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Home , Aldehyde dehydrogenase, BCKDHB, CBFA2T3, ELTD1, EMP1, Ets variant 5

Pulmonary Arteriole Expression Signature in Idiopathic Pulmonary Fibrosis

Nina M. Patel1, Steven M. Kawut2, Selim M. Arcasoy1, Sanja Jelic1, David J. Lederer1,

Alain C. Borczuk1

Division of Pulmonary, Allergy & Critical Care Medicine, Columbia University, College

of Physicians and Surgeons1

Department of Medicine and the Center for Clinical Epidemiology and Biostatistics,

University of Pennsylvania School of Medicine, Philadelphia, PA2

Online Data Supplement

Methods:

RNA Isolation, Microarray processing

The RNAqueous-Micro Kit (Ambion) was utilized to isolate RNA. The Agilent

Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) was used to assess the

quantity, quality and purity of the extracted RNA. The modified Eberwine procedure was

used to amplify and biotinylate RNA for a minimum goal of 15 g RNA for hybridization. Target cRNA was hybridized to Affymetrix Hu133 2.0 Plus oligonucleotide arrays and processed at the Herbert Irving Comprehensive

Center.

Microarray Analysis

Quality assessment was performed using Bioconductor. BRB array tools software

v3.7.2. (National Cancer Institute, Dr. Richard Simon and Dr. Amy Lam) was used for

normalization, filtering and initial quality control assessment of the genechip data. The

Robust Multi-Array Average (RMA) algorithm was used to quantify the expression

values for each probe set. Unsupervised clustering was performed using BRB array tools.

Supervised analyses of differential between class assignments was

performed using univariate analyses with a p < 0.001. The univariate analyses were

performed utilizing 10,000 random permutations, with a global p < 0.01. The false

discovery rate for all comparisons was set at a q < 10%. Supervised clustering of genes

and scatterplot analysis between class assignments was also performed using BRB array

tools software. Gene lists generated by the supervised analyses were further categorized

into biological pathways using Ingenuity Pathways Analysis (IPA, Ingenuity Systems, www.ingenuity.com). The IPA Functional Analysis identified the biological functions

and/or diseases that were most significant to the data set. Molecules from the dataset that

were associated with biological functions and/or diseases in Ingenuity’s Knowledge Base

were considered for the analysis. Two-tailed Fisher’s exact test was used to calculate a p-

value determining the probability that each biological function and/or disease assigned to

that data set is due to chance alone. A data set containing gene identifiers and

corresponding expression values was uploaded into the IPA application. Each identifier

was mapped to its corresponding object in Ingenuity's Knowledge Base. Molecules,

whose expression was significantly differentially regulated, called Network Eligible

molecules, were overlaid onto a global molecular network developed from information contained in Ingenuity’s Knowledge Base. Networks of Network Eligible Molecules were then algorithmically generated based on their connectivity.

Immunohistochemical staining (IHC)

Paraffinized tissue blocks of IPF and normal lung were sectioned at thickness of < 5

m. was performed on 10 IPF cases and 5 normal donor lungs

using antibodies against SFRP2 (Sigma, monoclonal Rabbit anti-, 1:75 dilution),

SMOC2 (Lifespan Biosciences, polyclonal Rabbit anti human, 1:50 dilution) and STAT1

(Sigma rabbit anti human, monoclonal, 1:50 dilution). Antigen retrieval was performed using DAKO pH 6 (SFRP2 and SMOC2) or pH 9 (STAT1) retrieval buffer. Primary antibodies were incubated at room temperature for 1 hour, and developed using the

DAKO Envision Dual Link kit (Dako, Denmark) with DAB substrate and hematoxylin counterstain. Examination for statistical significance was performed using the Fisher’s

Exact Test (SPSS, v16.0).

