Supplementary Appendix
This appendix has been provided by the authors to give readers additional information about their work.
Supplement to: Biomarkers distinguish bacterial from viral pediatric clinical pneumonia in a malaria endemic setting
Methods 3 Study population 3 Sample Collection 3 Etiologic Diagnosis Classification 4 Ethics 4 Data analysis pipeline 5 Marker selection and model building 5 Differential marker selection 5 Identification of surrogate markers 6 Selection of the most predictive subset of markers through genetic algorithms 6 Evaluating the accuracy of a clinical signature: ALMANACH 7 Biological processes and pathways 7 Results 10 Study population 10 Differentially expressed markers 10 Discussion 13 Figures 17 Fig. S1 Single etiology patient classification 17 Fig. S2 Heatmaps of unsupervised hierarchical clustering of all 1107 proteins and BvVM markers (n=151) 18 Fig. S3 Protein marker overlap of the 30 highest ranking markers. 20 Fig. S4 Box and whisker plots of the 100 Top markers. 21 Fig. S5 Model accuracy when switching out surrogates for comparisons of interests 23 Fig. S6 RBM multiplexed Immunoassay, RNA-sequencing and SOMAscan assay comparisons with Venn diagrams and marker lists 25 Fig. S7 Heatmap of all 24 overlapping SOMAScan (BvVM) and RNA-sequencing markers. 29 Fig. S8 Malarial markers shared between SOMAScan and RNA-sequencing. 30 Fig. S9 Enrichment Heatmap of the three-way comparison (Bacteria vs Malaria vs Virus). 31 Fig. S10 Heatmap of the Bacteria vs Virus model. (A) Hierarchically clustered heatmap of normalized SOMAscan expression values for 219 significant markers (FDR<0.01) from the SOMAScan Bacteria vs Virus (BvV) comparison in the space of all single etiology bacterial and viral samples in this study. 32 Tables 33
1 Table S1 Patient demographic and disease characteristics at admission for Bacterial and PCR Bacterial samples. 33 Table S2 Single etiology sample designations and distributions for training (n=120) and validation sets (n=47). 35 Table S3 Mixed infection sample designation sample distribution. 36 Table S4 List of markers for Bacteria vs Virus (n=219) and Bacteria vs Virus or Malaria (n=151). 38 Table S5 Single Etiology validation statistics for BvV and BvVM marker sets (A to D), and SOMAScan assay and RNA-Sequencing overlapping marker set (n=24) for RF and EN models (E and F) 55 Table S6 Mixed infection set without controls (n=23) (Random Forest) 60 Table S7 ALgorithm for MANagement of Childhood illnesses (ALMANACH). 62 References 64
2 Methods
Study population
Exclusion criteria are identical to those in Valim et. al., 20161,2: use of antimalarial drugs in the preceding 2 weeks, established or suspected pulmonary tuberculosis (based on a history of cough of more than 2 weeks’ duration or history of direct contact with a patient with active tuberculosis), ongoing participation in conflicting studies, and severe hypoxemia (oxyhemoglobin saturation
≤85% or less) to reduce the likelihood of Pneumocystis jirovecii infection. Exclusion of suspected infections by Mycobacterium tuberculosis and Pneumocystis jirovecii aimed to improve the specificity of case definitions.
Healthy community controls were matched to cases by sex, age, and neighborhood and identified through a demographic surveillance system, which allowed for selection of a random sample of children from the same age distribution and geographic area as the study patients. Control patients were examined and excluded if they presented with fever or respiratory symptoms, if they had taken any medication in the previous 30 days, or if they had a positive malaria microscopy exam.
Operators blinded to diagnosis and clinical status processed all laboratory tests and samples. All clinical, laboratory, and radiologic data were used to classify all patients enrolled in the study as having bacterial, viral, or malaria infection, into either single or mixed etiologies (both used in this study).2
Sample Collection
Before the initiation of antimicrobial treatment, a nasopharyngeal aspirate (NPA) was obtained to determine viral respiratory infections through a real-time polymerase chain reaction (RT-PCR)
3 test. Additionally, venous blood was collected for blood culture, bacterial PCR for respiratory pathogens (referred to as “PCR Bacteria samples” if positive), human immunodeficiency virus
(HIV) testing, malaria detection by smear microscopy, and SOMAScan protein assay. Pleural fluid, when available, was also submitted for culture. Coagulase-negative staphylococci, Bacillus species, or Micrococci were considered contaminants. Bacterial RT-PCR was performed for
Haemophilus influenzae (HiB) and Streptococcus pneumoniae (pneumococcus), the two most common causes of bacterial pneumonia in this pediatric population.2 Detection of the bexA gene was considered diagnostic for HiB3, while the ply and wzg genes identified pneumococcus if confirmed by at least one positive hit in two independent PCRs. 3,4 In 32 out of 58 tested samples both ply and wzg were positive.
Etiologic Diagnosis Classification
Single etiology cases generally required absence of evidence of other etiologies, and definitions were mutually exclusive. However, the bacteria and malaria classifications allowed concurrent viral infections in the NPA. A comprehensive flow chart for patient single etiology classification can be found in Fig. S1.
Ethics
This study was reviewed and approved by the Mozambique National Bioethics committee
(reference No. 262/CNBS/10), the Institutional Review Board of the Broad Institute/MIT
Committee on the Use of Humans as Experimental Subjects (reference No. 1003003765), and the
Hospital Clinic’s Ethics committee in Barcelona, Spain (reference No. 2010/5590). A signed informed consent of parent or guardian was obtained prior to study participation. The presence of a witness was required in case of illiterate guardians.
4 Data analysis pipeline
Marker selection and model building
Single etiology samples (n=167) were randomly divided into a training set (70% of samples, n=120) for model building and an independent validation set (30% of samples, n=47, after excluding 4 repeated samples to prevent information leak from the training data) (Table S2).
Markers selected in the training set were used to train models that were evaluated in the validation set. The same models were also tested in a separate sample set comprising the 23 mixed infection samples, 13 healthy controls, and 3 replicates (Table S3). Fig. 1 shows an overview of the data analysis workflow for single etiology and mixed infection samples. Because the critical focus was on identifying bacterial samples to guide antibiotic therapy, markers were selected and evaluated by two different 2-class comparisons of diagnosis groups: bacteria versus virus (BvV) and bacteria versus malaria or virus (BvVM).
Differential marker selection
Markers were first selected based on statistical significance of differences in their distributions in the BvV and BvVM comparisons estimated through SAM (Significance Analysis of Microarrays), with p-values corrected for multiple testing through the Benjamini-Hochberg FDR (False
Discovery Rate) approach.5 SAM analysis and statistical significance determination were performed in R using the samr library. Markers that were statistically significant (FDR < 0.01) were then used as input to train multiple classifiers including partial least squares, partitioning around medioids, random forests (RF), and elastic nets (EN). The importance of each input marker to overall classifier accuracy was determined using variable importance metrics from each of the
5 4 classifiers. The ranking of markers based on SAM and classifier variable importance were combined into a single final rank using robust rank aggregation.6 Classifier training and variable importance determination were coded using the caret library in R.7
Identification of surrogate markers
We sought surrogates for all markers with FDR<0.01 by calculating the mutual information-based information correlation (IC) between each marker and all other proteins in the dataset. Any protein with IC>0.75 was considered a surrogate for the corresponding marker 8. This analysis provided important latitude for final assay construction, as a surrogate marker could replace its companion candidate marker in a diagnostic test to address challenges such as reagent availability or inadequate analytical performance.
Selection of the most predictive subset of markers through genetic algorithms
As assays with fewer markers are generally easier to deploy, we aimed to identify subsets of markers that efficiently captured our classifications of interest -- distinguishing bacteria from virus, and bacteria from virus or malaria. The goals were to identify a small number of markers that effectively classified the samples, to assess the effect of adding more markers on model performance, and to compare reduced marker models to those trained using all statistically significant markers. To this end, we applied genetic algorithms to find the best subset of N markers
(with N = 5, 10, 15, 25, 50, 100) for RF and EN classifiers. The genetic algorithm was implemented in R using the rgenoud library.9 The BvV or BvVM protein marker sets and their surrogates (Data file S3) were the input markers to the non-deterministic genetic algorithm. The fitness function (or objective function) for the genetic algorithm was based on the accuracy of RF or EN models trained using the marker subset under consideration, and evaluated on a held-aside subset of the input
6 training dataset. As the marker subsets evolved, the fitness function was maximized to obtain the best subset of N markers.
Once the genetic algorithm identified the best markers for each N, repeated 10 times with random restarts, we ranked the markers based on the cumulative frequency with which they were identified in all runs. We selected the N most frequently identified markers based on this ranking, and used them to refit a random forest and elastic net model using the entire training dataset. The models were then applied to the validation set of subjects, and the predicted class of each sample based on each classifier was recorded and the misclassification rate of each classifier determined.
To contend with potential situations in which a particular selected marker could not be included in an assay (for instance, due to reagent availability, or difficulty measuring the marker in a clinical setting), we assessed model performance when randomly selected subsets of 10% or 20% of differential markers were replaced by their corresponding best surrogate markers.
Evaluating the accuracy of a clinical signature: ALMANACH
To compare the effectiveness of clinical parameters alone for assigning pathogenic etiology of febrile respiratory distress in our sample set, we used available clinical variables from our sample population in the context of the ALMANACH (ALgorithm for MANagement of Childhood illnesses)10 algorithm to differentiate between bacterial and viral pneumonia (see Table S7).
Biological processes and pathways
Marker lists (FDR<0.01) derived from SAM-based marker selection were mapped to a single gene name for each marker. The Metascape Gene Annotation and Analysis Resource was used to query multiple ontology resources. Binary markers were assigned fold change values; proteins higher in
7 bacterial or viral samples were assigned to Bacteria or Virus, respectively. Markers in the three- way comparison were assigned contrast scores, which represent standardized differences between the class mean and the overall mean. Proteins with positive contrast scores in a class were considered to be enriched in that class. Therefore, in the binary comparison proteins were uniquely assigned to one class, whereas in the three-way comparison proteins could be shared by two (but not all three) classes. The resulting networks can be probed in greater detail to identify individual node terms, associated Benjamini-Hochberg corrected q-values, etc. by importing the accompanying .cys file into Cytoscape (supplementary data file “Cytoscape B vs M vs V 3-class network”).
Verifying Consistency of Our Selected Markers - Comparative marker analysis between technologies
We first derived differential marker gene lists from markers identified in: a) the BvV and BvVM comparisons within SOMAScan protein assay data (Data file S2); and b) 2-class single marker comparisons of the groups Bacteria vs Virus (BvV), Bacteria vs Malaria, and Virus vs Malaria within a multiplex immunoassay.2 Since our prior RNA sequencing study1 included the same
Bacteria vs Virus and Malaria (BvVM) 2-class comparison that we used in the SOMAScan analysis, the resulting gene marker sets could be used without modification in these comparisons.
Our 151 SOMAScan BvVM markers were mapped to 156 genes and compared with the RNA- sequencing BvVM 431 gene marker set (see overlap depiction in Fig. 4), as well as with other sets from that analysis (Fig. S6). The combined significant markers from our RNA-sequencing and multiplex immunoassay were compared to the SOMAScan BvVM (n=156 genes) or to the BvV
8 gene marker sets (n=226). Most of these comparisons between marker sets and resulting Venn diagrams can be found in Fig. S6.
9 Results
Study population
No significant differences in patient demographic and disease characteristics were identified between Bacteria and PCR Bacteria samples (Table 1), except neutrophil levels, suggesting that positivity in RT-PCR for bacteria allowed inclusion of a wider spectrum of disease severity in the bacteria group.
Differentially expressed markers
We performed marker selection to identify proteins that were differentially abundant between bacterial and viral samples (BvV), and bacterial vs the combined viral and malaria samples
(BvVM). Statistically significant markers were used as input to train our models. The markers were ranked by a combination of their differential protein expression and contribution in accurately classifying samples into appropriate subgroups.
The highest ranking 10 proteins (Fig. 2B) were (gene names in parentheses): Phospholipase A2
(PLA2G2A), Lipocalin 2 (LCN2, also known as neutrophil gelatinase-associated lipocalin or
NGAL11), C-C motif chemokine 23 (CCL23), Interleukin-1 receptor-like 1 (ILRL1),
Myeloperoxidase (MPO), Fractalkine (CX3CL1), Resistin (RETN), Interleukin-6 (IL6), Netrin-4
(NTN4), and Kallistatin (SERPINA4). The 10 highest scoring proteins were Haptoglobin (HP),
Fractalkine, Resistin, Granulocyte colony-stimulating factor (CSF3), LCN2, Secretory Leukocyte
Protease Inhibitor (SLPI), S-formylglutathione hydrolase (ESD), Kynureninase (KYNU),
Interleukin-6, and Protein S100-A9 (S100A9).
10 Seventeen of the 30 top ranking protein markers were common to both the BvV and BvVM comparisons (Fig. S3). Fractalkine, Interleukin-6, and Resistin were amongst the top 10 markers for both models. Lipocalin 2 ranked within the top 5 markers in both models. Surrogate markers for Lipocalin 2 are Myeloperoxidase and Resistin (Data File S3). Expression values for the 100 top-ranking protein markers for each comparison are depicted in Fig. S4.
Clinical algorithms underperform protein-based predictive models in differentiating bacterial from other causes of pediatric respiratory distress
To test the effectiveness of clinical parameters alone for assigning pathogenic etiology of pediatric respiratory distress in our sample set, we used available clinical variables from our sample population in the context of the ALMANACH (ALgorithm for MANagement of Childhood illnesses 10 algorithm for “Assessment of FEBRILE Childhood Illness" and sub-algorithm on
“Cough-Related diagnoses”. As our focus was on guiding antibiotic administration, we used the two clinical variables that led to a directive for antibiotics: respiratory rate above 50 breaths per minute in a calm child and “Chest indrawing or stridor in a calm child”, indicative in the algorithm of “pneumonia” or “severe pneumonia”, respectively. In our data, stridor overlapped completely with indrawing or elevated respiratory rate and was therefore not used. The implementation of the
ALMANACH algorithm for this dataset was:
Given fever and cough or difficulty breathing (present in all of our subjects): If
chest indrawing is present or sustained respiratory rate is greater than 50 breaths
per minute, assign a “bacteria” etiology; otherwise assign an “other” etiology
11 (where “other” can be either “malaria or virus” or “virus” depending on the
specific comparison).
Both two-way (BvV) and three-way (BvMV) comparisons were included, and predictive accuracy in the relevant test set was compared to the protein-based predictive models. Resulting confusion matrices, statistics, and additional details can be found in Table S7.
The performance accuracy for both sample sets was poor (0.55 to 0.74), worse than our Somalogic models, and partially below the No Information Rate (NIR) for the BvVM sample set. Sensitivity was high (93%) in the BvV sample set in which a presumptive bacterial infection (pneumonia or severe pneumonia) was clinically assessed by the presence of either positive chest indrawing or a respiratory rate of over 50/min, but specificity was unacceptably low at 23%. Classifiers based on these two clinical variables separately had higher specificity and lower sensitivity than the combination. While chest indrawing as a single predictor for pneumonia performed best overall amongst the clinically-based models (accuracy 0.67, NIR 0.52, sensitivity 86%, specificity 46%), none of the models approached the specifications needed for a diagnostic assay for bacterial pneumonia and none competed with the Somalogic-based models.
12 Discussion
Since clinical parameters continue to be used to attempt to distinguish causes of fever in resource- limited settings, as for instance in the ALMANACH implementation10, comparison of their performance to that of our predictive models is important. Taking an ALMANACH recommendation for antibiotic administration as a functional surrogate for bacterial etiology, we compared the accuracy of ALMANACH predictions to those of our protein-based models. The clinical models were uniformly inferior to our molecular predictors, with a particularly dramatic loss of specificity (see Table S7 for details). We did not attempt to incorporate clinical parameters into our protein-marker based models for disease etiology, as our goal was a test for the presence or absence of bacterial cause of febrile respiratory illness that did not rely on either resource- intensive testing (such as blood culture or radiography) or subjective clinical assessments that are often unreliable in community health settings. Furthermore, laboratory parameters (such as leukocyte count) contributed to our definition of single etiology samples, so their inclusion would generate biased models. Of note, neutrophil counts have been shown in previous studies not to differentiate disease etiologies in febrile children.12,13
Neutrophils, part of the innate immune system 14,15, migrate to sites of inflammation to help to eliminate bacteria, and play a central role in the pathogenesis of many respiratory diseases.16,17
Though neutrophil infiltration in the lower respiratory tract is a hallmark of bacterial infection 17,18, their role in the pathological mechanisms of disease is not fully understood.
Evidence for other biologically important pathways can also be seen in these data, but the details are beyond the scope of this paper. For example, “interleukin-4 and interleukin-13” signaling was
13 enriched in markers from both the SOMAScan and RNA-sequencing studies. A three-way comparison (Bacterial vs Virus vs Malaria) revealed additional, largely expected, pathways involved in each of the three disease etiologies (Fig. S9). Hemostasis signals were increased in all types of infection; thrombosis is a well-known and dangerous complication especially of bacterial and viral sepsis.19 The appearance of a matrisome-associated protein signal in plasma, especially in bacterial infections, suggests ECM degradation. Invasive pathogens breach the basal lamina, bind to ECM and can degrade interstitial ECM proteins using proteases.20
Other ontologies were more strongly enriched in one or two of the categories. Especially potent cytokine production and inflammatory response signatures were shared by malaria and bacterial infections. Hemozoin and other toxic factors from the parasites may stimulate monocytes and macrophages in a fashion comparable to that of bacterial endotoxin, though other mechanisms of inflammatory induction may differ.21 High levels of predominantly proinflammatory cytokines are responsible for the high fevers associated with blood-stage malaria infection, while elevations of both pro- and anti-inflammatory cytokines are associated with severe bacterial pneumonia and attendant respiratory failure and multi-system organ dysfunction that can accompany bacterial pneumonia.22,23 Regulation of cell adhesion was strongly upregulated in malaria. These gene products have been suggested to contribute to the virulence of P. falciparum relative to other human malaria parasites 24, and to the clinical presentation of severe relative to asymptomatic malaria.25 The potential significance of upregulation of Cell Adhesion Molecules (CAMs) in Virus is twofold; CAMs are often upregulated in the host defense against microorganisms26, but can also function as viral receptors and promote infection and viral internalization.27 Although antibodies are the principal adaptive response against both extracellular viral and bacterial pathogens, humoral immune response was most strongly represented in bacteria samples. Regulation of
14 endopeptidase activity, which plays a critical regulatory role in both immune activation and inactivation28 was also especially robust in bacteria samples.