Supplemental Table E1:

Gene Names Expression Values Endothelial adrenomedullin 1532 ± 943 thrombomodulin 1110 ± 575 endothelin type A 3623 ± 1236 SMAD family member 6 744 ± 368 Epithelial Genes 15 72 ± 176 mucin 4, cell surface associated 77 ± 258 189 ± 190 surfactant A1B 39 ± 114

Values are mean normalized expression values rounded to the nearest integer ± standard deviation

Supplemental Table E2: Univariate analysis comparing gene expression in NPH-IPF vs. PH-IPF arterioles

Gene symbol Probe set Description Parametric FDR Fold- p-value change

CCR1 205099_s_at chemokine (C-C motif) receptor 1 0.001158 0.9913072 0.4500061

PTMS 218045_x_at parathymosin 0.0011904 0.9913072 1.7440695

NPL 240440_at N-acetylneuraminate pyruvate 0.0016084 0.9913072 0.5080298 (dihydrodipicolinate synthase)

NA 241838_at NA 0.0022076 0.9913072 0.5771265

NA 238156_at NA 0.0029903 0.9913072 0.388007

PDGFRA 203131_at platelet-derived growth factor receptor, 0.0031531 0.9913072 0.6256235 alpha polypeptide

FLT1 222033_s_at fms-related tyrosine 1 (vascular 0.0033705 0.9913072 0.5934558 endothelial growth factor/vascular permeability factor receptor)

TEF 225840_at thyrotrophic embryonic factor 0.0033854 0.9913072 2.3365277

NA 239808_at NA 0.0036163 0.9913072 0.395203

NA 1568983_a_at NA 0.0040027 0.9913072 0.5144699

NA 235172_at NA 0.0040874 0.9913072 0.3932263

NA 240690_at NA 0.0041938 0.9913072 0.5613011

NLGN4X 221933_at neuroligin 4, X-linked 0.0043912 0.9913072 0.4889389

ELTD1 219134_at EGF, and seven transmembrane 0.0045867 0.9913072 0.4041308 domain containing 1

NA 239862_at NA 0.0045982 0.9913072 0.595371

B2M 232311_at beta-2-microglobulin 0.0046597 0.9913072 0.438037

ND6 1553575_at NADH , subunit 6 (complex 0.0046924 0.9913072 0.5143606 I)

NA 1564077_at NA 0.0048054 0.9913072 0.4258312

SPTBN1 226765_at , beta, non-erythrocytic 1 0.0048557 0.9913072 0.4490491

ZNF827 226764_at protein 827 0.0048903 0.9913072 1.8218937

NEURL1B 225355_at neuralized homolog 1B (Drosophila) 0.0050316 0.9913072 1.49516

CDC14A 210742_at CDC14 cell division cycle 14 homolog A (S. 0.0053101 0.9913072 0.314476 cerevisiae)

POM121L9P 222253_s_at POM121 membrane glycoprotein-like 9 (rat) 0.0053544 0.9913072 0.4984525 pseudogene

6-Sep 212413_at septin 6 0.0057778 0.9913072 0.5310485

NA 235274_at NA 0.0057811 0.9913072 0.5455783

NA 236592_at NA 0.0059805 0.9913072 0.5788008

PNKP 218961_s_at polynucleotide kinase 3@#$%&- 0.0062114 0.9913072 1.6995573 phosphatase

THSD7A 214920_at thrombospondin, type I, domain containing 0.0062364 0.9913072 0.3822614 7A

CPM 235019_at carboxypeptidase M 0.0066804 0.9913072 0.3709829 KCTD11 235857_at potassium channel tetramerisation domain 0.0067233 0.9913072 2.0062071 containing 11

KRR1 232441_at KRR1, small subunit (SSU) processome 0.00704 0.9913072 0.5056537 component, homolog (yeast)

PITPNC1 219155_at phosphatidylinositol transfer protein, 0.0073711 0.9913072 0.5961627 cytoplasmic 1

NA 213705_at NA 0.007495 0.9913072 0.4530666

LOC100132430 214182_at hypothetical LOC100132430 0.0078264 0.9913072 0.5352828

HP1BP3 229204_at heterochromatin protein 1, binding protein 3 0.00794 0.9913072 0.58305

TNFRSF10A 231775_at tumor necrosis factor receptor superfamily, 0.0080608 0.9913072 0.5099776 member 10a

NA 231484_at NA 0.0082447 0.9913072 0.4695896

PRMT1 206445_s_at protein arginine methyltransferase 1 0.0085897 0.9913072 1.7887033

CNN3 228297_at calponin 3, acidic 0.0088275 0.9913072 0.455391

STAT3 243213_at signal transducer and activator of 0.0088678 0.9913072 0.4965778 3 (acute-phase response factor)

FAM86B1 65585_at family with sequence similarity 86, member 0.0091584 0.9913072 1.85688 B1

SH3KBP1 235692_at SH3-domain kinase binding protein 1 0.0093252 0.9913072 0.591637

NA 239907_at NA 0.0093355 0.9913072 0.3655385

HGF 209960_at hepatocyte growth factor (hepapoietin A; 0.0093767 0.9913072 0.4720159 scatter factor)

NA 242397_at NA 0.0095407 0.9913072 0.377448

CATSPER2 1561405_s_at cation channel, sperm associated 2 0.0098016 0.9913072 1.6568168

ERO1L 222646_s_at ERO1-like (S. cerevisiae) 0.0099056 0.9913072 0.6118214

IDH3G 202471_s_at isocitrate dehydrogenase 3 (NAD+) gamma 0.0103207 0.9913072 1.5550527

NA 226365_at NA 0.0105412 0.9913072 0.6073307

GPRIN3 1556698_a_at GPRIN family member 3 0.0105564 0.9913072 0.6549646

NA 1566342_at NA 0.0108587 0.9913072 0.4650578

PPP2R5C 1557718_at protein phosphatase 2, regulatory subunit 0.0110155 0.9913072 0.5251526 B@#$%&, gamma isoform

FYB 211794_at FYN binding protein (FYB-120/130) 0.0112537 0.9913072 0.5614993

TWIST1 213943_at twist homolog 1 (Drosophila) 0.0116602 0.9913072 0.5350974

OBFC2A 233085_s_at oligonucleotide/oligosaccharide-binding fold 0.0118959 0.9913072 0.4534448 containing 2A

NA 232835_at NA 0.0119891 0.9913072 0.6310771

DNAJC13 1560020_at DnaJ (Hsp40) homolog, subfamily C, 0.0123426 0.9913072 1.5664626 member 13

SYK 244023_at spleen tyrosine kinase 0.0124291 0.9913072 0.3928391

SYNPO2L 243313_at synaptopodin 2-like 0.0124683 0.9913072 1.6573898

STEAP1 205542_at six transmembrane epithelial antigen of the 0.0125049 0.9913072 0.4392555 prostate 1

ACOX2 205364_at acyl-Coenzyme A oxidase 2, branched chain 0.0127468 0.9913072 1.5880573

CTSC 225646_at cathepsin C 0.0130762 0.9913072 0.4501248

DCP2 244777_at DCP2 decapping homolog (S. 0.0130986 0.9913072 0.6262102 cerevisiae)

FBXL3 242829_x_at F-box and leucine-rich repeat protein 3 0.0132872 0.9913072 0.3470831 NA 236921_at NA 0.0134885 0.9913072 0.5898935

ZC3H12D 1559263_s_at zinc finger CCCH-type containing 12D 0.0135231 0.9913072 0.6001638

DLC1 220512_at deleted in liver cancer 1 0.013525 0.9913072 0.5404732

HIVEP3 235122_at human immunodeficiency virus type I 0.0136699 0.9913072 0.5747972 enhancer binding protein 3

LMO7 241140_at LIM domain 7 0.0136915 0.9913072 0.5051105

NA 240232_at NA 0.0137634 0.9913072 0.4723528

ASMTL 36554_at acetylserotonin O-methyltransferase-like 0.0138443 0.9913072 2.1604545