Our study shares with other biomarker studies in clinical pneumonia the difficulty of confidently assigning a bacterial or viral etiology to the clinical syndrome.29,30 Bacterial culture is insensitive and may be associated with severity of disease; therefore a bacterial class definition based on culture may bias results towards severity rather than etiology. To circumvent this problem and generate a more representative bacterial class, we included samples positive by blood-based RT-
PCR for bacterial respiratory pathogens, and followed other authors in using “probable diagnosis” criteria based on expert panel review of clinical, radiologic and laboratory information 31. Though such “probable bacteria” samples were in the minority, this greater inclusivity could result in false positive detection of bacterial etiology and misclassification bias. However, these biases would generally lead to underestimating differences across groups and not to false discovery of markers.
There are additional limitations. Genetic algorithms (GAs) used for marker selection are not deterministic, so repeated runs are likely to reach different solutions, especially when the candidate marker population is large.9,32 Relatedly, GAs do not exhaustively explore the feature landscape, so while they should achieve well-performing models, it cannot be claimed that their output results in the best possible predictor. These factors contribute to the observation that the 24 marker model based on overlapping features from multiple datasets with partially different markers (see Table
S6 E and F) has equivalent performance to the GA-optimized 25 marker model (see Table S6 A to
E, Table 1 and 2). Our markers were selected and models trained on single etiology samples, which importantly allowed virus-positive NPAs in the bacterial and malarial classes. While a bacterial signature could still be detected in other mixed infection samples, it is likely that performance in
15 those mixed infections could be further enhanced by specifically training on that population.
Finally, the generalizability of the model would be better assessed in the context of a larger, more ethnically and geographically diverse sample population drawn from areas with and without endemic malaria.
16 Figures
Fig. S1 Single etiology patient classification
Patient classification into three single etiology groups (bacteria, virus, and malaria). Negative tests included those that had contaminant bacteria, those that were missing results, and those that did not meet the microscopic parasitemia threshold. Chest X-ray results were classified as (1) normal, (2) infiltrates other than endpoint pneumonia, and (3) lobar consolidation or pleural effusion (endpoint pneumonia). PCR = polymerase chain reaction; WBC = white blood cells; Culture = bacterial blood or pleural fluid culture for respiratory pathogens (contaminants excluded).
17 Fig. S2 Heatmaps of unsupervised hierarchical clustering of all 1107 proteins and BvVM markers (n=151)
(A) Heatmap from unsupervised hierarchical clustering of all 1107 proteins measured in the space of all 171 single etiology samples from the training and validation set.
18 row min row max somalogic-data-combined-modeling+validation BACTERIA MALARIA VIRUS
id EID128100 EID128216 EID128247 EID128158 EID128222 EID128117 EID128194 EID128224 EID128184 EID128131 EID128115 EID128134 EID128156 EID128135 EID128136 EID128253 EID128205 EID128227 EID128188 EID128101 EID128141 EID128104 EID128133 EID128236 EID128107 EID128251 EID128198 EID128242 EID128098 EID128237 EID128124 EID128155 EID128118 EID128249 EID128226 EID128096 EID128173 EID128215 EID128113 EID128152 EID128109 EID128233 EID128119 EID128181 EID128159 EID128094 EID128097 EID128139 EID128232 EID128193 EID128197 EID128176 EID128250 EID128165 EID128151 EID128213 EID128110 EID128234 EID128125 EID128235 EID128231 EID128254 EID128225 EID128244 EID128228 EID128241 EID128206 EID128211 EID128180 EID128212 EID128239 EID128208 EID128178 EID128217 EID128108 EID128199 EID128229 EID128243 EID128138 EID128111 EID128195 EID128207 EID128209 EID128089 EID128127 EID128103 EID128160 EID128168 EID128126 EID128189 EID128186 EID128202 X1161398.5 EID128196 X1192032.8 EID128112 X1323012.8 X1191859.3 EID128192 X1042680.7 EID128099 X1192877.5 EID128154 X1394322.6 EID128120 X1292921.4 EID128121 X1292901.6 EID128201 EID128203 EID128204 EID128114 EID128214 EID128146 EID128145 EID128122 EID128150 EID128218 EID128190 EID128147 EID128223 EID128177 EID128187 EID128153 EID128129 EID128095 EID128221 EID128219 EID128091 EID128220 EID128175 EID128172 EID128090 EID128130 EID128102 EID128185 EID128238 EID128230 EID128210 EID128128 EID128169 EID128149 EID128240 X1161393 EID128191 X1191774.8 EID128252 EID128137 EID128105 EID128106 EID128140 EID128092 EID128093 EID128171 EID128132 EID128174 EID128116 EID128245 X1138395.6 X1042543.5 X1042570.1 X1042594.7 X1138459.5 X1042565.7 X1042651.7 X1083282 X1138474.8 X1323034 EID128246 X1323030.3 X1394327.1 somalogic-data-combined-modeling+validation # id Description 1 CHEK2 Serine/threonine-protein kinase Chk2 2 HIPK3 Homeodomain-interacting protein kinase 3 3 A2M Alpha-2-macroglobulin 4 F2 Thrombin 5 C4A.C4B Complement C4b 6 C3 Complement C3b, inactivated 7 LTA4H Leukotriene A-4 hydrolase 8 TPSG1 Tryptase gamma 9 PDE4D cAMP-specific 3',5'-cyclic phosphodiesterase 4D 10 HGFAC Hepatocyte growth factor activator 11 LEPR Leptin receptor 12 C3.3 Complement C3b 13 C5.1 C5a anaphylatoxin 14 KLK3 Prostate-specific antigen 15 C1R Complement C1r subcomponent 16 NXPH1 Neurexophilin-1 17 FGF10 Fibroblast growth factor 10 18 Human.virus.1 Protein E7_HPV18 19 APOE.1 Apolipoprotein E (isoform E3) 20 APOE.2 Apolipoprotein E (isoform E4) 21 APOE.3 Apolipoprotein E (isoform E2) 22 C3.1 Complement C3 23 C3.2 C3a anaphylatoxin des Arginine 24 CCL23.1 Ck-beta-8-1 25 C4A.C4B.1 Complement C4 26 F2.1 Prothrombin 27 FN1.1 Fibronectin Fragment 4 28 LTA.LTB.1 Lymphotoxin alpha2:beta1 29 RASA1 Ras GTPase-activating protein 1 30 DCTN2 Dynactin subunit 2 31 EHMT2 Histone-lysine N-methyltransferase EHMT2 32 RBP4 Retinol-binding protein 4 33 PTH Parathyroid hormone 34 MED1 Mediator of RNA polymerase II transcription subunit 1 35 FCN3 Ficolin-3 36 PRDX5 Peroxiredoxin-5, mitochondrial 37 FN1 Fibronectin Fragment 3 38 FN1.2 Fibronectin 39 ENPP7 Ectonucleotide pyrophosphatase/phosphodiesterase family member 7 40 NTF3 Neurotrophin-3 41 FETUB Fetuin-B 42 FGF19 Fibroblast growth factor 19 43 FABP3 Fatty acid-binding protein, heart 44 CKB.CKM Creatine kinase M-type:Creatine kinase B-type heterodimer 45 CKM Creatine kinase M-type 46 MB Myoglobin 47 FGF20 Fibroblast growth factor 20 48 SEMA3E Semaphorin-3E 49 COL8A1 Collagen alpha-1(VIII) chain 50 KLK5 Kallikrein-5 51 ARTN Artemin 52 FGF17 Fibroblast growth factor 17 53 FUT3 Galactoside 3(4)-L-fucosyltransferase 54 CDNF Cerebral dopamine neurotrophic factor 55 FGF18 Fibroblast growth factor 18 56 NOG Noggin 57 BCL2L1 Bcl-2-like protein 1 58 DSG1 Desmoglein-1 59 NOV Protein NOV homolog 60 ERP29 Endoplasmic reticulum resident protein 29 61 IL17F Interleukin-17F 62 CYP3A4 Cytochrome P450 3A4 63 F11 Coagulation Factor XI 64 ECE1 Endothelin-converting enzyme 1 65 CPB2 Carboxypeptidase B2 66 BMP1 Bone morphogenetic protein 1 67 PLG Angiostatin 68 ENTPD5 Ectonucleoside triphosphate diphosphohydrolase 5 69 HPX Hemopexin 70 CFB Complement factor B 71 CFI Complement factor I 72 CFH Complement factor H 73 CRP C-reactive protein 74 CLEC4M C-type lectin domain family 4 member M 75 LYZ Lysozyme C 76 AIMP1 Endothelial monocyte-activating polypeptide 2 77 GOT1 Aspartate aminotransferase, cytoplasmic 78 C1QBP Complement component 1 Q subcomponent-binding protein, mitochondrial 79 SCGB2A1 Mammaglobin-B 80 TXNDC12 Thioredoxin domain-containing protein 12 81 FOLH1 Glutamate carboxypeptidase 2 82 APCS Serum amyloid P-component 83 C2 Complement C2 84 CCL21 C-C motif chemokine 21 85 AMH Muellerian-inhibiting factor 86 HP Haptoglobin 87 PROS1 Vitamin K-dependent protein S 88 SERPIND1 Heparin cofactor 2 89 IFNA2 Interferon alpha-2 90 CD70 CD70 antigen 91 ARG1 Arginase-1 92 OSM Oncostatin-M 93 CCL1 C-C motif chemokine 1 94 ERBB4 Receptor tyrosine-protein kinase erbB-4 95 CA10 Carbonic anhydrase-related protein 10 96 KLK13 Kallikrein-13 97 KLK12 Kallikrein-12 98 BIRC5 Baculoviral IAP repeat-containing protein 5 99 CAMK1D Calcium/calmodulin-dependent protein kinase type 1D 100 CD97 CD97 antigen 101 CTF1 Cardiotrophin-1 102 CA4 Carbonic anhydrase 4 103 TPM2 Tropomyosin beta chain 104 C8A.C8B.C8G Complement component C8 105 IL37 Interleukin-37 106 RAD51 DNA repair protein RAD51 homolog 1 107 TNFRSF11B Tumor necrosis factor receptor superfamily member 11B 108 LTBR Tumor necrosis factor receptor superfamily member 3 109 PAK3 Serine/threonine-protein kinase PAK 3 110 ZAP70 Tyrosine-protein kinase ZAP-70 111 KLK6 Kallikrein-6 112 PRSS3 Trypsin-3 113 CRLF1.CLCF1 Cytokine receptor-like factor 1:Cardiotrophin-like cytokine factor 1 Complex 114 FGF1 Fibroblast growth factor 1 115 SPON1 Spondin-1 116 WFIKKN1 WAP, kazal, immunoglobulin, kunitz and NTR domain-containing protein 1 117 TNFSF18 Tumor necrosis factor ligand superfamily member 18 118 FAM107A Protein FAM107A 119 FABP5 Fatty acid-binding protein, epidermal 120 ETHE1 Persulfide dioxygenase ETHE1, mitochondrial 121 SEMA3A Semaphorin-3A 122 CXCL16 C-X-C motif chemokine 16 123 MFGE8 Lactadherin 124 IL18R1 Interleukin-18 receptor 1 125 SLPI Antileukoproteinase 126 VEGFA Vascular endothelial growth factor A 127 PIGR Polymeric immunoglobulin receptor 128 LGALS3BP Galectin-3-binding protein 129 SERPINF2 Alpha-2-antiplasmin 130 C6 Complement component C6 131 CFP Properdin 132 NAAA N-acylethanolamine-hydrolyzing acid amidase 133 BMPR1A Bone morphogenetic protein receptor type-1A 134 CADM3 Cell adhesion molecule 3 135 IL1A Interleukin-1 alpha 136 ALB Serum albumin 137 APOA1 Apolipoprotein A-I 138 CDK8.CCNC Cyclin-dependent kinase 8:Cyclin-C complex 139 CPE Carboxypeptidase E 140 KIRREL3 Kin of IRRE-like protein 3 141 CD209 CD209 antigen 142 CTSC Dipeptidyl peptidase 1 143 ADAMTS13 A disintegrin and metalloproteinase with thrombospondin motifs 13 144 MBL2 Mannose-binding protein C 145 CST1 Cystatin-SN 146 CST2 Cystatin-SA 147 PDCD1LG2 Programmed cell death 1 ligand 2 148 GHR Growth hormone receptor 149 HRG Histidine-rich glycoprotein 150 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 151 KNG1 Kininogen-1 152 PAPPA Pappalysin-1 153 CYCS Cytochrome c 154 DIABLO Diablo homolog, mitochondrial 155 CCL16 C-C motif chemokine 16 156 IL6R Interleukin-6 receptor subunit alpha 157 CTSV Cathepsin L2 158 SIGLEC1 Sialoadhesin 159 CKAP2 Cytoskeleton-associated protein 2 160 ITGA2B.ITGB3 Integrin alpha-IIb: beta-3 complex 161 LIN7B Protein lin-7 homolog B 162 ARSB Arylsulfatase B 163 BCAM Basal Cell Adhesion Molecule 164 COLEC11 Collectin-11 165 CST5 Cystatin-D 166 AGER Advanced glycosylation end product-specific receptor, soluble 167 PRSS22 Brain-specific serine protease 4 168 BOC Brother of CDO 169 COL18A1 Endostatin 170 IL1R1 Interleukin-1 receptor type 1 171 IL19 Interleukin-19 172 LRIG3 Leucine-rich repeats and immunoglobulin-like domains protein 3 173 MMP2 72 kDa type IV collagenase 174 CAST Calpastatin 175 CDH3 Cadherin-3 176 LTA.LTB Lymphotoxin alpha1:beta2 177 SOD2 Superoxide dismutase [Mn], mitochondrial 178 DPT Dermatopontin 179 MIA Melanoma-derived growth regulatory protein 180 KLK7 Kallikrein-7 181 GPNMB Transmembrane glycoprotein NMB 182 CD200 OX-2 membrane glycoprotein 183 HFE2 Hemojuvelin 184 RGMA Repulsive guidance molecule A 185 CNTN2 Contactin-2 186 CNTN5 Contactin-5 187 CNTFR Ciliary neurotrophic factor receptor subunit alpha 188 POSTN Periostin 189 CA6 Carbonic anhydrase 6 190 CDON Cell adhesion molecule-related/down-regulated by oncogenes 191 MRC2 C-type mannose receptor 2 192 HAPLN1 Hyaluronan and proteoglycan link protein 1 193 CD109 CD109 antigen 194 CADM1 Cell adhesion molecule 1 195 ACAN Aggrecan core protein 196 NTRK3 NT-3 growth factor receptor 197 EFNA5 Ephrin-A5 198 SLITRK5 SLIT and NTRK-like protein 5 199 KLK8 Kallikrein-8 200 SHH Sonic hedgehog protein 201 ALCAM CD166 antigen 202 LSAMP Limbic system-associated membrane protein 203 FGFR1 Fibroblast growth factor receptor 1 204 IL6ST Interleukin-6 receptor subunit beta 205 CHL1 Neural cell adhesion molecule L1-like protein 206 NCAM1 Neural cell adhesion molecule 1, 120 kDa isoform 207 CNTN4 Contactin-4 208 NTRK2 BDNF/NT-3 growth factors receptor 209 L1CAM Neural cell adhesion molecule L1 210 CDH5 Cadherin-5 211 NOTCH1 Neurogenic locus notch homolog protein 1 212 ROBO2 Roundabout homolog 2 213 EPHA2 Ephrin type-A receptor 2 214 EPHB6 Ephrin type-B receptor 6 215 EPHB2 Ephrin type-B receptor 2 216 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 217 BCAN Brevican core protein 218 NRCAM Neuronal cell adhesion molecule 219 NRXN1 Neurexin-1-beta 220 UNC5D Netrin receptor UNC5D 221 ROR1 Tyrosine-protein kinase transmembrane receptor ROR1 222 UNC5C Netrin receptor UNC5C 223 LRP8 Low-density lipoprotein receptor-related protein 8 224 LPO Lactoperoxidase 225 SERPING1 Plasma protease C1 inhibitor 226 SPINT1 Kunitz-type protease inhibitor 1 227 IL22RA2 Interleukin-22 receptor subunit alpha-2 228 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 229 GDF2 Growth/differentiation factor 2 230 IL17B Interleukin-17B 231 SPINT2 Kunitz-type protease inhibitor 2 232 TGFBI Transforming growth factor-beta-induced protein ig-h3 233 CST6 Cystatin-M 234 TFF3 Trefoil factor 3 235 EFNA4 Ephrin-A4 236 ESAM Endothelial cell-selective adhesion molecule 237 TGFBR3 Transforming growth factor beta receptor type 3 238 NRXN3 Neurexin-3-beta 239 RGMB RGM domain family member B 240 EPHA1 Ephrin type-A receptor 1 241 KLK11 Kallikrein-11 242 NBL1 Neuroblastoma suppressor of tumorigenicity 1 243 PDGFRB Platelet-derived growth factor receptor beta 244 ICAM5 Intercellular adhesion molecule 5 245 ECM1 Extracellular matrix protein 1 246 MASP1 Mannan-binding lectin serine protease 1 247 FLT4 Vascular endothelial growth factor receptor 3 248 KDR Vascular endothelial growth factor receptor 2 249 BST1 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 250 IGF1R Insulin-like growth factor 1 receptor 251 INSR Insulin receptor 252 TLR4.LY96 Toll-like receptor 4:Lymphocyte antigen 96 complex 253 DKK3 Dickkopf-related protein 3 254 ERBB3 Receptor tyrosine-protein kinase erbB-3 255 GRN Granulins 256 IGFBP7 Insulin-like growth factor-binding protein 7 257 APOB Apolipoprotein B 258 ASAH2 Neutral ceramidase 259 EGFR Epidermal growth factor receptor 260 KIT Mast/stem cell growth factor receptor Kit 261 IL1RAP Interleukin-1 Receptor accessory protein 262 OMD Osteomodulin 263 IL13RA1 Interleukin-13 receptor subunit alpha-1 264 EDA Ectodysplasin-A, secreted form 265 RET Proto-oncogene tyrosine-protein kinase receptor Ret 266 WIF1 Wnt inhibitory factor 1 267 PLAU Urokinase-type plasminogen activator 268 TEK Angiopoietin-1 receptor, soluble 269 SPARCL1 SPARC-like protein 1 270 ERAP1 Endoplasmic reticulum aminopeptidase 1 271 ICOS Inducible T-cell costimulator 272 MAPK9 Mitogen-activated protein kinase 9 273 BMP7 Bone morphogenetic protein 7 274 BGN Biglycan 275 IDS Iduronate 2-sulfatase 276 ENG Endoglin 277 SEMA6A Semaphorin-6A 278 LY9 T-lymphocyte surface antigen Ly-9 279 IL34 Interleukin-34 280 TYRO3 Tyrosine-protein kinase receptor TYRO3 281 ICAM2 Intercellular adhesion molecule 2 282 PCSK7 Proprotein convertase subtilisin/kexin type 7 283 TNFSF13B Tumor necrosis factor ligand superfamily member 13B 284 INHBA Inhibin beta A chain 285 AHSG Alpha-2-HS-glycoprotein 286 GSN Gelsolin 287 SHBG Sex hormone-binding globulin 288 IGFBP3 Insulin-like growth factor-binding protein 3 289 AFM Afamin 290 SERPINA4 Kallistatin 291 KLKB1 Plasma kallikrein 292 SERPINC1 Antithrombin-III 293 LEP Leptin 294 SERPINA5 Plasma serine protease inhibitor 295 TPSB2 Tryptase beta-2 296 GFRA2 GDNF family receptor alpha-2 297 CHST15 Carbohydrate sulfotransferase 15 298 TIE1 Tyrosine-protein kinase receptor Tie-1, soluble 299 MET Hepatocyte growth factor receptor 300 FCER2 Low affinity immunoglobulin epsilon Fc receptor 301 CD200R1 Cell surface glycoprotein CD200 receptor 1 302 JAG1 Protein jagged-1 303 CD86 T-lymphocyte activation antigen CD86 304 TNFSF8 Tumor necrosis factor ligand superfamily member 8 305 IL27RA Interleukin-27 receptor subunit alpha 