PER3 1569701_at period homolog 3 (Drosophila) 0.013992 0.9913072 2.3551093

ROR1 205805_s_at receptor tyrosine kinase-like 0.0143093 0.9913072 2.0305321 1

STAT4 206118_at signal transducer and activator of 0.0144971 0.9913072 0.556929 transcription 4

LZTS1 47550_at , putative tumor suppressor 1 0.0145891 0.9913072 0.5121251

TM4SF18 228489_at transmembrane 4 L six family member 18 0.0145942 0.9913072 0.4841238

CCDC102A 232051_at coiled-coil domain containing 102A 0.0152067 0.9913072 1.5958458

NA 240019_at NA 0.0154648 0.9913072 0.4546053

MLF2 200948_at myeloid leukemia factor 2 0.0155736 0.9913072 1.6586876

FAM149A 214889_at family with sequence similarity 149, 0.0157888 0.9913072 1.7287745 member A

NA 242968_at NA 0.0158339 0.9913072 0.5183042

MYOZ1 219509_at myozenin 1 0.0159267 0.9913072 1.55115

RFX6 1552673_at regulatory factor X, 6 0.0160027 0.9913072 0.8947108

FAM85A 227917_at family with sequence similarity 85, member 0.016082 0.9913072 1.6639345 A

MRPL38 225103_at mitochondrial ribosomal protein L38 0.0162002 0.9913072 1.5571097

THBS1 201109_s_at 0.0163735 0.9913072 0.5349754

NA 1558299_at NA 0.0164316 0.9913072 0.6720068

ANXA6 200982_s_at annexin A6 0.0165673 0.9913072 1.7850808

ERI3 208973_at exoribonuclease 3 0.016719 0.9913072 1.5941935

TTN 242771_at 0.0167691 0.9913072 1.6518375

CCDC69 212886_at coiled-coil domain containing 69 0.016813 0.9913072 1.507653

C1orf86 229113_s_at 1 open reading frame 86 0.0169767 0.9913072 1.5080523

IL1A 208200_at interleukin 1, alpha 0.0170529 0.9913072 0.5507049

DGCR14 204383_at DiGeorge syndrome critical region gene 14 0.0172718 0.9913072 1.5724772

RPL27A 212044_s_at ribosomal protein L27a 0.0173191 0.9913072 0.574372

NA 236571_at NA 0.0174376 0.9913072 0.4114869

VEGFA 210512_s_at vascular endothelial growth factor A 0.0174886 0.9913072 0.5904196

ADAP2 222876_s_at ArfGAP with dual PH domains 2 0.0177546 0.9913072 0.6413053

RASGRF2 228109_at Ras protein-specific guanine nucleotide- 0.0178562 0.9913072 0.6280951 releasing factor 2

FAM101B 226876_at family with sequence similarity 101, 0.0179484 0.9913072 0.5402046 member B

NCAM1 212843_at neural cell adhesion molecule 1 0.0180103 0.9913072 0.4943807

POLE3 208828_at polymerase (DNA directed), epsilon 3 (p17 0.0180366 0.9913072 1.5910197 subunit)

NA 235743_at NA 0.0180406 0.9913072 0.5092879 KRT4 213240_s_at 0.0181636 0.9913072 1.8456264

NTRK3 217377_x_at neurotrophic tyrosine kinase, receptor, type 0.0183369 0.9913072 1.8392137 3

E2F3 203693_s_at 3 0.0184495 0.9913072 0.5888585

NA 243183_at NA 0.0184839 0.9913072 0.5561876

EEF1D 214395_x_at eukaryotic translation elongation factor 1 0.01863 0.9913072 0.5200997 delta (guanine nucleotide exchange protein)

LOC727820 231247_s_at hypothetical protein LOC727820 0.0187138 0.9913072 0.5557303