306 PLXNC1 Plexin-C1 307 VCAM1 Vascular cell adhesion protein 1 308 TNFRSF9 Tumor necrosis factor receptor superfamily member 9 309 ITGAV.ITGB5 Integrin alpha-V: beta-5 complex 310 TNFSF9 Tumor necrosis factor ligand superfamily member 9 311 APOE Apolipoprotein E 312 CFD Complement factor D 313 PSPN Persephin 314 ANG Angiogenin 315 FUT5 Alpha-(1,3)-fucosyltransferase 5 316 PROC Vitamin K-dependent protein C 317 CAMK1 Calcium/calmodulin-dependent protein kinase type 1 318 F5 Coagulation Factor V 319 CGA.TSHB Thyroid Stimulating Hormone 320 RARRES2 Retinoic acid receptor responder protein 2 321 AGRP Agouti-related protein 322 CCL15 C-C motif chemokine 15 323 MMP7 Matrilysin 324 PI3 Elafin 325 GCG Glucagon 326 PYY Peptide YY 327 WFIKKN2 WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 328 B2M Beta-2-microglobulin 329 CST3 Cystatin-C 330 IGFBP6 Insulin-like growth factor-binding protein 6 331 RELT Tumor necrosis factor receptor superfamily member 19L 332 IGFBP4 Insulin-like growth factor-binding protein 4 333 IGFBP5 Insulin-like growth factor-binding protein 5 334 CGA.FSHB Follicle stimulating hormone 335 CCL25 C-C motif chemokine 25 336 GNS N-acetylglucosamine-6-sulfatase 337 ADIPOQ Adiponectin 338 CNTN1 Contactin-1 339 THBS4 Thrombospondin-4 340 NOTCH3 Neurogenic locus notch homolog protein 3 341 CTSA Lysosomal protective protein 342 GPC3 Glypican-3 343 PTN Pleiotrophin 344 PRL Prolactin 345 MMP13 Collagenase 3 346 SCARF1 Scavenger receptor class F member 1 347 RTN4R Reticulon-4 receptor 348 TIMP2 Metalloproteinase inhibitor 2 349 ANGPT2 Angiopoietin-2 350 IBSP Bone sialoprotein 2 351 CCDC80 Coiled-coil domain-containing protein 80 352 MATN2 Matrilin-2 353 THBS2 Thrombospondin-2 354 TNC Tenascin 355 CLEC11A Stem Cell Growth Factor-beta 356 NLGN4X Neuroligin-4, X-linked 357 TNNI3 Troponin I, cardiac muscle 358 CTLA4 Cytotoxic T-lymphocyte protein 4 359 OLFM4 Olfactomedin-4 360 MST1 Hepatocyte growth factor-like protein 361 IL17RA Interleukin-17 receptor A 362 ADAMTS4 A disintegrin and metalloproteinase with thrombospondin motifs 4 363 CD27 CD27 antigen 364 AMN Protein amnionless 365 FGFR4 Fibroblast growth factor receptor 4 366 PTHLH Parathyroid hormone-related protein 367 CALR Calreticulin 368 NPPA Atrial natriuretic factor 369 GRAP2 GRB2-related adapter protein 2 370 CCNB1 G2/mitotic-specific cyclin-B1 371 KRT18 Keratin, type I cytoskeletal 18 372 PIM1 Serine/threonine-protein kinase pim-1 373 PRKCG Protein kinase C gamma type 374 TNFRSF14 Tumor necrosis factor receptor superfamily member 14 375 TNFSF14 Tumor necrosis factor ligand superfamily member 14 376 IL17RC Interleukin-17 receptor C 377 SNRPF Small nuclear ribonucleoprotein F 378 SIGLEC9 Sialic acid-binding Ig-like lectin 9 379 DBNL Drebrin-like protein 380 DDR1 Epithelial discoidin domain-containing receptor 1 381 MICA MHC class I polypeptide-related sequence A 382 PPY Pancreatic hormone 383 CDKN1B Cyclin-dependent kinase inhibitor 1B 384 CSNK2A2.CSNK2B Casein kinase II 2-alpha':2-beta heterotetramer 385 EREG Epiregulin 386 F3 Tissue Factor 387 FAM107B Protein FAM107B 388 HCK Tyrosine-protein kinase HCK 389 CD274 Programmed cell death 1 ligand 1 390 GSTA3 Glutathione S-transferase A3 391 CA9 Carbonic anhydrase 9 392 GPC5 Glypican-5 393 MAPK12 Mitogen-activated protein kinase 12 394 PTK6 Protein-tyrosine kinase 6 395 CRTAM Cytotoxic and regulatory T-cell molecule 396 CSF2 Granulocyte-macrophage colony-stimulating factor 397 MAPK11 Mitogen-activated protein kinase 11 398 NOTCH2 Neurogenic locus notch homolog protein 2 399 CD226 CD226 antigen 400 TGFBR2 TGF-beta receptor type-2 401 IL1RAPL2 X-linked interleukin-1 receptor accessory protein-like 2 402 CDH2 Cadherin-2 403 CST4 Cystatin-S 404 MSN Moesin 405 PRKCQ Protein kinase C theta type 406 AGR2 Anterior gradient protein 2 homolog 407 BRF1 Transcription factor IIIB 90 kDa subunit 408 PRLR Prolactin receptor 409 ROBO3 Roundabout homolog 3 410 EDA2R Tumor necrosis factor receptor superfamily member 27 411 IL7R Interleukin-7 receptor subunit alpha 412 FGF5 Fibroblast growth factor 5 413 FGFR3 Fibroblast growth factor receptor 3 414 GDF9 Growth/differentiation factor 9 415 LTA Lymphotoxin-alpha 416 MATK Megakaryocyte-associated tyrosine-protein kinase 417 KLRK1 NKG2-D type II integral membrane protein 418 HMGCR 3-hydroxy-3-methylglutaryl-coenzyme A reductase 419 POMC Beta-endorphin 420 SST Somatostatin-28 421 CASP2 Caspase-2 422 PTEN Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN 423 CKB Creatine kinase B-type 424 KIR3DL2 Killer cell immunoglobulin-like receptor 3DL2 425 WNT7A Protein Wnt-7a 426 FYN Tyrosine-protein kinase Fyn 427 GP1BA Platelet glycoprotein Ib alpha chain 428 FASLG Tumor necrosis factor ligand superfamily member 6, soluble form 429 EPHA5 Ephrin type-A receptor 5 430 TNFRSF19 Tumor necrosis factor receptor superfamily member 19 431 IFNGR1 Interferon gamma receptor 1 432 FGFR2 Fibroblast growth factor receptor 2 433 PDE9A High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A 434 AMICA1 Junctional adhesion molecule-like 435 BIRC3 Baculoviral IAP repeat-containing protein 3 436 ARPP19 cAMP-regulated phosphoprotein 19 437 CA2 Carbonic anhydrase 2 438 LGALS8 Galectin-8 439 FCAR Immunoglobulin alpha Fc receptor 440 NPPB Brain natriuretic peptide 32 441 NR1D1 Nuclear receptor subfamily 1 group D member 1 442 SPTAN1 Spectrin alpha chain, non-erythrocytic 1 443 FLT3LG Fms-related tyrosine kinase 3 ligand 444 HNRNPK Heterogeneous nuclear ribonucleoprotein K 445 PRKAA1.PRKAB1..PRKAG1 AMP Kinase (alpha1beta1gamma1) 446 PDK1 [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial 447 RB1 Retinoblastoma-associated protein 448 ULBP1 NKG2D ligand 1 449 DDX19B ATP-dependent RNA helicase DDX19B 450 KIR3DS1 Killer cell immunoglobulin-like receptor 3DS1 451 AURKA Aurora kinase A 452 IL13 Interleukin-13 453 PGF Placenta growth factor 454 KLRF1 Killer cell lectin-like receptor subfamily F member 1 455 SCARF2 Scavenger receptor class F member 2 456 SCARB2 Lysosome membrane protein 2 457 POMC.1 Corticotropin 458 MAPKAPK5 MAP kinase-activated protein kinase 5 459 GCKR Glucokinase regulatory protein 460 FGR Tyrosine-protein kinase Fgr 461 TNFRSF6B Tumor necrosis factor receptor superfamily member 6B 462 IL4R Interleukin-4 receptor subunit alpha 463 SCT Secretin 464 GFAP Glial fibrillary acidic protein 465 PDGFC Platelet-derived growth factor C 466 PSME3 Proteasome activator complex subunit 3 467 KRAS GTPase KRas 468 MMP14 Matrix metalloproteinase-14 469 TNF Tumor necrosis factor 470 JAG2 Protein jagged-2 471 TNFRSF12A Tumor necrosis factor receptor superfamily member 12A 472 LGALS2 Galectin-2 473 TPM1 Tropomyosin alpha-1 chain 474 DSC3 Desmocollin-3 475 IL20RA Interleukin-20 receptor subunit alpha 476 MAPK13 Mitogen-activated protein kinase 13 477 TNFRSF18 Tumor necrosis factor receptor superfamily member 18 478 EPHA10 Ephrin type-A receptor 10 479 INS Insulin 480 PTK2 Focal adhesion kinase 1 481 CGA.CGB Human Chorionic Gonadotropin 482 NCK1 Cytoplasmic protein NCK1 483 ULBP2 NKG2D ligand 2 484 HIBADH 3-hydroxyisobutyrate dehydrogenase, mitochondrial 485 TNFRSF4 Tumor necrosis factor receptor superfamily member 4 486 MMP1 Interstitial collagenase 487 TYMS Thymidylate synthase 488 IL12RB2 Interleukin-12 receptor subunit beta-2 489 NCR1 Natural cytotoxicity triggering receptor 1 490 LILRB1 Leukocyte immunoglobulin-like receptor subfamily B member 1 491 SIGLEC14 Sialic acid-binding Ig-like lectin 14 492 SORCS2 VPS10 domain-containing receptor SorCS2 493 TGM3 Protein-glutamine gamma-glutamyltransferase E 494 CCL8 C-C motif chemokine 8 495 CCL7 C-C motif chemokine 7 496 CXCL10 C-X-C motif chemokine 10 497 CX3CL1 Fractalkine 498 CCL2 C-C motif chemokine 2 499 CXCL8 Interleukin-8 500 CXCL11 C-X-C motif chemokine 11 501 CTSS Cathepsin S 502 LGMN Legumain 503 ESM1 Endothelial cell-specific molecule 1 504 IL1RL2 Interleukin-1 receptor-like 2 505 LAMA1.LAMB1..LAMC1 Laminin 506 TNFAIP6 Tumor necrosis factor-inducible gene 6 protein 507 CTSZ Cathepsin Z 508 IL18BP Interleukin-18-binding protein 509 PCSK9 Proprotein convertase subtilisin/kexin type 9 510 SAA1 Serum amyloid A-1 protein 511 ADAM9 Disintegrin and metalloproteinase domain-containing protein 9 512 CD4 T-cell surface glycoprotein CD4 513 ENTPD1 Ectonucleoside triphosphate diphosphohydrolase 1 514 PSMD7 26S proteasome non-ATPase regulatory subunit 7 515 CSF1 Macrophage colony-stimulating factor 1 516 PLAUR Urokinase plasminogen activator surface receptor 517 CD84 SLAM family member 5 518 LAYN Layilin 519 IL10RB Interleukin-10 receptor subunit beta 520 DLL4 Delta-like protein 4 521 TNFSF15 Tumor necrosis factor ligand superfamily member 15 522 FCN1 Ficolin-1 523 KPNA2 Importin subunit alpha-1 524 SPOCK2 Testican-2 525 CCL18 C-C motif chemokine 18 526 CCL3L1 C-C motif chemokine 3-like 1 527 CCL3 C-C motif chemokine 3 528 CFHR5 Complement factor H-related protein 5 529 IL5RA Interleukin-5 receptor subunit alpha 530 C9 Complement component C9 531 F9 Coagulation factor IX 532 F9.1 Coagulation factor IXab 533 FCN2 Ficolin-2 534 F10 Coagulation factor Xa 535 F10.1 Coagulation Factor X 536 ITIH4 Inter-alpha-trypsin inhibitor heavy chain H4 537 JAK2 Tyrosine-protein kinase JAK2 538 CCL11 Eotaxin 539 CCL19 C-C motif chemokine 19 540 CCL27 C-C motif chemokine 27 541 CDH1 Cadherin-1 542 CXCL12 Stromal cell-derived factor 1 543 CXCL13 C-X-C motif chemokine 13 544 TFPI Tissue factor pathway inhibitor 545 CHRDL1 Chordin-like protein 1 546 FRZB Secreted frizzled-related protein 3 547 GFRA1 GDNF family receptor alpha-1 548 MDK Midkine 549 ACP5 Tartrate-resistant acid phosphatase type 5 550 PAK6 Serine/threonine-protein kinase PAK 6 551 C5 Complement C5 552 C5.C6 Complement C5b-C6 complex 553 C7 Complement component C7 554 CAPG Macrophage-capping protein 555 PLA2G1B Phospholipase A2 556 PRSS1 Trypsin-1 557 PRSS2 Trypsin-2 558 C1QA.C1QB..C1QC Complement C1q subcomponent 559 FGF2 Fibroblast growth factor 2 560 DPP7 Dipeptidyl peptidase 2 561 CNDP1 Beta-Ala-His dipeptidase 562 IGHD..IGK..IGL. Immunoglobulin D 563 IGHE.IGK..IGL. Immunoglobulin E 564 LGALS3 Galectin-3 565 CD5L CD5 antigen-like 566 IGHM.IGJ.IGK..IGL. Immunoglobulin M 567 IGHG1.IGHG2.IGHG3.IGHG4.IGK..IGL. Immunoglobulin G 568 DSG2 Desmoglein-2 569 TNFRSF25 Tumor necrosis factor receptor superfamily member 25 570 RTN4 Reticulon-4 571 TNFRSF17 Tumor necrosis factor receptor superfamily member 17 572 SLAMF7 SLAM family member 7 573 MICB MHC class I polypeptide-related sequence B 574 TNNI2 Troponin I, fast skeletal muscle 575 BMPR2 Bone morphogenetic protein receptor type-2 576 CTSH Cathepsin H 577 CCL14 C-C motif chemokine 14 578 Human.virus.3 gp41 C34 peptide, HIV 579 CTSE Cathepsin E 580 FGA.FGB.FGG Fibrinogen 581 FGG Fibrinogen gamma chain 582 SET Protein SET 583 CHIT1 Chitotriosidase-1 584 BPI Bactericidal permeability-increasing protein 585 HGF Hepatocyte growth factor 586 ALPL Alkaline phosphatase, tissue-nonspecific isozyme 587 LTF Lactotransferrin 588 MMP9 Matrix metalloproteinase-9 589 OLR1 Oxidized low-density lipoprotein receptor 1 590 CSF3 Granulocyte colony-stimulating factor 591 IL6 Interleukin-6 592 HAMP Hepcidin 593 CST7 Cystatin-F 594 LCN2 Neutrophil gelatinase-associated lipocalin 595 RETN Resistin 596 S100A9 Protein S100-A9 597 PGLYRP1 Peptidoglycan recognition protein 1 598 ADAMTS15 A disintegrin and metalloproteinase with thrombospondin motifs 15 599 LCMT1 Leucine carboxyl methyltransferase 1 600 LY86 Lymphocyte antigen 86 601 CXCL5 C-X-C motif chemokine 5 602 CBX5 Chromobox protein homolog 5 603 STAB2 Stabilin-2 604 C1S Complement C1s subcomponent 605 ASGR1 Asialoglycoprotein receptor 1 606 HINT1 Histidine triad nucleotide-binding protein 1 607 IL12B.IL23A Interleukin-23 608 IL17A Interleukin-17A 609 GDF11 Growth/differentiation factor 11 610 LYN.1 Tyrosine-protein kinase Lyn 611 FGA.FGB.FGG.1 D-dimer 612 HSPA8 Heat shock cognate 71 kDa protein 613 Human.virus.2 Protein Rev_HV2BE 614 PLG.1 Plasmin 615 VEGFA.1 Vascular endothelial growth factor A, isoform 121 616 PLG.2 Plasminogen 617 MMP8 Neutrophil collagenase 618 PRKCD Protein kinase C delta type 619 NGF beta-nerve growth factor 620 BIRC7 Baculoviral IAP repeat-containing protein 7 Isoform beta 621 HS6ST1 Heparan-sulfate 6-O-sulfotransferase 1 622 PLK1 Serine/threonine-protein kinase PLK1 623 TGFB3 Transforming growth factor beta-3 624 PIK3CG Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform 625 DAPK2 Death-associated protein kinase 2 626 PRSS27 Serine protease 27 627 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 628 GZMH Granzyme H 629 FCRL3 Fc receptor-like protein 3 630 GAS1 Growth arrest-specific protein 1 631 TNFSF12 Tumor necrosis factor ligand superfamily member 12 632 CCL20 C-C motif chemokine 20 633 CD207 C-type lectin domain family 4 member K 634 ADAM12 Disintegrin and metalloproteinase domain-containing protein 12 635 ABL1 Tyrosine-protein kinase ABL1 636 IFNL2 Interferon lambda-2 637 TMPRSS15 Enteropeptidase 638 CA7 Carbonic anhydrase 7 639 TGFB2 Transforming growth factor beta-2 640 IL20 Interleukin-20 641 AURKB Aurora kinase B 642 NTF4 Neurotrophin-4 643 SPHK2 Sphingosine kinase 2 644 LRRTM3 Leucine-rich repeat transmembrane neuronal protein 3 645 STK16 Serine/threonine-protein kinase 16 646 CHST6 Carbohydrate sulfotransferase 6 647 IL17RD Interleukin-17 receptor D 648 PLA2G10 Group 10 secretory phospholipase A2 649 HDAC8 Histone deacetylase 8 650 TPO Thyroid peroxidase 651 IL24 Interleukin-24 652 TG Thyroglobulin 653 IL25 Interleukin-25 654 ERBB2 Receptor tyrosine-protein kinase erbB-2 655 RPSA 40S ribosomal protein SA 656 LCORL Ligand-dependent nuclear receptor corepressor-like protein 657 MEPE Matrix extracellular phosphoglycoprotein 658 CHEK1 Serine/threonine-protein kinase Chk1 659 PLA2G2E Group IIE secretory phospholipase A2 660 IL18RAP Interleukin-18 receptor accessory protein 661 Human.virus Protein E7_HPV16 662 NCR2 Natural cytotoxicity triggering receptor 2 663 IGFBP1 Insulin-like growth factor-binding protein 1 664 BMX Cytoplasmic tyrosine-protein kinase BMX 665 PTPN2 Tyrosine-protein phosphatase non-receptor type 2 666 IL2 Interleukin-2 667 PCNA Proliferating cell nuclear antigen 668 MMP3 Stromelysin-1 669 PDE7A High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A 670 ARSA Arylsulfatase A 671 ACY1 Aminoacylase-1 672 POR NADPH--cytochrome P450 reductase 673 HTRA2 Serine protease HTRA2, mitochondrial 674 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 675 HSPD1 60 kDa heat shock protein, mitochondrial 676 ITGA1.ITGB1 Integrin alpha-I: beta-1 complex 677 P4HB Protein disulfide-isomerase 678 AGT Angiotensinogen 679 CD55 Complement decay-accelerating factor 680 IGFBP2 Insulin-like growth factor-binding protein 2 681 ICAM1 Intercellular adhesion molecule 1 682 IGF2R Cation-independent mannose-6-phosphate receptor 683 LYVE1 Lymphatic vessel endothelial hyaluronic acid receptor 1 684 NRP1 Neuropilin-1 685 CD163 Scavenger receptor cysteine-rich type 1 protein M130 686 CD33 Myeloid cell surface antigen CD33 687 CSF1R Macrophage colony-stimulating factor 1 receptor 688 SELL L-Selectin 689 GNLY Granulysin 690 CD300C CMRF35-like molecule 6 691 DCTPP1 dCTP pyrophosphatase 1 692 CD48 CD48 antigen 693 GZMA Granzyme A 694 LAG3 Lymphocyte activation gene 3 protein 695 TNFRSF8 Tumor necrosis factor receptor superfamily member 8 696 SLAMF6 SLAM family member 6 697 ELANE Neutrophil elastase 698 CCL4L1 C-C motif chemokine 4-like 699 IL10 Interleukin-10 700 GZMB Granzyme B 701 CD36 Platelet glycoprotein 4 702 MMP12 Macrophage metalloelastase 703 DLL1 Delta-like protein 1 704 HAVCR2 Hepatitis A virus cellular receptor 2 705 TNFRSF1A Tumor necrosis factor receptor superfamily member 1A 706 TNFRSF1B Tumor necrosis factor receptor superfamily member 1B 707 FSTL3 Follistatin-related protein 3 708 TIMP1 Metalloproteinase inhibitor 1 709 CTSB Cathepsin B 710 FCGR3B Low affinity immunoglobulin gamma Fc region receptor III-B 711 LILRB2 Leukocyte immunoglobulin-like receptor subfamily B member 2 712 MRC1 Macrophage mannose receptor 1 713 SIGLEC7 Sialic acid-binding Ig-like lectin 7 714 PGAM1 Phosphoglycerate mutase 1 715 NAMPT Nicotinamide phosphoribosyltransferase 716 TLR2 Toll-like receptor 2 717 IL27.EBI3 Interleukin-27 718 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 719 MBD4 Methyl-CpG-binding domain protein 4 720 BMPER BMP-binding endothelial regulator protein 721 COL23A1 Collagen alpha-1(XXIII) chain 722 MDM2 E3 ubiquitin-protein ligase Mdm2 723 PAK7 Serine/threonine-protein kinase PAK 7 724 CD80 T-lymphocyte activation antigen CD80 725 FGF8 Fibroblast growth factor 8 isoform B 726 OCIAD1 OCIA domain-containing protein 1 727 ADCYAP1 Pituitary adenylate cyclase-activating polypeptide 27 728 ADCYAP1.1 Pituitary adenylate cyclase-activating polypeptide 38 729 IL12A.IL12B Interleukin-12 730 TDGF1 Teratocarcinoma-derived growth factor 1 731 MAPT Microtubule-associated protein tau 732 MMP10 Stromelysin-2 733 CLU Clusterin 734 GDF5 Growth/differentiation factor 5 735 ADAMTS1 A disintegrin and metalloproteinase with thrombospondin motifs 1 736 IL17D Interleukin-17D 737 CDH12 Cadherin-12 738 PES1 Pescadillo homolog 739 DNAJC19 Mitochondrial import inner membrane translocase subunit TIM14 740 CSF3R Granulocyte colony-stimulating factor receptor 741 IL11 Interleukin-11 742 IL1B Interleukin-1 beta 743 PPIB Peptidyl-prolyl cis-trans isomerase B 744 NTRK1 High affinity nerve growth factor receptor 745 CDC42BPB Serine/threonine-protein kinase MRCK beta 746 CASP10 Caspase-10 747 BMP10 Bone morphogenetic protein 10 748 DDR2 Discoidin domain-containing receptor 2 749 ESR1 Estrogen receptor 750 FCGR1A High affinity immunoglobulin gamma Fc receptor I 751 HMOX2 Heme oxygenase 2 752 ANGPTL3 Angiopoietin-related protein 3 753 MATN3 Matrilin-3 754 CLEC7A C-type lectin domain family 7 member A 755 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 756 GREM1 Gremlin-1 757 CTSG Cathepsin G 758 EFNB3 Ephrin-B3 759 H2AFZ Histone H2A.z 760 BDNF Brain-derived neurotrophic factor 761 MMP17 Matrix metalloproteinase-17 762 KAT6A Histone acetyltransferase KAT6A 763 PRKCZ Protein kinase C zeta type 764 GFRA3 GDNF family receptor alpha-3 765 ENTPD3 Ectonucleoside triphosphate diphosphohydrolase 3 766 PECAM1 Platelet endothelial cell adhesion molecule 767 IL22RA1 Interleukin-22 receptor subunit alpha-1 768 CCL13 C-C motif chemokine 13 769 RBM39 RNA-binding protein 39 770 SERPINE2 Glia-derived nexin 771 MFRP Membrane frizzled-related protein 772 TGFB1 Transforming growth factor beta-1 773 IL15RA Interleukin-15 receptor subunit alpha 774 COMMD7 COMM domain-containing protein 7 775 STX1A Syntaxin-1A 776 APOD Apolipoprotein D 777 PTPN1 Tyrosine-protein phosphatase non-receptor type 1 778 BCL2A1 Bcl-2-related protein A1 779 HPGD 15-hydroxyprostaglandin dehydrogenase [NAD(+)] 780 CDH6 Cadherin-6 781 BSG Basigin 782 EPHB4 Ephrin type-B receptor 4 783 SMPDL3A Acid sphingomyelinase-like phosphodiesterase 3a 784 PDE2A cGMP-dependent 3',5'-cyclic phosphodiesterase 785 IMPDH2 Inosine-5'-monophosphate dehydrogenase 2 786 RSPO2 R-spondin-2 787 DKKL1 Dickkopf-like protein 1 788 PPP3R1 Calcineurin subunit B type 1 789 KLK14 Kallikrein-14 790 OPCML Opioid-binding protein/cell adhesion molecule 791 PDIA3 Protein disulfide-isomerase A3 792 WISP1 WNT1-inducible-signaling pathway protein 1 793 SFN 14-3-3 protein sigma 794 SH2D1A SH2 domain-containing protein 1A 795 GPC2 Glypican-2 796 KLK4 Kallikrein-4 797 GPT Alanine aminotransferase 1 798 ANGPT4 Angiopoietin-4 799 TNFRSF13B Tumor necrosis factor receptor superfamily member 13B 800 TOP1 DNA topoisomerase 1 801 CRISP3 Cysteine-rich secretory protein 3 802 ACVR1B Activin receptor type-1B 803 PROK1 Prokineticin-1 804 FGF12 Fibroblast growth factor 12 805 EPO Erythropoietin 806 FGF23 Fibroblast growth factor 23 807 SERPINE1 Plasminogen activator inhibitor 1 808 CAPN1.CAPNS1 Calpain I 809 HBA1.HBB Hemoglobin 810 KYNU Kynureninase 811 LDHB L-lactate dehydrogenase B chain 812 NAGK N-acetyl-D-glucosamine kinase 813 AIF1 Allograft inflammatory factor 1 814 IL16 Interleukin-16 815 ADRBK1 beta-adrenergic receptor kinase 1 816 CSK Tyrosine-protein kinase CSK 817 CMA1 Chymase 818 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 819 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 820 RPS7 40S ribosomal protein S7 821 MAPK14 Mitogen-activated protein kinase 14 822 FLT3 Receptor-type tyrosine-protein kinase FLT3 823 YES1 Tyrosine-protein kinase Yes 824 HSP90AA1.HSP90AB1 Heat shock protein HSP 90-alpha/beta 825 YWHAB.YWHAE.YWHAG.YWHAH.YWHAQ.YWHAZ.SFN 14-3-3 protein family 826 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 827 PTPN6 Tyrosine-protein phosphatase non-receptor type 6 828 UCHL1 Ubiquitin carboxyl-terminal hydrolase isozyme L1 829 SSRP1 FACT complex subunit SSRP1 830 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 831 MAPKAPK3 MAP kinase-activated protein kinase 3 832 PKM2 Pyruvate kinase PKM 833 PGD 6-phosphogluconate dehydrogenase, decarboxylating 834 LRPAP1 alpha-2-macroglobulin receptor-associated protein 835 GPI Glucose-6-phosphate isomerase 836 CDK2.CCNA2 Cyclin-dependent kinase 2:Cyclin-A2 complex 837 TK1 Thymidine kinase, cytosolic 838 PSMA2 Proteasome subunit alpha type-2 839 CTSD Cathepsin D 840 PPP3CA.PPP3R1 Calcineurin 841 NID1 Nidogen-1 842 NID2 Nidogen-2 843 HDGFRP2 Hepatoma-derived growth factor-related protein 2 844 HIST1H1C Histone H1.2 845 ICOSLG ICOS ligand 846 CCL23 C-C motif chemokine 23 847 PLA2G2A Phospholipase A2, membrane associated 848 IL1RL1 Interleukin-1 receptor-like 1 849 MPO Myeloperoxidase 850 PRTN3 Myeloblastin 851 NTN4 Netrin-4 852 SERPINA1 Alpha-1-antitrypsin 853 PDE11A Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A 854 PLAT Tissue-type plasminogen activator 855 VWF von Willebrand factor 856 STC1 Stanniocalcin-1 857 LBP Lipopolysaccharide-binding protein 858 REN Renin 859 MMEL1 Membrane metallo-endopeptidase-like 1 860 NME1 Nucleoside diphosphate kinase A 861 TEC Tyrosine-protein kinase Tec 862 PLA2G7 Platelet-activating factor acetylhydrolase 863 CHST2 Carbohydrate sulfotransferase 2 864 CNDP2 Cytosolic non-specific dipeptidase 865 MST1R Macrophage-stimulating protein receptor 866 IL12RB1 Interleukin-12 receptor subunit beta-1 867 TBP TATA-box-binding protein 868 ICAM3 Intercellular adhesion molecule 3 869 XCL1 Lymphotactin 870 LRRTM1 Leucine-rich repeat transmembrane neuronal protein 1 871 SIGLEC6 Sialic acid-binding Ig-like lectin 6 872 IL7 Interleukin-7 873 MPL Thrombopoietin Receptor 874 NANOG Homeobox protein NANOG 875 PON1 Serum paraoxonase/arylesterase 1 876 TNFSF4 Tumor necrosis factor ligand superfamily member 4 877 COLEC12 Collectin-12 878 LIFR Leukemia inhibitory factor receptor 879 PROC.1 Activated Protein C 880 TNFRSF10A Tumor necrosis factor receptor superfamily member 10A 881 ACVRL1 Serine/threonine-protein kinase receptor R3 882 LCK Tyrosine-protein kinase Lck 883 TNFRSF13C Tumor necrosis factor receptor superfamily member 13C 884 CXCL1 Growth-regulated alpha protein 885 CXCL3.CXCL2 Gro-beta/gamma 886 CXCL6 C-X-C motif chemokine 6 887 CCL22 C-C motif chemokine 22 888 CCL28 C-C motif chemokine 28 889 DKK1 Dickkopf-related protein 1 890 DKK4 Dickkopf-related protein 4 891 CCL17 C-C motif chemokine 17 892 ANXA6 Annexin A6 893 THBS1 Thrombospondin-1 894 CLEC1B C-type lectin domain family 1 member B 895 ANGPT1 Angiopoietin-1 896 APP Amyloid beta A4 protein 897 CCL5 C-C motif chemokine 5 898 PDGFB Platelet-derived growth factor subunit B 899 PF4 Platelet factor 4 900 PPBP Neutrophil-activating peptide 2 901 PPBP.1 Connective tissue-activating peptide III 902 PDGFA Platelet-derived growth factor subunit A 903 SPARC SPARC 904 TIMP3 Metalloproteinase inhibitor 3 905 CA13 Carbonic anhydrase 13 906 DUSP3 Dual specificity protein phosphatase 3 907 CAMK2B Calcium/calmodulin-dependent protein kinase type II subunit beta 908 CAMK2A Calcium/calmodulin-dependent protein kinase type II subunit alpha 909 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 910 PPIF Peptidyl-prolyl cis-trans isomerase F, mitochondrial 911 CFL1 Cofilin-1 912 SPHK1 Sphingosine kinase 1 913 FER Tyrosine-protein kinase Fer 914 PRKCA Protein kinase C alpha type 915 BTK Tyrosine-protein kinase BTK 916 PRKCB Protein kinase C beta type (splice variant beta-II) 917 PDPK1 3-phosphoinositide-dependent protein kinase 1 918 METAP1 Methionine aminopeptidase 1 919 PPID Peptidyl-prolyl cis-trans isomerase D 920 LYN Tyrosine-protein kinase Lyn, isoform B 921 SRC Proto-oncogene tyrosine-protein kinase Src 922 SNX4 Sorting nexin-4 923 GP6 Platelet glycoprotein VI 924 PDE5A cGMP-specific 3',5'-cyclic phosphodiesterase 925 ACE2 Angiotensin-converting enzyme 2 926 ADAMTS5 A disintegrin and metalloproteinase with thrombospondin motifs 5 927 EPOR Erythropoietin receptor 928 HBEGF Heparin-binding EGF-like growth factor 929 CTGF Connective tissue growth factor 930 TACSTD2 Tumor-associated calcium signal transducer 2 931 DCN Decorin 932 EDAR Tumor necrosis factor receptor superfamily member EDAR 933 CFC1 Cryptic protein 934 JAM2 Junctional adhesion molecule B 935 IL23R Interleukin-23 receptor 936 IL22 Interleukin-22 937 ABL2 Abelson tyrosine-protein kinase 2 938 BCAR3 Breast cancer anti-estrogen resistance protein 3 939 MMP16 Matrix metalloproteinase-16 940 CDH15 Cadherin-15 941 DYRK3 Dual specificity tyrosine-phosphorylation-regulated kinase 3 942 ANGPTL4 Angiopoietin-related protein 4 943 SLC25A18 Mitochondrial glutamate carrier 2 944 MSR1 Macrophage scavenger receptor types I and II 945 AIP AH receptor-interacting protein 946 CMPK1 UMP-CMP kinase 947 TNFRSF11A Tumor necrosis factor receptor superfamily member 11A 948 IL2RA Interleukin-2 receptor subunit alpha 949 IL3 Interleukin-3 950 HSD17B1 Estradiol 17-beta-dehydrogenase 1 951 MAP3K7.TAB1 Mitogen-activated protein kinase kinase kinase 7:TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 fusion 952 MAPK1 Mitogen-activated protein kinase 1 953 MAPK3 Mitogen-activated protein kinase 3 954 IMPDH1 Inosine-5'-monophosphate dehydrogenase 1 955 HMGB1 High mobility group protein B1 956 SFTPD Pulmonary surfactant-associated protein D 957 STK17B Serine/threonine-protein kinase 17B 958 PTGS2 Prostaglandin G/H synthase 2 959 BMP6 Bone morphogenetic protein 6 960 IL5 Interleukin-5 961 PDE3A cGMP-inhibited 3',5'-cyclic phosphodiesterase A 962 TYK2 Non-receptor tyrosine-protein kinase TYK2 963 CSNK2A1 Casein kinase II subunit alpha 964 FGF8.1 Fibroblast growth factor 8 isoform A 965 CCL24 C-C motif chemokine 24 966 FGF4 Fibroblast growth factor 4 967 KREMEN2 Kremen protein 2 968 FST Follistatin 969 CD22 B-cell receptor CD22 970 LGALS4 Galectin-4 971 PLA2G5 Calcium-dependent phospholipase A2 972 LMNB1 Lamin-B1 973 PSMA1 Proteasome subunit alpha type-1 974 NR3C1 Glucocorticoid receptor 975 TBK1 Serine/threonine-protein kinase TBK1 976 FTH1.FTL Ferritin 977 ACP1 Low molecular weight phosphotyrosine protein phosphatase 978 HAT1 Histone acetyltransferase type B catalytic subunit 979 CA1 Carbonic anhydrase 1 980 CA3 Carbonic anhydrase 3 981 CDC37 Hsp90 co-chaperone Cdc37 982 IGF1 Insulin-like growth factor I 983 AKR1A1 Alcohol dehydrogenase [NADP(+)] 984 PSME1 Proteasome activator complex subunit 1 985 CAT Catalase 986 GDI2 Rab GDP dissociation inhibitor beta 987 MDH1 Malate dehydrogenase, cytoplasmic 988 METAP2 Methionine aminopeptidase 2 989 SHC1 SHC-transforming protein 1 990 EPB41 Protein 4.1 991 AZU1 Azurocidin 992 CRLF2 Cytokine receptor-like factor 2 993 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 994 BCL2 Apoptosis regulator Bcl-2 995 SOD1 Superoxide dismutase [Cu-Zn] 996 EIF5 Eukaryotic translation initiation factor 5 997 CGA.LHB Luteinizing hormone 998 IFNG Interferon gamma 999 IL3RA Interleukin-3 receptor subunit alpha 1000 DHH Desert hedgehog protein N-product 1001 FGF7 Fibroblast growth factor 7 1002 ARID3A AT-rich interactive domain-containing protein 3A 1003 SEZ6L2 Seizure 6-like protein 2 1004 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 1005 EEF1B2 Elongation factor 1-beta 1006 CSNK2A1.CSNK2B Casein kinase II 2-alpha:2-beta heterotetramer 1007 AK1 Adenylate kinase isoenzyme 1 1008 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 1009 IL2RG Cytokine receptor common subunit gamma 1010 FLRT1 Leucine-rich repeat transmembrane protein FLRT1 1011 FGF16 Fibroblast growth factor 16 1012 AREG Amphiregulin 1013 PDXP Pyridoxal phosphate phosphatase 1014 PSMA6 Proteasome subunit alpha type-6 1015 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 1016 JAM3 Junctional adhesion molecule C 1017 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1018 PEBP1 Phosphatidylethanolamine-binding protein 1 1019 NAPA Alpha-soluble NSF attachment protein 1020 PA2G4 Proliferation-associated protein 2G4 1021 UBE2N Ubiquitin-conjugating enzyme E2 N 1022 STIP1 Stress-induced-phosphoprotein 1 1023 PRDX6 Peroxiredoxin-6 1024 PRDX1 Peroxiredoxin-1 1025 TKT Transketolase 1026 TPI1 Triosephosphate isomerase 1027 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1028 ING1 Inhibitor of growth protein 1 1029 PRKCI Protein kinase C iota type 1030 RAC1 Ras-related C3 botulinum toxin substrate 1 1031 SBDS Ribosome maturation protein SBDS 1032 NACA Nascent polypeptide-associated complex subunit alpha 1033 ULBP3 NKG2D ligand 3 1034 SKP1 S-phase kinase-associated protein 1 1035 KIR2DL4 Killer cell immunoglobulin-like receptor 2DL4 1036 CLIC1 Chloride intracellular channel protein 1 1037 CPNE1 Copine-1 1038 GSK3A.GSK3B Glycogen synthase kinase-3 alpha/beta 1039 TPT1 Translationally-controlled tumor protein 1040 PPIA Peptidyl-prolyl cis-trans isomerase A 1041 UBE2I SUMO-conjugating enzyme UBC9 1042 DNAJB1 DnaJ homolog subfamily B member 1 1043 RPS27A Ubiquitin+1, truncated mutation for UbB 1044 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1045 RAN GTP-binding nuclear protein Ran 1046 RPS27A.1 Ubiquitin 1047 MIF Macrophage migration inhibitory factor 1048 PRKAA2.PRKAB2.PRKAG1 AMP Kinase (alpha2beta2gamma1) 1049 INHBA.INHBB Inhibin beta A chain:Inhibin beta B chain heterodimer 1050 CD40LG CD40 ligand 1051 IFNL1 Interferon lambda-1 1052 IL4 Interleukin-4 1053 TSLP Thymic stromal lymphopoietin 1054 FGF6 Fibroblast growth factor 6 1055 VIP Vasoactive Intestinal Peptide 1056 MSLN Mesothelin 1057 SERPINA6 Corticosteroid-binding globulin 1058 MAPKAPK2 MAP kinase-activated protein kinase 2 1059 ATP5B ATP synthase subunit beta, mitochondrial 1060 RPS3 40S ribosomal protein S3 1061 SPOCK1 Testican-1 1062 EIF4A3 Eukaryotic initiation factor 4A-III 1063 MAPK8 Mitogen-activated protein kinase 8 1064 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1065 PPIE Peptidyl-prolyl cis-trans isomerase E 1066 KIF23 Kinesin-like protein KIF23 1067 VEGFC Vascular endothelial growth factor C 1068 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1069 COTL1 Coactosin-like protein 1070 SFRP1 Secreted frizzled-related protein 1 1071 ANXA1 Annexin A1 1072 ANXA2 Annexin A2 1073 DYNLRB1 Dynein light chain roadblock-type 1 1074 ADSL Adenylosuccinate lyase 1075 GSTP1 Glutathione S-transferase P 1076 CASP3 Caspase-3 1077 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1078 EIF5A Eukaryotic translation initiation factor 5A-1 1079 CRK Adapter molecule crk 1080 KPNB1 Importin subunit beta-1 1081 NSFL1C NSFL1 cofactor p47 1082 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 1083 UFM1 Ubiquitin-fold modifier 1 1084 IDE Insulin-degrading enzyme 1085 PPA1 Inorganic pyrophosphatase 1086 NME2 Nucleoside diphosphate kinase B 1087 ESD S-formylglutathione hydrolase 1088 XPNPEP1 Xaa-Pro aminopeptidase 1 1089 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1090 NUDCD3 NudC domain-containing protein 3 1091 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1092 PRKACA cAMP-dependent protein kinase catalytic subunit alpha 1093 PFDN5 Prefoldin subunit 5 1094 XRCC6 X-ray repair cross-complementing protein 6 1095 PGK1 Phosphoglycerate kinase 1 1096 CDK5.CDK5R1 Cyclin-dependent kinase 5:Cyclin-dependent kinase 5 activator 1 complex 1097 CDC2.CCNB1 Cyclin-dependent kinase 1:G2/mitotic-specific cyclin-B1 complex 1098 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 1099 NCR3 Natural cytotoxicity triggering receptor 3 1100 PLCG1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 1101 EPHA3 Ephrin type-A receptor 3 1102 FGF9 Fibroblast growth factor 9 1103 DYNLL1 Dynein light chain 1, cytoplasmic 1104 TNFSF11 Tumor necrosis factor ligand superfamily member 11 1105 DDC Aromatic-L-amino-acid decarboxylase 1106 SERPINA3 Alpha-1-antichymotrypsin 1107 TF Serotransferrin (B) Heatmap for the Bacteria vs Virus or Malaria model with all 151 significant markers, hierarchically clustered with all single etiology bacteria, virus, and control samples from the training and validation set (n=171).