NA 237176_at NA 0.0187555 0.9913072 0.6820739

MED29 225708_at mediator complex subunit 29 0.0188131 0.9913072 1.6882892

TMEFF2 224321_at transmembrane protein with EGF-like and 0.0188362 0.9913072 0.4949167 two -like domains 2

IDH2 210046_s_at isocitrate dehydrogenase 2 (NADP+), 0.0188468 0.9913072 1.7712324 mitochondrial

NA 1557632_at NA 0.0188898 0.9913072 0.5419998

LOC440944 1555858_at hypothetical LOC440944 0.0190277 0.9913072 1.6439497

RNF125 235199_at ring finger protein 125 0.0191633 0.9913072 0.4636918

PYGB 201481_s_at phosphorylase, glycogen; brain 0.0191895 0.9913072 1.7767896

NA 213048_s_at NA 0.0191977 0.9913072 0.4831417

RPL27A 223707_at ribosomal protein L27a 0.019244 0.9913072 1.5343023

NA 227665_at NA 0.0193841 0.9913072 0.6220426

LEAP2 1552362_a_at liver expressed antimicrobial peptide 2 0.0195025 0.9913072 0.6327363

OBFC2A 222872_x_at oligonucleotide/oligosaccharide-binding fold 0.019516 0.9913072 0.4905981 containing 2A

FAM149A 214890_s_at family with sequence similarity 149, 0.0196238 0.9913072 1.8613193 member A

FAM101B 226905_at family with sequence similarity 101, 0.0198607 0.9913072 0.5394198 member B

NA 243756_at NA 0.0200941 0.9913072 0.3647235

ABL2 231907_at v-abl Abelson murine leukemia viral 0.0203484 0.9913072 1.6987097 oncogene homolog 2 (arg, Abelson-related gene)

NA 216246_at NA 0.0203603 0.9913072 0.5334423

APLP2 228520_s_at (A4) precursor-like protein 2 0.0204158 0.9913072 0.5920002

RPS27A 242214_at ribosomal protein S27a 0.0205283 0.9913072 0.582027

NA 213813_x_at NA 0.0205306 0.9913072 0.5337055

ROBO2 226709_at roundabout, axon guidance receptor, 0.020715 0.9913072 0.5642216 homolog 2 (Drosophila)

NA 1558605_at NA 0.0207527 0.9913072 1.4906206

NA 238009_at NA 0.0209136 0.9913072 0.5929444

NA 215029_at NA 0.0209194 0.9913072 0.5766432

PAPPA 1559400_s_at pregnancy-associated plasma protein A, 0.0209715 0.9913072 0.4928106 pappalysin 1

PCDH7 210273_at protocadherin 7 0.0210958 0.9913072 2.1332432

QKI 241938_at quaking homolog, KH domain RNA binding 0.0212625 0.9913072 0.3483255 (mouse)

EHBP1L1 91703_at EH domain binding protein 1-like 1 0.0216188 0.9913072 2.0069868

HMG20B 210719_s_at high-mobility group 20B 0.0216659 0.9913072 1.6078151

NA 213879_at NA 0.0217621 0.9913072 0.6297194 NAIP 204860_s_at NLR family, apoptosis inhibitory protein 0.022266 0.9913072 0.5299025

NA 230959_at NA 0.0223002 0.9913072 0.5261256

CTSC 231234_at cathepsin C 0.0223494 0.9913072 0.5963279

LOC144571 1564139_at hypothetical protein LOC144571 0.0224991 0.9913072 0.6046607

PEBP1 211941_s_at phosphatidylethanolamine binding protein 1 0.0225327 0.9913072 1.5998284

NA 237104_at NA 0.0225993 0.9913072 0.6323796

VDR 204254_s_at vitamin D (1,25- dihydroxyvitamin D3) 0.022637 0.9913072 0.4576312 receptor

NTRK3 217033_x_at neurotrophic tyrosine kinase, receptor, type 0.0227025 0.9913072 1.801638 3

LDOC1 204454_at leucine zipper, down-regulated in cancer 1 0.0229187 0.9913072 1.5847795