19
Fig. S3 Protein marker overlap of the 30 highest ranking markers.
SOMAScan Bacteria vs Virus (BvV) and Bacteria vs Virus and Malaria (BvVM) marker sets.
Comparison Markers Venn Diagram
SOMAScan CSF3 (BvV) and CTF1 SOMAScan CX3CL1 (BvVM) CXCL13 ESD FABP5 HGF
IL1RL1 IL6 LCN2 MPO PIK3CG PLA2G2A RETN S100A9 SERPINA4 SLPI
20 Fig. S4 Box and whisker plots of the 100 Top markers.
Distribution of the logarithm of Relative Fluorescence Units (RFU) for BvV and BvVM marker
sets. RFUs are directly proportional to the amount of target protein in the initial sample. B =
Bacteria, V = Virus, V+M = Virus or Malaria
(A) Box and whisker plots of 100 Top Markers in Bacteria vs Virus or Malaria
21 (B) Box and whisker plots of 100 Top Markers in Bacteria vs Virus
22 Fig. S5 Model accuracy when switching out surrogates for comparisons of interests
Model classification accuracy assessed on validation data for Bacteria vs Virus and Bacteria vs
Virus or Malaria using two different classification algorithms (Random Forest and Elastic Net).
The plots show classifier accuracy with increasing numbers of biomarkers used in training the model. The panels show how model performance changes when 10% or 20% of markers are substituted with their corresponding surrogate markers.
(A) Bacteria vs Virus with 5, 10, 15, 25, 50, 100 and all (219) markers
23 (B) Bacteria vs Malaria or Virus with 5, 10, 15, 25, 50, 100 and all (151) markers
24 Fig. S6 RBM multiplexed Immunoassay, RNA-sequencing and SOMAscan assay comparisons with Venn diagrams and marker lists
(A) Table of differential markers (genes) shared between this study and the previous RNA-
Sequencing study of the same population.1,2 SOMAScan protein markers were converted into their gene names to compare markers between studies.
Marker sets (genes) represented are SOMAScan BvV (n=226), SOMAScan BvVM (n=156), and
RNA-Sequencing BvVM, Malaria vs Virus or Malaria (MvBV), and Virus vs Bacteria or Malaria
(VvBM) (n=431, n=99, and n=70, respectively).
Comparison Markers Venn Diagram
RNA- ALPL Sequencing C3* (BvVM, MvVB, CCL3 VvBM) and CD274 SOMAScan CHIT1 (BvVM) CST7 GZMB The 25 gene HBA1+ marker overlap HBB+ translates to 24 HGF protein markers HP IL18R1 +HBA1 and HBB IL18RAP is hemoglobin LAG3 LCN2 *C3a in LTF SOMAScan MMP8 MPO OSM PGLYRP1 PLXNC1
25 RETN S100A9 SERPINA1 SLPI
SOMAScan ALPL (BvVM) and CHIT1 RNA- CST7 Sequencing HGF (BvVM) HP IL18R1 depicted in Fig. 4 IL18RAP B LCN2 LTF MMP8 MPO OSM PGLYRP1 PLXNC1 RETN S100A9 SERPINA1 SLPI
26 RNA- ALPL Sequencing BPI (BvVM) and CHIT1 CST7 SOMAScan HGF (BvV) HP IL18R1 IL1R1 ITGA2B ITGB3 LCN2 LTF MAPK14 MPO PGD PGLYRP1 PLXNC1 RETN S100A9 SERPINA1 SLPI SMPDL3A
RNA- C3* Sequencing CCL3 (MvVB) and CD274 SOMAScan GZMB (BvVM) HBA1+ HBB+ 7 gene marker LAG3 overlap translates to 6 protein markers depicted in Supplemental File 6C
*C3a in SOMAScan + HBA1 and HBB is hemoglobin
27 (B) Table of differential markers (genes) shared between this study and previous RBM protein multiplex immunoassay of the same population 1,2. RBM and SOMAScan protein aliases were converted into their gene names to compare markers between studies.
Marker sets (genes) represented are SOMAScan BvV (n=226), SOMAScan BvVM (n=156), RBM multiplex assay 2-class comparisons (BvV, BvM, VvM with n=15, n=9, and n=22, respectively) and RBM multiplex assay 3-class comparison Bacteria vs Virus vs Malaria (n=16).
Comparison Markers Venn Diagram
SOMAScan (BvV) CKM and RBM (BvV) HP IL6 depicted in Fig. 3 MPO SERPINA1
SOMAScan (BvVM) APCS and RBM (BvV, HP BvM) IL6 MPO SERPINA1 VCAM1
28 Fig. S7 Heatmap of all 24 overlapping SOMAScan (BvVM) and RNA-sequencing markers.
Hierarchically clustered heatmap of normalized SOMAscan expression values for the 24 overlapping protein markers from the RNA-Sequencing study and the SOMAScan Bacteria vs
Malaria or Virus comparison in the space of all available single etiology samples used in this study
(n=167). The markers depicted are ALPL, CHIT1, C3a, CCL3, CD274, CST7, GZMB,
HBA1.HBB (hemoglobin), HGF, HP, IL18R1, IL18RAP, LAG3, LCN2, LTF, MMP8, MPO,
OSM, PGLYRP1, PLXNC1, RETN, S100A9, SERPINA1, and SLPI.
29 Fig. S8 Malarial markers shared between SOMAScan and RNA-sequencing.
Differential markers shared between this study and previous RNA-sequencing study of the same population. Shown are six protein markers shared between this study (SOMAScan BvVM) and
RNA-sequencing Malaria vs Bacteria or Virus (MvVB). Red = upregulated in bacterial samples, black = upregulated in malarial samples, dark blue = upregulated in malaria or virus samples.
30 Fig. S9 Enrichment Heatmap of the three-way comparison (Bacteria vs Malaria vs Virus). In this comparison individual protein markers could be shared by two, but not all three etiologies.
31 Fig. S10 Heatmap of the Bacteria vs Virus model. (A) Hierarchically clustered heatmap of normalized SOMAscan expression values for 219 significant markers (FDR<0.01) from the SOMAScan Bacteria vs Virus (BvV) comparison in the space of all single etiology bacterial and viral samples in this study.
32 row min row max top-markers-heatmap-data-L BACTERIA VIRUS
id EID128131 EID128184 EID128237 EID128188 EID128192 EID128101 EID128092 EID128115 EID128247 EID128119 EID128160 EID128242 EID128134 EID128104 EID128116 EID128234 EID128205 EID128158 EID128100 EID128227 EID128154 EID128254 EID128233 EID128252 EID128206 EID128159 EID128222 EID128156 EID128098 EID128181 EID128120 EID128118 EID128249 EID128211 EID128121 EID128236 EID128136 EID128251 EID128226 EID128102 EID128199 EID128135 EID128103 EID128133 X1191859.3 X1042570.1 X1138395.6 X1042543.5 X1042594.7 X1042680.7 X1042651.7 X1292901.6 X1394322.6 X1083282 EID128198 EID128155 EID128215 EID128132 EID128137 EID128193 EID128107 EID128106 EID128099 EID128245 EID128105 EID128124 EID128093 EID128117 X1292921.4 X1138459.5 X1323030.3 X1323034 X1042565.7 X1192877.5 X1138474.8 EID128110 EID128213 EID128244 EID128165 EID128231 EID128212 EID128196 EID128094 EID128178 EID128141 EID128207 EID128113 EID128253 EID128225 EID128239 EID128202 EID128195 EID128109 EID128138 EID128250 EID128125 EID128171 EID128241 EID128235 EID128112 EID128224 EID128204 EID128189 EID128228 EID128176 EID128128 EID128209 EID128111 EID128127 EID128108 X1192032.8 X1161398.5 X1323012.8 EID128217 EID128174 EID128229 EID128186 EID128232 EID128208 EID128180 EID128139 EID128126 EID128089 EID128243 EID128140 EID128168
top-markers-heatmap-data-L id Description
HBA1.HBB Hemoglobin CX3CL1 Fractalkine CCL7 C-C motif chemokine 7 CXCL1 Growth-regulated alpha protein CXCL3.CXCL2 Gro-beta/gamma LTA.LTB.1 Lymphotoxin alpha2:beta1 FN1.2 Fibronectin MET Hepatocyte growth factor receptor ESD S-formylglutathione hydrolase XPNPEP1 Xaa-Pro aminopeptidase 1 EPHA1 Ephrin type-A receptor 1 PAPPA Pappalysin-1 TPSB2 Tryptase beta-2 LEP Leptin PLXNC1 Plexin-C1 SERPINA5 Plasma serine protease inhibitor LTA.LTB Lymphotoxin alpha1:beta2 CDH3 Cadherin-3 CAST Calpastatin SERPING1 Plasma protease C1 inhibitor SHBG Sex hormone-binding globulin CA6 Carbonic anhydrase 6 SERPINA4 Kallistatin AFM Afamin KLKB1 Plasma kallikrein GSN Gelsolin IGFBP3 Insulin-like growth factor-binding protein 3 AHSG Alpha-2-HS-glycoprotein KLK8 Kallikrein-8 SLITRK5 SLIT and NTRK-like protein 5 CDON Cell adhesion molecule-related/down-regulated by oncogenes MRC2 C-type mannose receptor 2 NTRK3 NT-3 growth factor receptor CD109 CD109 antigen HAPLN1 Hyaluronan and proteoglycan link protein 1 ACAN Aggrecan core protein CADM1 Cell adhesion molecule 1 EFNA5 Ephrin-A5 SHH Sonic hedgehog protein LRIG3 Leucine-rich repeats and immunoglobulin-like domains protein 3 CNTFR Ciliary neurotrophic factor receptor subunit alpha TNFRSF21 Tumor necrosis factor receptor superfamily member 21 EPHB2 Ephrin type-B receptor 2 EPHB6 Ephrin type-B receptor 6 UNC5D Netrin receptor UNC5D NRXN1 Neurexin-1-beta NRCAM Neuronal cell adhesion molecule BCAN Brevican core protein ROR1 Tyrosine-protein kinase transmembrane receptor ROR1 UNC5C Netrin receptor UNC5C EPHA2 Ephrin type-A receptor 2 L1CAM Neural cell adhesion molecule L1 KIT Mast/stem cell growth factor receptor Kit NCAM1 Neural cell adhesion molecule 1, 120 kDa isoform CHL1 Neural cell adhesion molecule L1-like protein NTRK2 BDNF/NT-3 growth factors receptor CNTN4 Contactin-4 CDH5 Cadherin-5 LSAMP Limbic system-associated membrane protein FGFR1 Fibroblast growth factor receptor 1 NOTCH1 Neurogenic locus notch homolog protein 1 ALCAM CD166 antigen SERPINC1 Antithrombin-III OMD Osteomodulin LRP8 Low-density lipoprotein receptor-related protein 8 CNTN2 Contactin-2 EPHA5 Ephrin type-A receptor 5 CD200 OX-2 membrane glycoprotein RGMB RGM domain family member B DKK3 Dickkopf-related protein 3 LPO Lactoperoxidase KLK7 Kallikrein-7 DPT Dermatopontin CNTN1 Contactin-1 THBS4 Thrombospondin-4 NOTCH3 Neurogenic locus notch homolog protein 3 IL1R1 Interleukin-1 receptor type 1 SPINT1 Kunitz-type protease inhibitor 1 WIF1 Wnt inhibitory factor 1 PDCD1LG2 Programmed cell death 1 ligand 2 ITGA2B.ITGB3 Integrin alpha-IIb: beta-3 complex CKM Creatine kinase M-type HP Haptoglobin CDC2.CCNB1 Cyclin-dependent kinase 1:G2/mitotic-specific cyclin-B1 complex PGLYRP1 Peptidoglycan recognition protein 1 TOP1 DNA topoisomerase 1 RB1 Retinoblastoma-associated protein SIRT2 NAD-dependent protein deacetylase sirtuin-2 PIK3CG Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform MST1R Macrophage-stimulating protein receptor CTF1 Cardiotrophin-1 ZAP70 Tyrosine-protein kinase ZAP-70 SERPINE1 Plasminogen activator inhibitor 1 EPO Erythropoietin FGF23 Fibroblast growth factor 23 STC1 Stanniocalcin-1 SAA1 Serum amyloid A-1 protein CCL14 C-C motif chemokine 14 ETHE1 Persulfide dioxygenase ETHE1, mitochondrial SEMA3A Semaphorin-3A PLA2G2A Phospholipase A2, membrane associated CCL23 C-C motif chemokine 23 IL1RL1 Interleukin-1 receptor-like 1 SLPI Antileukoproteinase RETN Resistin NTN4 Netrin-4 SERPINA1 Alpha-1-antitrypsin MPO Myeloperoxidase PRTN3 Myeloblastin REN Renin PDE11A Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A TNFRSF1A Tumor necrosis factor receptor superfamily member 1A FSTL3 Follistatin-related protein 3 TIMP1 Metalloproteinase inhibitor 1 LBP Lipopolysaccharide-binding protein IL6 Interleukin-6 CSF3 Granulocyte colony-stimulating factor HAMP Hepcidin LCN2 Neutrophil gelatinase-associated lipocalin S100A9 Protein S100-A9 HGF Hepatocyte growth factor BPI Bactericidal permeability-increasing protein LTF Lactotransferrin ALPL Alkaline phosphatase, tissue-nonspecific isozyme CST7 Cystatin-F VEGFA Vascular endothelial growth factor A IL18R1 Interleukin-18 receptor 1 CCL3 C-C motif chemokine 3 CCL19 C-C motif chemokine 19 CXCL13 C-X-C motif chemokine 13 CXCL12 Stromal cell-derived factor 1 TFPI Tissue factor pathway inhibitor CCL27 C-C motif chemokine 27 GFRA1 GDNF family receptor alpha-1 CFHR5 Complement factor H-related protein 5 CCL18 C-C motif chemokine 18 CCL3L1 C-C motif chemokine 3-like 1 FABP5 Fatty acid-binding protein, epidermal ITIH4 Inter-alpha-trypsin inhibitor heavy chain H4 JAK2 Tyrosine-protein kinase JAK2 FCN2 Ficolin-2 F9.1 Coagulation factor IXab F9 Coagulation factor IX IGHD..IGK..IGL. Immunoglobulin D MRC1 Macrophage mannose receptor 1 LILRB2 Leukocyte immunoglobulin-like receptor subfamily B member 2 MAPK14 Mitogen-activated protein kinase 14 TNFRSF25 Tumor necrosis factor receptor superfamily member 25 DSG2 Desmoglein-2 RTN4 Reticulon-4 SLAMF7 SLAM family member 7 FGF12 Fibroblast growth factor 12 CRISP3 Cysteine-rich secretory protein 3 PRSS1 Trypsin-1 PRSS2 Trypsin-2 IGFBP2 Insulin-like growth factor-binding protein 2 AGT Angiotensinogen CASP10 Caspase-10 F10 Coagulation factor Xa F10.1 Coagulation Factor X CHIT1 Chitotriosidase-1 HSD17B1 Estradiol 17-beta-dehydrogenase 1 MAPK1 Mitogen-activated protein kinase 1 PPID Peptidyl-prolyl cis-trans isomerase D IMPDH1 Inosine-5'-monophosphate dehydrogenase 1 ADRBK1 beta-adrenergic receptor kinase 1 HMGB1 High mobility group protein B1 SFTPD Pulmonary surfactant-associated protein D STK17B Serine/threonine-protein kinase 17B DAPK2 Death-associated protein kinase 2 PGD 6-phosphogluconate dehydrogenase, decarboxylating CDK2.CCNA2 Cyclin-dependent kinase 2:Cyclin-A2 complex MAPKAPK3 MAP kinase-activated protein kinase 3 MATN3 Matrilin-3 Human.virus.2 Protein Rev_HV2BE PLG.1 Plasmin HSPA8 Heat shock cognate 71 kDa protein FGA.FGB.FGG.1 D-dimer TDGF1 Teratocarcinoma-derived growth factor 1 PRKCD Protein kinase C delta type GFRA3 GDNF family receptor alpha-3 IL12A.IL12B Interleukin-12 ADCYAP1.1 Pituitary adenylate cyclase-activating polypeptide 38 ADCYAP1 Pituitary adenylate cyclase-activating polypeptide 27 BIRC7 Baculoviral IAP repeat-containing protein 7 Isoform beta MDM2 E3 ubiquitin-protein ligase Mdm2 OCIAD1 OCIA domain-containing protein 1 CCL13 C-C motif chemokine 13 PECAM1 Platelet endothelial cell adhesion molecule IL22RA1 Interleukin-22 receptor subunit alpha-1 RBM39 RNA-binding protein 39 H2AFZ Histone H2A.z PRKCZ Protein kinase C zeta type MMP17 Matrix metalloproteinase-17 KAT6A Histone acetyltransferase KAT6A CTSG Cathepsin G FLT3 Receptor-type tyrosine-protein kinase FLT3 HSP90AA1.HSP90AB1 Heat shock protein HSP 90-alpha/beta ANGPTL4 Angiopoietin-related protein 4 HDGFRP2 Hepatoma-derived growth factor-related protein 2 RSPO2 R-spondin-2 HIST1H1C Histone H1.2 RPS7 40S ribosomal protein S7 ICOSLG ICOS ligand KLK14 Kallikrein-14 DKKL1 Dickkopf-like protein 1 PPP3R1 Calcineurin subunit B type 1 PDE2A cGMP-dependent 3',5'-cyclic phosphodiesterase SMPDL3A Acid sphingomyelinase-like phosphodiesterase 3a WISP1 WNT1-inducible-signaling pathway protein 1 APOD Apolipoprotein D LCMT1 Leucine carboxyl methyltransferase 1 ERBB2 Receptor tyrosine-protein kinase erbB-2 CCL20 C-C motif chemokine 20 IL17D Interleukin-17D IFNL2 Interferon lambda-2 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B MMEL1 Membrane metallo-endopeptidase-like 1 ANGPT2 Angiopoietin-2 Tables
Table S1 Patient demographic and disease characteristics at admission for Bacterial and PCR
Bacterial samples.
The “Bacteria” group includes blood or pleural fluid culture positive samples and “probable bacteria” samples that were culture negative but had leukocytosis and radiographic endpoint pneumonia and were independently judged by two clinical experts as probable bacterial infections.
Patient Demographic and Disease Characteristics at admission Features on admission (signs, symptoms, and laboratory Bacteria No. PCR BacteriaΩ No. P† results) Age (month), mean (SD) 30.5 (30.9) 42 28.4 (27.5) 27 0.87 Female sex, n (%) 19 (45.2) 42 12 (44.4) 27 0.79 Clinical Examination results on arrival Weight (kg), mean (SD) 10.1 (4.6) 42 10.2 (5.2) 27 0.69 Height (cm), mean (SD) 81.3 (18.8) 42 78.8 (18.8) 26 0.57 MUAC (cm), mean (SD) 13.4 (2.1) 42 13.56 (1.8) 27 0.86 Temperature (°C), mean (SD) 38.5 (1.0) 42 37.69 (1.3) 27 0.050 Respiratory rate (cycles per min), mean (SD) 61 (14.9) 42 60 (14.7) 27 0.77 Nutritional status WAZ > -1 SD 11 (26.2) 42 6 (22.2) 27 WAZ -1 SD to -3 SD, n (%) (low to severe 20 (47.6) 42 16 (59.3) 27 underweight) WAZ < -3 SD, n (%) (severe underweight) 11 (26.2) 42 5 (18.5) 27 WAZ: Mean (SD) -2 (1.8) 42 -2 (1.7) 27 0.92 Anaemia status on admission Hemoglobin (g/dL), mean (SD) 8.7 (2.4) 42 8.5 (1.7) 25 0.85 Packed cell volume (%), mean (SD) 26 (6.8) 42 26.3 (5.1) 25 0.44 No anaemia (hct > 33%), n (%) 2 (4.8) 42 2 (0.08) 25 Mild anaemia (hct 25 - | 33%), n (%) 19 (45.2) 42 12 (0.5) 25 Moderate anaemia (hct 15 - | 25%), n (%) 21 (50) 42 11 (0.4) 25 Severe anaemia (hct ≤ 15%), n (%) 0 (0.000) 42 0 (0.000) 25 Micro-biology and other laboratory results on admission
33 HIV status positive, n (%) 16 (38.1) 42 9 (33.3) 27 0.59 Positive blood culture, n (%) 29 (69) 42 0 (0) 27 <0.0001 WBC count (103/uL), mean (SD) 23.9 (15.1) 42 17 (7) 25 0.68 Neutrophil granulocytes (103/uL), mean (SD) 16.2 (10.7) 35 9.8 (6.6) 22 0.02 Plasmodium density (parasites/uL), geometric mean 0 (0) 42 0 (0) 27 (SD) Malaria positive 0 (0) 42 0 (0) 27 Chest X-Ray results >0.99 Normal X-ray, n (%) 5 (13.5) 37 4 (17.4) 23 Other infiltrate/abnormality, n (%) 2 (5.4) 37 4 (17.4) 23 Primary endpoint pneumonia, n (%) 30 (81.1) 37 15 (65.2) 23
Evolution during admission Duration of admission (days): Median (IQR) 5.1 (2.5-8.2) 42 3.7 (2-5.1) 27 0.18 Case fatality rate (in hospital death) 3 (7.1) 42 0 (0) 27 0.24
HCT= hematocrit; IQR= Interquartile Range; MUAC=middle upper arm circumference; SD= Standard Deviation; WAZ
= weight-for-age Z score. † P-values for continuous variables were estimated through analysis of Mann-Whitney U test.
P-values for categorical variables used Fisher’s exact test.
34 Table S2 Single etiology sample designations and distributions for training (n=120) and validation sets (n=47).
167 blood samples (including 8 replicates) were assayed using the SOMAScan platform. Replicate samples were included in the training set but not in the validation set.
Sample designation counts Training sample counts Validation sample counts
Bacteria 73* 54 (45%) 19 (40%)
Malaria 43** 28 (23%) 15 (32%)
Virus 51*** 38 (32%) 13 (28%)
Total 167 120 (100%) 47 (100%)
* Bacteria samples include 31 Bacteria (culture-positive), 27 PCR-Bacteria (PCR-positive), and 11 Probable Bacteria samples (strong clinical evidence of bacterial infection including leukocytosis and radiographic endpoint pneumonia without direct culture or PCR evidence). Four samples, including 3 PCR-Bacteria and 1 Bacteria etiology, were repeated in the second SOMAScan assay.
** Malaria samples include 42 analyzed in the first SOMAScan assay and 1 repeated in the second SOMAScan assay.
*** Virus samples include 48 analyzed in the first SOMAScan assay and 3 repeated in the second SOMAScan assay.
35 Table S3 Mixed infection sample designation sample distribution.
In addition to the groups defined as single etiology per previous methods 2, several mixed infection groups were defined. These included the following classifications: bacteria and malaria, bacteria and virus, malaria and virus, and malaria and other. Mixed samples comprised a separate test set and were not used for model training or primary validation.
Sample designation counts
Control1 13
Repeat Valid control2 3
Bacteria & Malaria3 9
Virus & probable Bacterial secondary co-infection4 11
Malaria & Other5 1
Malaria & Virus6 2
Total number (%) 39 (100%)
1 Control samples were analyzed in the first SOMAScan assay
2 Repeat valid controls are control samples from the first SOMAScan assay that were repeated in the second
SOMAScan assay
3 Bacteria & Malaria patients had confirmed malaria parasitemia according to the pre-specified age thresholds, but with a lobar consolidation on chest x-ray (“endpoint pneumonia”) or with a positive (not contaminated) blood culture; hence not fulfilling the case definition for either malaria or bacteria single etiology group.
4 Virus & probable secondary bacterial co-infection. Patients were confirmed viral positive (in the nasopharyngeal aspirate), were culture and PCR-negative for bacteria but with leukocytosis and radiographic endpoint pneumonia, suggestive of a secondary bacterial infection.
36 5 Malaria & Other patients had confirmed malaria parasitemia but with parasite density not fulfilling the pre-specified parasitemia age-thresholds (i.e. less than 2,500 asexual parasites/ml of blood in children over 1 year of age), or were patients with confirmed malaria parasitemia according to the pre-specified age-thresholds, but with infiltrates in the chest X ray and no evidence of positive blood culture, hence not not fulfilling the case definition for single etiology malaria.
6 Malaria & Virus patients fulfilled the same criteria as Malaria & Other, but were positive for virus in the nasopharyngeal aspirate.
37
Table S4 List of markers for Bacteria vs Virus (n=219) and Bacteria vs Virus or Malaria
(n=151).
List of markers, selected using SAM 5 with FDR<0.01, and ranked using marker aggregation, for the two comparisons: Bacteria vs Virus and Bacteria vs Malaria or Virus, with 219 and 151 biomarkers, respectively. Each marker is assigned a score “score(d)” based on the difference (d) in gene expression, relative to the standard deviation of repeated measurements for that gene.
Genes with scores greater than the threshold are deemed potentially significant. The q-value represents the FDR (in percent) and is an approximation (hence, when SAM is invoked with an
FDR threshold of 0.01, some markers have a resulting q-value slightly larger than 1.00%; see documentation for the SAM function in 33. The “fold-change” is the change of gene expression from one group (bacteria, virus, virus and malaria) to another.5 The “score” for each marker is derived from the rank aggregation algorithm to determine a global consensus ranking for each marker (“final rank”).
(A) All 219 protein markers for the Bacteria vs Virus comparison (FDR < 0.01)
Biomarker Description score(d) fold q-value score Final change (%) rank
PLA2G2A Phospholipase A2, membrane associated -6.272 0.141 0 539 1
LCN2 Neutrophil gelatinase-associated -5.248 0.309 0 5629 2 lipocalin
CCL23 C-C motif chemokine 23 -5.105 0.373 0 72528 3
IL1RL1 Interleukin-1 receptor-like 1 -5.194 0.256 0 75304 4
MPO Myeloperoxidase -4.75 0.56 0 122395 5
CX3CL1 Fractalkine 4.145 1.679 0 178304 6
RETN Resistin -4.542 0.477 0 210805 7
38 IL6 Interleukin-6 -4.062 0.248 0 372195 8
NTN4 Netrin-4 -4.326 0.537 0 410795 9
SERPINA4 Kallistatin 4.236 1.727 0 779067 10
CSF3 Granulocyte colony-stimulating factor -3.019 0.446 0 809589 11
CXCL13 C-X-C motif chemokine 13 -3.96 0.452 0 1144035 12
CA6 Carbonic anhydrase 6 4.052 4.145 0 1177340 13
EPO Erythropoietin -3.093 0.474 0 1492008 14
S100A9 Protein S100-A9 -3.726 0.575 0 2159784 15
SERPINA1 Alpha-1-antitrypsin -4.197 0.512 0 2284000 16
ITIH4 Inter-alpha-trypsin inhibitor heavy chain -3.879 0.609 0 4599539 17 H4
HAMP Hepcidin -3.31 0.372 0 6823232 18
FABP5 Fatty acid-binding protein, epidermal -3.707 0.619 0 7156875 19
SLPI Antileukoproteinase -3.56 0.688 0 8165000 20
SERPINA5 Plasma serine protease inhibitor 2.585 2.23 0.439 9812352 21
PDE11A Dual 3',5'-cyclic-AMP and -GMP -3.028 0.757 0 10829973 22 phosphodiesterase 11A
CDC2.CC Cyclin-dependent kinase 1:G2/mitotic- -1.917 0.809 1.782 11202365 23 NB1 specific cyclin-B1 complex
PIK3CG Phosphatidylinositol 4,5-bisphosphate 3- -2.287 0.81 0.439 12178053 24 kinase catalytic subunit gamma isoform
CCL3 C-C motif chemokine 3 -2.792 0.686 0 12523072 25
CTF1 Cardiotrophin-1 -2.281 0.81 0.439 12617096 26
IMPDH1 Inosine-5'-monophosphate -3.597 0.603 0 13490256 27 dehydrogenase 1
ESD S-formylglutathione hydrolase 3.23 1.683 0 16598579 28
ROR1 Tyrosine-protein kinase transmembrane 3.597 1.627 0 17099712 29 receptor ROR1
HGF Hepatocyte growth factor -3.82 0.506 0 17694336 30
KLK8 Kallikrein-8 3.337 1.895 0 21939160 31
PAPPA Pappalysin-1 3.129 1.89 0 22683136 32
39 SLITRK5 SLIT and NTRK-like protein 5 3.166 2.011 0 23984160 33
HIST1H1C Histone H1.2 -3.656 0.499 0 25727355 34
CDON Cell adhesion molecule-related/down- 3.442 2.177 0 27024015 35 regulated by oncogenes
SHBG Sex hormone-binding globulin 3.267 1.735 0 42887296 36
LTA.LTB. Lymphotoxin alpha2:beta1 2.698 2.153 0 43073024 37 1
TNFRSF21 Tumor necrosis factor receptor 3.657 1.56 0 46155057 38 superfamily member 21
IL1R1 Interleukin-1 receptor type 1 2.906 1.971 0 55924937 39
HSD17B1 Estradiol 17-beta-dehydrogenase 1 -3.011 0.702 0 60892608 40
MAPK1 Mitogen-activated protein kinase 1 -2.163 0.748 0.95 68465256 41
CCL18 C-C motif chemokine 18 -3.314 0.569 0 70039553 42
PGLYRP1 Peptidoglycan recognition protein 1 -2.713 0.451 0 83894265 43
LTA.LTB Lymphotoxin alpha1:beta2 3.218 1.866 0 85042953 44
KIT Mast/stem cell growth factor receptor Kit 2.956 1.53 0 86318715 45
AFM Afamin 3.643 1.512 0 87402621 46
MATN3 Matrilin-3 -2.246 0.772 0.95 91152909 47
Human.vir Protein Rev_HV2BE -2.281 0.55 0.439 97576185 48 us.2
MRC2 C-type mannose receptor 2 3.373 1.843 0 99867485 49
JAK2 Tyrosine-protein kinase JAK2 -3.075 0.649 0 99941040 50
MST1R Macrophage-stimulating protein receptor -2.066 0.833 0.95 1.11E+08 51
HP Haptoglobin -2.398 0.359 0.439 1.15E+08 52
SERPINC1 Antithrombin-III 2.367 1.198 0.95 1.15E+08 53
SPINT1 Kunitz-type protease inhibitor 1 3.253 1.755 0 1.3E+08 54
HBA1.HB Hemoglobin 2.181 2.521 1.782 1.36E+08 55 B
RB1 Retinoblastoma-associated protein -2.092 0.741 0.95 1.43E+08 56
REN Renin -2.772 0.622 0 1.44E+08 57
40 CXCL1 Growth-regulated alpha protein 2.335 1.631 0.95 1.45E+08 58
ERBB2 Receptor tyrosine-protein kinase erbB-2 -2.13 0.674 0.95 1.49E+08 59
LTF Lactotransferrin -2.86 0.626 0 1.5E+08 60
SAA1 Serum amyloid A-1 protein -2.474 0.355 0.439 1.5E+08 61
LEP Leptin 2.313 1.51 0.95 1.51E+08 62
ITGA2B.I Integrin alpha-IIb: beta-3 complex 2.587 1.681 0.439 1.55E+08 63 TGB3
L1CAM Neural cell adhesion molecule L1 2.699 1.49 0 1.6E+08 64
CCL14 C-C motif chemokine 14 -2.707 0.67 0 1.61E+08 65
CCL19 C-C motif chemokine 19 -2.404 0.664 0.439 1.64E+08 66
MRC1 Macrophage mannose receptor 1 -3.052 0.664 0 1.64E+08 67
CCL20 C-C motif chemokine 20 -2.226 0.722 0.95 1.66E+08 68
HMGB1 High mobility group protein B1 -2.658 0.679 0 1.81E+08 69
PLG.1 Plasmin -2.109 0.483 0.95 2.01E+08 70
IGHD..IG Immunoglobulin D -1.923 0.508 1.782 2.09E+08 71 K..IGL.