CRY2 212695_at cryptochrome 2 (photolyase-like) 0.0230588 0.9913072 1.365966

LOC100133484 238900_at similar to Major histocompatibility complex, 0.0230606 0.9913072 0.3591865 class II, DR beta 4

NA 238920_at NA 0.0233162 0.9913072 0.7322632

CYP1B1 202436_s_at P450, family 1, subfamily B, 0.0233227 0.9913072 0.3554015 polypeptide 1

NA 243561_at NA 0.0233613 0.9913072 0.4538001

NTRK3 215115_x_at neurotrophic tyrosine kinase, receptor, type 0.0233621 0.9913072 1.7565984 3

C1orf144 212005_at open reading frame 144 0.0235095 0.9913072 1.8460611

NA 237172_at NA 0.0235696 0.9913072 1.3823695

NA 1559436_x_at NA 0.0236591 0.9913072 0.5686513

ABCC9 1557374_at ATP-binding cassette, sub-family C 0.0236662 0.9913072 0.5417522 (CFTR/MRP), member 9

THBS1 201110_s_at thrombospondin 1 0.0239809 0.9913072 0.446528

BACH2 236796_at BTB and CNC homology 1, basic leucine 0.0242891 0.9913072 0.5254527 zipper transcription factor 2

LILRB1 229937_x_at leukocyte immunoglobulin-like receptor, 0.0246479 0.9913072 0.5940855 subfamily B (with TM and ITIM domains), member 1

DAB2 201280_s_at disabled homolog 2, mitogen-responsive 0.0246569 0.9913072 0.4128252 phosphoprotein (Drosophila)

NA 243366_s_at NA 0.0247143 0.9913072 0.4492646

C9orf33 217130_at open reading frame 33 0.0248148 0.9913072 0.6272287

SLC2A3 202497_x_at solute carrier family 2 (facilitated glucose 0.0248222 0.9913072 0.6278402 transporter), member 3

LOC100170939 214850_at glucuronidase, beta pseudogene 0.0248926 0.9913072 0.6077436

VPS18 223346_at vacuolar protein sorting 18 homolog (S. 0.0249083 0.9913072 1.5573457 cerevisiae)

MCPH1 1554155_at microcephalin 1 0.0250434 0.9913072 0.5560028

TM4SF18 230061_at transmembrane 4 L six family member 18 0.0254783 0.9913072 0.3455158

NA 229849_at NA 0.0258341 0.9913072 1.9354205

FBXL22 241350_at F-box and leucine-rich repeat protein 22 0.0258378 0.9913072 1.5344829

CCDC69 1553102_a_at coiled-coil domain containing 69 0.0260903 0.9913072 1.6983095

INHBC 207688_s_at inhibin, beta C 0.0261144 0.9913072 0.5992369 PTPRO 211600_at protein tyrosine phosphatase, receptor type, 0.0262174 0.9913072 1.6540914 O

MIRHG2 229437_at microRNA host gene 2 (non-protein coding) 0.0262211 0.9913072 0.4933694

NA 242480_at NA 0.0263602 0.9913072 0.4812714

RPL37A 214041_x_at ribosomal protein L37a 0.0265011 0.9913072 0.5956481

MCL1 214057_at myeloid cell leukemia sequence 1 (BCL2- 0.0265703 0.9913072 0.6237113 related)

TMEM132C 232313_at transmembrane protein 132C 0.0267488 0.9913072 0.6563002

TXN 216609_at thioredoxin 0.0268969 0.9913072 0.617715

ITGA6 201656_at integrin, alpha 6 0.0269621 0.9913072 0.4872863

NA 244054_at NA 0.0271453 0.9913072 0.6209078

BMP2K 59644_at BMP2 inducible kinase 0.0272504 0.9913072 0.553151

TMTC1 224397_s_at transmembrane and tetratricopeptide repeat 0.0272715 0.9913072 0.6595777 containing 1