CDH5 Cadherin-5 3.08 1.349 0 2.13E+08 72
CFHR5 Complement factor H-related protein 5 -2.644 0.609 0 2.15E+08 73
CDH3 Cadherin-3 2.605 1.363 0.439 2.2E+08 74
CDK2.CC Cyclin-dependent kinase 2:Cyclin-A2 -2.558 0.678 0 2.3E+08 75 NA2 complex
PRSS1 Trypsin-1 -2.398 0.682 0.439 2.33E+08 76
CNTN1 Contactin-1 3.022 1.405 0 2.34E+08 77
MET Hepatocyte growth factor receptor 2.137 1.24 1.782 2.45E+08 78
NTRK2 BDNF/NT-3 growth factors receptor 3.142 1.522 0 2.48E+08 79
NCAM1 Neural cell adhesion molecule 1, 120 2.732 1.438 0 2.54E+08 80 kDa isoform
PRSS2 Trypsin-2 -2.696 0.519 0 2.54E+08 81
SERPINE1 Plasminogen activator inhibitor 1 -2.126 0.594 0.95 2.58E+08 82
FGA.FGB. D-dimer -2.435 0.529 0.439 2.75E+08 83
41 FGG.1
PPID Peptidyl-prolyl cis-trans isomerase D -2.662 0.628 0 2.78E+08 84
XPNPEP1 Xaa-Pro aminopeptidase 1 2.467 1.557 0.439 2.96E+08 85
CADM1 Cell adhesion molecule 1 2.802 1.579 0 2.99E+08 86
LSAMP Limbic system-associated membrane 2.591 1.338 0.439 3.2E+08 87 protein
UNC5D Netrin receptor UNC5D 2.613 1.758 0.439 3.22E+08 88
FGF23 Fibroblast growth factor 23 -1.985 0.666 1.782 3.23E+08 89
ZAP70 Tyrosine-protein kinase ZAP-70 -2.013 0.825 1.782 3.24E+08 90
NTRK3 NT-3 growth factor receptor 2.727 1.517 0 3.28E+08 91
PLXNC1 Plexin-C1 2.249 1.248 0.95 3.29E+08 92
PRTN3 Myeloblastin -3.314 0.599 0 3.41E+08 93
CCL13 C-C motif chemokine 13 -2.471 0.685 0.439 3.52E+08 94
TFPI Tissue factor pathway inhibitor -3.09 0.61 0 3.54E+08 95
TNFRSF25 Tumor necrosis factor receptor -2.227 0.738 0.95 3.57E+08 96 superfamily member 25
ETHE1 Persulfide dioxygenase ETHE1, -2.449 0.762 0.439 3.62E+08 97 mitochondrial
TPSB2 Tryptase beta-2 2.201 1.512 1.782 3.68E+08 98
CCL7 C-C motif chemokine 7 2.398 1.7 0.439 3.71E+08 99
KLK7 Kallikrein-7 2.36 1.632 0.95 3.72E+08 100
H2AFZ Histone H2A.z -2.385 0.548 0.439 3.73E+08 101
RPS7 40S ribosomal protein S7 -2.058 0.701 0.95 3.96E+08 102
IGFBP3 Insulin-like growth factor-binding 3.114 1.507 0 3.96E+08 103 protein 3
RGMB RGM domain family member B 2.153 1.207 1.782 3.97E+08 104
CHIT1 Chitotriosidase-1 -2.205 0.655 0.95 4.01E+08 105
STK17B Serine/threonine-protein kinase 17B -2.195 0.772 0.95 4.03E+08 106
CXCL3.C Gro-beta/gamma 2.133 1.647 1.782 4.07E+08 107 XCL2
42 PECAM1 Platelet endothelial cell adhesion -2.097 0.819 0.95 4.08E+08 108 molecule
CNTFR Ciliary neurotrophic factor receptor 2.445 1.427 0.439 4.14E+08 109 subunit alpha
EPHB2 Ephrin type-B receptor 2 3.234 1.517 0 4.16E+08 110
IL12A.IL1 Interleukin-12 -2.444 0.701 0.439 4.21E+08 111 2B
HSPA8 Heat shock cognate 71 kDa protein -2.042 0.639 0.95 4.25E+08 112
HAPLN1 Hyaluronan and proteoglycan link 2.503 1.65 0.439 4.27E+08 113 protein 1
SHH Sonic hedgehog protein 2.615 1.56 0.439 4.32E+08 115
ICOSLG ICOS ligand -2.206 0.702 0.95 4.37E+08 116
OCIAD1 OCIA domain-containing protein 1 -2.162 0.688 0.95 4.38E+08 117
EPHA2 Ephrin type-A receptor 2 2.524 1.418 0.439 4.42E+08 118
RBM39 RNA-binding protein 39 -2.391 0.752 0.439 4.42E+08 119
EPHA5 Ephrin type-A receptor 5 2.745 1.508 0 4.5E+08 120
TNFRSF1 Tumor necrosis factor receptor -2.746 0.708 0 4.51E+08 121 A superfamily member 1A
SFTPD Pulmonary surfactant-associated protein -2.507 0.642 0 4.73E+08 122 D
CD109 CD109 antigen 2.715 1.589 0 4.74E+08 123
ANGPT2 Angiopoietin-2 -2.212 0.766 0.95 4.77E+08 124
LRP8 Low-density lipoprotein receptor-related 2.561 1.367 0.439 4.81E+08 125 protein 8
DKK3 Dickkopf-related protein 3 2.647 1.407 0 4.82E+08 126
ACAN Aggrecan core protein 2.322 1.508 0.95 4.83E+08 127
KLK14 Kallikrein-14 -2.281 0.818 0.439 4.89E+08 128
FGFR1 Fibroblast growth factor receptor 1 3.237 1.451 0 4.89E+08 129
PRKCZ Protein kinase C zeta type -2.524 0.731 0 4.98E+08 130
LRIG3 Leucine-rich repeats and 2.409 1.373 0.439 4.98E+08 131 immunoglobulin-like domains protein 3
ADCYAP1 Pituitary adenylate cyclase-activating -2.532 0.652 0 5E+08 132
43 .1 polypeptide 38
CAST Calpastatin 2.848 1.526 0 5.01E+08 133
PGD 6-phosphogluconate dehydrogenase, -1.967 0.652 1.782 5.02E+08 134 decarboxylating
TOP1 DNA topoisomerase 1 -2 0.704 1.782 5.05E+08 135
MAPKAP MAP kinase-activated protein kinase 3 -2.578 0.731 0 5.08E+08 136 K3
CHL1 Neural cell adhesion molecule L1-like 2.582 1.41 0.439 5.1E+08 137 protein
DSG2 Desmoglein-2 -2.013 0.762 1.782 5.12E+08 138
BIRC7 Baculoviral IAP repeat-containing -2.105 0.805 0.95 5.21E+08 139 protein 7 Isoform beta
VEGFA Vascular endothelial growth factor A -2.076 0.813 0.95 5.24E+08 140
EPHB6 Ephrin type-B receptor 6 2.591 1.32 0.439 5.26E+08 141
NOTCH1 Neurogenic locus notch homolog protein 2.251 1.195 0.95 5.28E+08 142 1
LPO Lactoperoxidase 2.303 1.765 0.95 5.38E+08 143
GSN Gelsolin 2.851 1.33 0 5.4E+08 144
LILRB2 Leukocyte immunoglobulin-like receptor -1.895 0.755 1.782 5.6E+08 145 subfamily B member 2
FLT3 Receptor-type tyrosine-protein kinase -2.032 0.754 0.95 5.76E+08 146 FLT3
EFNA5 Ephrin-A5 2.569 1.384 0.439 5.84E+08 147
BPI Bactericidal permeability-increasing -2.817 0.57 0 5.91E+08 148 protein
FCN2 Ficolin-2 -2.557 0.724 0 5.96E+08 149
SIRT2 NAD-dependent protein deacetylase -2.177 0.727 0.95 6E+08 150 sirtuin-2
FSTL3 Follistatin-related protein 3 -1.978 0.768 1.782 6.01E+08 151
PDCD1LG Programmed cell death 1 ligand 2 2.373 1.318 0.95 6.03E+08 152 2
CXCL12 Stromal cell-derived factor 1 -2.679 0.639 0 6.09E+08 153
44 CNTN2 Contactin-2 2.308 1.37 0.95 6.27E+08 154
TDGF1 Teratocarcinoma-derived growth factor 1 -2.168 0.764 0.95 6.39E+08 155
CD200 OX-2 membrane glycoprotein 2.364 1.308 0.95 6.48E+08 156
ALPL Alkaline phosphatase, tissue-nonspecific -2.578 0.711 0 6.91E+08 157 isozyme
FGF12 Fibroblast growth factor 12 -2.017 0.804 1.782 6.91E+08 158
FN1.2 Fibronectin 2.136 1.625 1.782 6.93E+08 159
CST7 Cystatin-F -2.045 0.646 0.95 6.96E+08 160
IL22RA1 Interleukin-22 receptor subunit alpha-1 -2.092 0.729 0.95 7.08E+08 161
SEMA3A Semaphorin-3A -2.378 0.716 0.439 7.19E+08 162
IGFBP2 Insulin-like growth factor-binding -2.777 0.674 0 7.3E+08 163 protein 2
GFRA1 GDNF family receptor alpha-1 -2.236 0.728 0.95 7.46E+08 164
F9.1 Coagulation factor IXab -2.335 0.786 0.439 7.77E+08 165
KAT6A Histone acetyltransferase KAT6A -2.228 0.793 0.95 7.94E+08 166
HSP90AA Heat shock protein HSP 90-alpha/beta -1.933 0.774 1.782 8.31E+08 167 1.HSP90A B1
ADRBK1 beta-adrenergic receptor kinase 1 -2.635 0.73 0 8.36E+08 168
RTN4 Reticulon-4 -2.057 0.767 0.95 8.77E+08 169
DAPK2 Death-associated protein kinase 2 -2.298 0.78 0.439 8.86E+08 170
MMEL1 Membrane metallo-endopeptidase-like 1 -2.221 0.78 0.95 8.87E+08 171
OMD Osteomodulin 2.11 1.368 1.782 8.92E+08 172
IL18R1 Interleukin-18 receptor 1 -2.022 0.779 0.95 8.96E+08 173
EPHA1 Ephrin type-A receptor 1 2.198 1.577 1.782 9.36E+08 174
SERPING1 Plasma protease C1 inhibitor 2.582 1.413 0.439 9.38E+08 175
ALCAM CD166 antigen 2.52 1.27 0.439 9.38E+08 176
DKKL1 Dickkopf-like protein 1 -2.283 0.795 0.439 9.81E+08 177
AHSG Alpha-2-HS-glycoprotein 2.568 1.351 0.439 9.96E+08 178
CCL3L1 C-C motif chemokine 3-like 1 -2.289 0.778 0.439 1.02E+09 179
45 NOTCH3 Neurogenic locus notch homolog protein 2.141 1.275 1.782 1.03E+09 180 3
HDGFRP2 Hepatoma-derived growth factor-related -2.38 0.769 0.439 1.05E+09 181 protein 2
MMP17 Matrix metalloproteinase-17 -2.42 0.732 0.439 1.05E+09 182
PPP3R1 Calcineurin subunit B type 1 -2.257 0.804 0.95 1.07E+09 183
SLAMF7 SLAM family member 7 -1.928 0.776 1.782 1.07E+09 184
UNC5C Netrin receptor UNC5C 2.245 1.249 0.95 1.08E+09 185
ANGPTL4 Angiopoietin-related protein 4 -2.32 0.714 0.439 1.1E+09 186
DPT Dermatopontin 2.21 1.449 0.95 1.1E+09 187
F10 Coagulation factor Xa -2.252 0.805 0.95 1.11E+09 188
PDE2A cGMP-dependent 3',5'-cyclic -2.017 0.802 1.782 1.11E+09 189 phosphodiesterase
CTSG Cathepsin G -1.993 0.766 1.782 1.12E+09 190
WISP1 WNT1-inducible-signaling pathway -2.119 0.8 0.95 1.12E+09 191 protein 1
LCMT1 Leucine carboxyl methyltransferase 1 -2.108 0.785 0.95 1.12E+09 192
KLKB1 Plasma kallikrein 2.182 1.267 1.782 1.13E+09 193
LBP Lipopolysaccharide-binding protein -1.975 0.71 1.782 1.13E+09 194
IL17D Interleukin-17D -1.964 0.819 1.782 1.15E+09 195
SMPDL3A Acid sphingomyelinase-like -2.038 0.778 0.95 1.15E+09 196 phosphodiesterase 3a
BCAN Brevican core protein 2.418 1.494 0.439 1.15E+09 197
PRKCD Protein kinase C delta type -2.138 0.806 0.95 1.17E+09 198
CNTN4 Contactin-4 2.227 1.286 0.95 1.18E+09 199
THBS4 Thrombospondin-4 2.446 1.45 0.439 1.2E+09 200
NRXN1 Neurexin-1-beta 2.38 1.446 0.95 1.24E+09 201
ANP32B Acidic leucine-rich nuclear -1.974 0.822 1.782 1.25E+09 202 phosphoprotein 32 family member B
ADCYAP1 Pituitary adenylate cyclase-activating -2.2 0.72 0.95 1.25E+09 203 polypeptide 27
46 IFNL2 Interferon lambda-2 -1.899 0.822 1.782 1.26E+09 204
WIF1 Wnt inhibitory factor 1 2.235 1.363 0.95 1.33E+09 205
F10.1 Coagulation Factor X -1.891 0.838 1.782 1.34E+09 206
TIMP1 Metalloproteinase inhibitor 1 -2.037 0.709 0.95 1.35E+09 207
CKM Creatine kinase M-type 2.274 1.467 0.95 1.37E+09 208
MDM2 E3 ubiquitin-protein ligase Mdm2 -2.336 0.815 0.439 1.48E+09 209
AGT Angiotensinogen -1.895 0.762 1.782 1.48E+09 210
CASP10 Caspase-10 -1.901 0.866 1.782 1.49E+09 211
MAPK14 Mitogen-activated protein kinase 14 -2.062 0.801 0.95 1.5E+09 212
CRISP3 Cysteine-rich secretory protein 3 -1.914 0.836 1.782 1.51E+09 213
STC1 Stanniocalcin-1 -1.972 0.768 1.782 1.57E+09 214
GFRA3 GDNF family receptor alpha-3 -1.911 0.779 1.782 1.64E+09 215
RSPO2 R-spondin-2 -1.91 0.787 1.782 1.86E+09 216
F9 Coagulation factor IX -1.958 0.835 1.782 1.87E+09 217
APOD Apolipoprotein D -2.05 0.833 0.95 1.88E+09 218
CCL27 C-C motif chemokine 27 -2.15 0.8 0.95 1.93E+09 219
47 (B) All 151 protein markers for the Bacteria vs Virus or Malaria comparison (FDR < 0.01)
Biomarker Description score(d) fold q-value score Final change (%) rank
HP Haptoglobin -4.624 0.097 0 3817 1
CX3CL1 Fractalkine 4.894 1.752 0 4217 2
RETN Resistin -4.98 0.512 0 7053 3
CSF3 Granulocyte colony-stimulating factor -4.377 0.386 0 27321 4
LCN2 Neutrophil gelatinase-associated -5.398 0.367 0 30544 5 lipocalin
SLPI Antileukoproteinase -4.457 0.66 0 79632 6
ESD S-formylglutathione hydrolase 4.17 1.78 0 103631 7
KYNU Kynureninase 3.819 1.786 0 207560 8
IL6 Interleukin-6 -4.184 0.304 0 240832 9
S100A9 Protein S100-A9 -4.857 0.543 0 250112 10
HBA1.HB Hemoglobin 4.248 7.32 0 332432 11 B
PLA2G2A Phospholipase A2, membrane associated -3.912 0.309 0 443185 12
SERPINA4 Kallistatin 4.253 1.571 0 507115 13
PIK3CG Phosphatidylinositol 4,5-bisphosphate 3- -3.155 0.783 0 631496 14 kinase catalytic subunit gamma isoform
CXCL13 C-X-C motif chemokine 13 -3.886 0.516 0 671021 15
FABP5 Fatty acid-binding protein, epidermal -4.271 0.626 0 770688 16
CD36 Platelet glycoprotein 4 3.768 2.829 0 906752 17
PAPPA Pappalysin-1 3.399 1.825 0 2123200 18
FGF17 Fibroblast growth factor 17 -2.456 0.775 0.619 2471135 19
HGF Hepatocyte growth factor -4.516 0.523 0 2516560 20
GZMB Granzyme B 3.107 1.933 0 3226520 21
NAGK N-acetyl-D-glucosamine kinase 3.556 1.641 0 3750264 22
CD274 Programmed cell death 1 ligand 1 2.777 1.422 0 5022381 23
48 IL1RL1 Interleukin-1 receptor-like 1 -3.371 0.433 0 5061257 24
LTA.LTB. Lymphotoxin alpha2:beta1 3.274 2.046 0 7261947 25 1
BIRC7 Baculoviral IAP repeat-containing -3.29 0.756 0 7726488 26 protein 7 Isoform beta
MPO Myeloperoxidase -3.561 0.669 0 8970291 27
LAG3 Lymphocyte activation gene 3 protein 3.672 1.958 0 9707152 28
FGA.FGB. D-dimer -3.351 0.501 0 12127520 29 FGG.1
CTF1 Cardiotrophin-1 -2.757 0.796 0 12407197 30
HAMP Hepcidin -3.041 0.429 0 12572847 31
CFHR5 Complement factor H-related protein 5 -3.044 0.62 0 14080573 32
ETHE1 Persulfide dioxygenase ETHE1, -3.282 0.73 0 14145024 33 mitochondrial
CCL21 C-C motif chemokine 21 -3.064 0.7 0 15049216 34
IGFBP3 Insulin-like growth factor-binding 3.235 1.449 0 15969024 35 protein 3
HSD17B1 Estradiol 17-beta-dehydrogenase 1 -2.573 0.764 0 17290496 36
PLG.1 Plasmin -2.847 0.471 0 17838352 37
PTPN11 Tyrosine-protein phosphatase non- 3.081 1.445 0 18420931 38 receptor type 11
RB1 Retinoblastoma-associated protein -2.135 0.774 0.994 18433605 39
MST1R Macrophage-stimulating protein receptor -2.643 0.823 0 20582656 40
PRDX6 Peroxiredoxin-6 2.924 1.651 0 21192460 41
Human.vir Protein Rev_HV2BE -3.175 0.527 0 21518796 42 us.2
C4A.C4B.1 Complement C4 2.634 3.126 0.619 22014388 43
CCL3 C-C motif chemokine 3 -2.604 0.747 0 22561200 44
F2.1 Prothrombin 2.744 2.463 0 23337369 45
CCL7 C-C motif chemokine 7 2.641 1.625 0.619 26251264 46
HSPA8 Heat shock cognate 71 kDa protein -3.295 0.565 0 29458053 47
49 XPNPEP1 Xaa-Pro aminopeptidase 1 2.926 1.581 0 35900928 48
JAK2 Tyrosine-protein kinase JAK2 -2.951 0.696 0 37850112 49
ITIH4 Inter-alpha-trypsin inhibitor heavy chain -3.128 0.699 0 39478731 50 H4
PGLYRP1 Peptidoglycan recognition protein 1 -2.687 0.499 0 43464008 51
PRSS2 Trypsin-2 -2.621 0.579 0 47073468 52
FN1.1 Fibronectin Fragment 4 2.51 2.088 0.994 49025934 53
ERBB2 Receptor tyrosine-protein kinase erbB-2 -2.655 0.672 0 50269135 54
PLXNC1 Plexin-C1 2.917 1.298 0 51597600 55
CCL23 C-C motif chemokine 23 -3.052 0.572 0 51770916 56
KIT Mast/stem cell growth factor receptor Kit 2.433 1.346 1.541 55683456 57
CST7 Cystatin-F -3.28 0.568 0 56863744 58
ADCYAP1 Pituitary adenylate cyclase-activating -2.695 0.692 0 57811648 59 .1 polypeptide 38
SAA1 Serum amyloid A-1 protein -2.3 0.443 0.994 57814700 60
GZMA Granzyme A 3.127 1.715 0 57857019 61
IL12B.IL2 Interleukin-23 -2.654 0.702 0 62266512 62 3A
CXCL6 C-X-C motif chemokine 6 2.445 1.528 0.994 62403279 63
ANGPT2 Angiopoietin-2 -2.801 0.761 0 68371275 64
AMH Muellerian-inhibiting factor -2.68 0.662 0 68765655 65
PDE11A Dual 3',5'-cyclic-AMP and -GMP -2.224 0.834 0.994 71374451 66 phosphodiesterase 11A
MMP12 Macrophage metalloelastase 2.603 1.72 0.619 71629448 67
CCL19 C-C motif chemokine 19 -2.543 0.701 0 75809104 68
REN Renin -2.526 0.697 0 77300480 69
CCL14 C-C motif chemokine 14 -3.021 0.684 0 77632147 70
IL18RAP Interleukin-18 receptor accessory protein -2.256 0.864 0.994 80479952 71
VCAM1 Vascular cell adhesion protein 1 3.265 1.462 0 80621568 72
LRP8 Low-density lipoprotein receptor-related 2.41 1.274 1.541 84357630 73
50 protein 8
NTN4 Netrin-4 -2.856 0.689 0 84643328 74
LDHB L-lactate dehydrogenase B chain 2.999 1.383 0 91042368 75
BIRC5 Baculoviral IAP repeat-containing -2.512 0.831 0 92105445 76 protein 5
MDH1 Malate dehydrogenase, cytoplasmic 2.613 1.355 0.619 93004548 77
MATN3 Matrilin-3 -2.308 0.798 0.994 93669087 78
CNTN1 Contactin-1 2.87 1.32 0 94727345 79
SEMA3A Semaphorin-3A -2.943 0.703 0 96847465 80
CCL28 C-C motif chemokine 28 -2.128 0.754 1.541 97300272 81
HPX Hemopexin -2.237 0.702 0.994 100470051 82
CAT Catalase 2.615 1.472 0.619 100571087 83
CHIT1 Chitotriosidase-1 -2.416 0.669 0.619 100753484 84
CD48 CD48 antigen 2.811 1.336 0 100837845 85
SPINT1 Kunitz-type protease inhibitor 1 2.426 1.429 1.541 101040423 86
GSN Gelsolin 2.456 1.236 0.994 105135723 87
EHMT2 Histone-lysine N-methyltransferase 2.443 1.317 0.994 108038980 88 EHMT2
FGF18 Fibroblast growth factor 18 -2.156 0.701 0.994 108245676 89
CSF1R Macrophage colony-stimulating factor 1 3.206 1.508 0 109648316 90 receptor
FN1.2 Fibronectin 2.5 1.59 0.994 110208276 91
SHBG Sex hormone-binding globulin 3.526 1.662 0 112985616 92
HIST1H1C Histone H1.2 -2.454 0.657 0.619 118866217 93
C2 Complement C2 -2.289 0.745 0.994 120470336 94
SERPINA1 Alpha-1-antitrypsin -3.066 0.651 0 122448161 95
C3.2 C3a anaphylatoxin des Arginine 2.425 1.682 1.541 123565862 96
IL18R1 Interleukin-18 receptor 1 -2.843 0.747 0 124216768 97
VEGFA Vascular endothelial growth factor A -2.701 0.781 0 130621440 98
51 CDH5 Cadherin-5 2.825 1.265 0 132077225 99
B2M Beta-2-microglobulin 2.398 1.282 1.541 141846650 100
OCIAD1 OCIA domain-containing protein 1 -2.164 0.742 0.994 142408170 101
PDCD1LG Programmed cell death 1 ligand 2 2.701 1.298 0 147354424 102 2
IGFBP2 Insulin-like growth factor-binding -2.373 0.743 0.619 155397250 103 protein 2
MMP7 Matrilysin -2.153 0.759 0.994 155548796 104
VEGFA.1 Vascular endothelial growth factor A, -2.375 0.57 0.619 167420205 105 isoform 121
CRLF1.CL Cytokine receptor-like factor -2.582 0.786 0 177490310 106 CF1 1:Cardiotrophin-like cytokine factor 1 Complex
ABL1 Tyrosine-protein kinase ABL1 -2.382 0.759 0.619 178015814 107
PROS1 Vitamin K-dependent protein S -2.282 0.84 0.994 180593480 108
AFM Afamin 2.915 1.348 0 188496175 109
ECE1 Endothelin-converting enzyme 1 -2.096 0.767 1.541 193310813 110
MMP8 Neutrophil collagenase -2.136 0.657 0.994 194324063 111
PON1 Serum paraoxonase/arylesterase 1 -2.119 0.778 1.541 199967425 112
PTPN6 Tyrosine-protein phosphatase non- 2.402 1.302 1.541 200334821 113 receptor type 6
TFPI Tissue factor pathway inhibitor -2.684 0.69 0 203267988 114
FGFR1 Fibroblast growth factor receptor 1 2.384 1.272 1.541 205188228 115
PRSS1 Trypsin-1 -2.464 0.706 0.619 214221360 116
TGFB3 Transforming growth factor beta-3 -2.151 0.785 0.994 215796832 117
ALPL Alkaline phosphatase, tissue-nonspecific -2.283 0.759 0.994 225378604 118 isozyme
AHSG Alpha-2-HS-glycoprotein 2.52 1.288 0.994 237444991 119
IL12A.IL1 Interleukin-12 -2.12 0.774 1.541 238871625 120 2B
LTF Lactotransferrin -2.401 0.698 0.619 244290928 121
NXPH1 Neurexophilin-1 -2.108 0.786 1.541 256912273 122
52 MRC2 C-type mannose receptor 2 2.548 1.487 0.994 258936128 123
EPHA5 Ephrin type-A receptor 5 2.716 1.426 0 261296460 124
IL17A Interleukin-17A -2.207 0.795 0.994 265322596 125
FCN2 Ficolin-2 -2.219 0.789 0.994 273131276 126
GFRA1 GDNF family receptor alpha-1 -2.437 0.744 0.619 280357585 127
CXCL12 Stromal cell-derived factor 1 -2.353 0.72 0.619 283038112 128
HINT1 Histidine triad nucleotide-binding protein -2.128 0.787 1.541 284657196 129 1
TXNDC12 Thioredoxin domain-containing protein -2.157 0.777 0.994 289318896 130 12
CCL3L1 C-C motif chemokine 3-like 1 -2.233 0.809 0.994 295039826 131
PRKCD Protein kinase C delta type -2.461 0.817 0.619 317039067 132
SPON1 Spondin-1 -2.108 0.8 1.541 320281250 133
ZAP70 Tyrosine-protein kinase ZAP-70 -2.271 0.825 0.994 322273663 134
APCS Serum amyloid P-component -2.563 0.806 0 331490535 135
CD97 CD97 antigen -2.063 0.872 1.541 344115038 136
CAPG Macrophage-capping protein -2.063 0.777 1.541 352255023 137
CCL27 C-C motif chemokine 27 -2.23 0.823 0.994 359256696 138
TDGF1 Teratocarcinoma-derived growth factor 1 -2.042 0.809 1.541 371548086 139
HS6ST1 Heparan-sulfate 6-O-sulfotransferase 1 -2.48 0.802 0.619 381908068 140
PRSS3 Trypsin-3 -2.205 0.823 0.994 389691303 141
F9.1 Coagulation factor IXab -2.721 0.794 0 407565957 142
ADAMTS1 A disintegrin and metalloproteinase with -2.102 0.834 1.541 410591411 143 5 thrombospondin motifs 15
OSM Oncostatin-M -2.242 0.844 0.994 426248646 144
ANP32B Acidic leucine-rich nuclear -2.286 0.818 0.994 426866823 145 phosphoprotein 32 family member B
CAMK1D Calcium/calmodulin-dependent protein -2.084 0.844 1.541 444783686 146 kinase type 1D
F10 Coagulation factor Xa -2.4 0.812 0.619 447143476 147
53 C8A.C8B. Complement component C8 -2.154 0.849 0.994 459197271 148 C8G
IL37 Interleukin-37 -2.274 0.828 0.994 466347158 149
IFNL2 Interferon lambda-2 -2.128 0.831 1.541 484511388 150
F9 Coagulation factor IX -2.189 0.845 0.994 487734706 151
54 Table S5 Single Etiology validation statistics for BvV and BvVM marker sets (A to D), and
SOMAScan assay and RNA-Sequencing overlapping marker set (n=24) for RF and EN models (E and F)
(A) Single Etiology validation set (n=32) for Bacteria vs Virus (Random Forest Model).
Performance statistics summary for 5, 10, 15, 25, 50, 100, and 219 markers. The validation set
(n=32) contains Bacteria (n=19) and Virus (n=13). The confusion matrix and other statistics are included in Table 1.
(B) Single Etiology validation set (n=47) for Bacteria vs Virus or Malaria (Random Forest
Model). Performance statistics summary for 5, 10, 15, 25, 50, 100, and 151 markers. The validation set (n=51) contains Bacteria (n=19), Malaria (n=15), and Virus (n=13). The confusion matrix and other statistics are included in Table 1.
55 (C) Single Etiology validation set (n=32) for Bacteria vs Virus (Elastic Net Model). Confusion matrices with all (219) and 5 markers and performance statistics summary for 5, 10,15, 25, 50,
100, and 219 markers including accuracy with 0%, 10% and 20% surrogates. The validation set
(n=32) contains Bacteria (n=19) and Virus (n=13).
56 (D) Single Etiology validation set (n=47) for Bacteria vs Malaria or Virus (Elastic Net Model).
Confusion matrices with all (151) and 5 markers and performance statistics summary for 5, 10,15,
25, 50, 100, and 151 markers including accuracy with 0%, 10% and 20% surrogates. The validation set (n=47) contains Bacteria (n=19), Malaria (n=15), and Virus (n=13).
57 (E) Single Etiology SOMAScan assay and RNA-Sequencing overlapping marker sets (n=24, see Fig. 4 B) predicted performance in the Bacteria vs Virus marker set (RF and EN models).
Confusion matrices and performance statistics summary depicted. The sample set (n=32) contains
Bacteria (n=19) and Virus (n=13).
58 (F) Single Etiology SOMAScan assay and RNA-Sequencing overlapping marker sets (n=24, see Fig. 4 B) predicted performance in the Bacteria vs Malaria or Virus sample set (RF and
EN models). Confusion matrices and performance statistics summary depicted. The validation set
(n=47) contains Bacteria (n=19), Malaria (n=15), and Virus (n=13).
59 Table S6 Mixed infection set without controls (n=23) (Random Forest)
The mixed infection test set (n=23) contains the following samples: Bacteria & Malaria (n=9),
Virus and probable Bacterial secondary co-infection (n=11), Malaria & Other (n=1), Malaria &
Virus (n=2). All samples that contain the term “bacteria” are considered bacteria-positive samples.
(A) Mixed infection test samples (n=23) for Bacteria vs Virus. Confusion matrices with 219 and 5 markers and performance statistics summary for 5, 10, 15, 25, 50, 100, and 219 markers.
60 (B) Mixed infection test samples (n=23) for Bacteria vs Malaria or Virus. Confusion matrices with 151 and 5 markers and performance statistics summary for 5, 10,15, 25, 50, 100, and 151 markers.
61 Table S7 ALgorithm for MANagement of Childhood illnesses (ALMANACH).
(A) ALMANACH prediction in single etiology specimens from the test set (n=27) including bacterial (n=14) and viral (n=13) samples. Confusion matrices based on ALMANACH metrics for pneumonia requiring antibiotic therapy, including chest indrawing alone, measured respiratory rate over 50 breaths/minute alone, or the presence of either indrawing or elevated respiratory rate.
See accompanying text for details.
62 (B) ALMANACH clinical assessment with single etiology specimens from the test set (n=40) with bacterial (n=14), viral (n=13), and malarial (n=13) samples. Confusion matrices based on
ALMANACH metrics for pneumonia requiring antibiotic therapy, including chest indrawing alone, measured respiratory rate over 50 breaths/minute alone, or the presence of either indrawing or elevated respiratory rate. See accompanying text for details.
63 References
1. Silterra J, Gillette MA, Lanaspa M, et al. Transcriptional Categorization of the Etiology of
Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis
2017;215(2):312–20.
2. Valim C, Ahmad R, Lanaspa M, et al. Responses to Bacteria, Virus, and Malaria Distinguish the
Etiology of Pediatric Clinical Pneumonia. Am J Respir Crit Care Med 2016;193(4):448–59.
3. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Fox AJ, Kaczmarski EB. Simultaneous
detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in
suspected cases of meningitis and septicemia using real-time PCR. J Clin Microbiol
2001;39(4):1553–8.
4. Laura Selva, Xavier Krauel, Roman Pallares, Carmen Muñoz-Almagro. Easy Diagnosis of Invasive
Pneumococcal Disease. Emerging Infectious Disease journal 2011;17(6):1125.
5. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing
radiation response. Proc Natl Acad Sci U S A 2001;98(9):5116–21.
6. Kolde R, Laur S, Adler P, Vilo J. Robust rank aggregation for gene list integration and meta-
analysis. Bioinformatics 2012;28(4):573–80.
7. Max Kuhn, Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony
Cooper, Zachary Mayer, Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang and Can Candan. caret: Classification and Regression
Training. R package version 6.0 [Internet]. 2016 [cited 2019 Feb 14];Available from: https://cran.r-
project.org/web/packages/caret/index.html
8. Kim JW, Botvinnik OB, Abudayyeh O, et al. Characterizing genomic alterations in cancer by
64 complementary functional associations. Nat Biotechnol 2016;34(5):539–46.
9. Mebane WR Jr, Sekhon JS, Others. Genetic optimization using derivatives: the rgenoud package for
R. J Stat Softw 2011;42(11):1–26.
10. Rambaud-Althaus C, Shao AF, Kahama-Maro J, Genton B, d’Acremont V. Managing the Sick Child
in the Era of Declining Malaria Transmission: Development of ALMANACH, an Electronic
Algorithm for Appropriate Use of Antimicrobials. PLoS One 2015;10(7):e0127674.
11. Abella V, Scotece M, Conde J, et al. The potential of lipocalin-2/NGAL as biomarker for
inflammatory and metabolic diseases. Biomarkers 2015;20(8):565–71.
12. Mahende C, Ngasala B, Lusingu J, et al. Profile of C-reactive protein, white cells and neutrophil
populations in febrile children from rural north-eastern Tanzania. Pan Afr Med J 2017;26:51.
13. Van den Bruel A, Thompson MJ, Haj-Hassan T, et al. Diagnostic value of laboratory tests in
identifying serious infections in febrile children: systematic review. BMJ 2011;342:d3082.
14. Summers C, Rankin SM, Condliffe AM, Singh N, Peters AM, Chilvers ER. Neutrophil kinetics in
health and disease. Trends Immunol 2010;31(8):318–24.
15. Dancey JT, Deubelbeiss KA, Harker LA, Finch CA. Neutrophil kinetics in man. J Clin Invest
1976;58(3):705–15.
16. Rosales C. Neutrophil: A Cell with Many Roles in Inflammation or Several Cell Types? Front
Physiol 2018;9:113.
17. Liu J, Pang Z, Wang G, et al. Advanced Role of Neutrophils in Common Respiratory Diseases. J
Immunol Res 2017;2017:6710278.
18. Craig A, Mai J, Cai S, Jeyaseelan S. Neutrophil recruitment to the lungs during bacterial pneumonia.
65 Infect Immun 2009;77(2):568–75.
19. Tapper H, Herwald H. Modulation of hemostatic mechanisms in bacterial infectious diseases. Blood
2000;96(7):2329–37.
20. Singh B, Fleury C, Jalalvand F, Riesbeck K. Human pathogens utilize host extracellular matrix
proteins laminin and collagen for adhesion and invasion of the host. FEMS Microbiol Rev
2012;36(6):1122–80.
21. Hensmann M, Kwiatkowski D. Cellular basis of early cytokine response to Plasmodium falciparum.
Infect Immun 2001;69(4):2364–71.
22. Torres A, Sibila O, Ferrer M, et al. Effect of corticosteroids on treatment failure among hospitalized
patients with severe community-acquired pneumonia and high inflammatory response: a randomized
clinical trial. JAMA 2015;313(7):677–86.
23. Kellum JA, Kong L, Fink MP, et al. Understanding the inflammatory cytokine response in
pneumonia and sepsis: results of the Genetic and Inflammatory Markers of Sepsis (GenIMS) Study.
Arch Intern Med 2007;167(15):1655–63.
24. Liu X, Wang Y, Liang J, et al. In-depth comparative analysis of malaria parasite genomes reveals
protein-coding genes linked to human disease in Plasmodium falciparum genome. BMC Genomics
2018;19(1):312.
25. Almelli T, Nuel G, Bischoff E, et al. Differences in gene transcriptomic pattern of Plasmodium
falciparum in children with cerebral malaria and asymptomatic carriers. PLoS One
2014;9(12):e114401.
26. Kerr JR. Cell adhesion molecules in the pathogenesis of and host defence against microbial
infection. Mol Pathol 1999;52(4):220–30.
66 27. Bhella D. The role of cellular adhesion molecules in virus attachment and entry. Philos Trans R Soc
Lond B Biol Sci 2015;370(1661):20140035.
28. Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to
the Chase. Mol Cell Proteomics 2017;16(4 suppl 1):S161–71.
29. Morpeth SC, Deloria Knoll M, Scott JAG, et al. Detection of pneumococcal DNA in blood by
polymerase chain reaction for diagnosing pneumococcal pneumonia in young children from low-and
middle-income countries. Clin Infect Dis 2017;64(suppl_3):S347–56.
30. Deloria Knoll M, Morpeth SC, Scott JAG, et al. Evaluation of Pneumococcal Load in Blood by
Polymerase Chain Reaction for the Diagnosis of Pneumococcal Pneumonia in Young Children in the
PERCH Study. Clin Infect Dis 2017;64(suppl_3):S357–67.
31. van Houten CB, de Groot JAH, Klein A, et al. A host-protein based assay to differentiate between
bacterial and viral infections in preschool children (OPPORTUNITY): a double-blind, multicentre,
validation study. Lancet Infect Dis 2017;17(4):431–40.
32. Holland JH. Adaptation in Natural and Artificial Systems [Internet]. 1992;Available from:
http://dx.doi.org/10.7551/mitpress/1090.001.0001
33. Tibshirani R, Seo MJ, Chu G, Narasimhan B, Li J, Tibshirani MR. Package “samr.” 2018;Available
from: ftp://64.50.236.52/.1/cran/web/packages/samr/samr.pdf
67