LPAR1 204037_at receptor 1 0.0275661 0.9913072 0.6423543

ITPKB 235213_at inositol 1,4,5-trisphosphate 3-kinase B 0.0276105 0.9913072 0.4044254

PDIA5 203857_s_at protein family A, 0.0276924 0.9913072 1.6385378 member 5

HAVCR2 235458_at hepatitis A virus cellular receptor 2 0.0277154 0.9913072 0.6542807

VARS 201797_s_at valyl-tRNA synthetase 0.0279616 0.9913072 1.58353

NA 1563075_s_at NA 0.0280708 0.9913072 0.543617

ATP6V0E2 213587_s_at ATPase, H+ transporting V0 subunit e2 0.0287273 0.9913072 1.470399

NA 233690_at NA 0.0287698 0.9913072 0.6187599

NA 230820_at NA 0.0289587 0.9913072 0.6113732

SMTN 209427_at smoothelin 0.0290671 0.9913072 2.1343983

KAT5 209192_x_at K() acetyltransferase 5 0.0293221 0.9913072 1.5682291

NA 1563473_at NA 0.0293493 0.9913072 0.6164532

ROD1 224618_at ROD1 regulator of differentiation 1 (S. 0.0295306 0.9913072 0.6156955 pombe)

PDLIM3 210170_at PDZ and LIM domain 3 0.029604 0.9913072 1.8060344

THRA 204100_at thyroid , alpha 0.0297535 0.9913072 1.5184773 (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)

NA 230733_at NA 0.0298742 0.9913072 0.4668269

ETV5 230102_at 0.0299641 0.9913072 0.6287517

TRIM26 242618_at tripartite motif-containing 26 0.0301526 0.9913072 0.6618969

FLJ32810 230047_at Rho-type GTPase-activating protein 0.0302694 0.9913072 0.576896 FLJ32810

NA 1559057_at NA 0.0304852 0.9913072 0.6526711

FAM120A 1555948_s_at family with sequence similarity 120A 0.0305233 0.9913072 0.6425512

DKFZP434L187 230861_at hypothetical LOC26082 0.0305529 0.9913072 0.5146465

SEMA5B 223610_at sema domain, seven thrombospondin repeats 0.0305863 0.9913072 1.4685478 (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B

NA 244665_at NA 0.0308025 0.9913072 0.4932473

FKBP1A 210187_at FK506 binding protein 1A, 12kDa 0.0308035 0.9913072 0.6063258 GMFB 202543_s_at glia maturation factor, beta 0.0309757 0.9913072 0.5405001

NA 232203_at NA 0.0310041 0.9913072 1.6455088

USP2 229337_at ubiquitin specific peptidase 2 0.0311736 0.9913072 1.6526199

AHNAK2 212992_at AHNAK nucleoprotein 2 0.0312118 0.9913072 1.5105114

NA 230913_at NA 0.0314103 0.9913072 0.5241051

KAT5 214258_x_at K(lysine) acetyltransferase 5 0.0314326 0.9913072 1.5757526

SYTL3 1562255_at synaptotagmin-like 3 0.0314332 0.9913072 0.5507314

FHOD3 218980_at formin homology 2 domain containing 3 0.0314488 0.9913072 2.0548185

CASC3 207842_s_at cancer susceptibility candidate 3 0.0315266 0.9913072 1.5518787

PLAGL2 202924_s_at pleiomorphic adenoma gene-like 2 0.0315591 0.9913072 1.5038006

NA 242021_at NA 0.0315778 0.9913072 0.5973007

RHOD 209885_at ras homolog gene family, member D 0.0316924 0.9913072 1.5170973

NA 1562468_at NA 0.0317142 0.9913072 0.624339

AHSA1 201491_at AHA1, activator of heat shock 90kDa 0.031948 0.9913072 1.6180226 protein ATPase homolog 1 (yeast)

NUDT16 235054_at nudix (nucleoside diphosphate linked moiety 0.0319657 0.9913072 1.3041277 X)-type motif 16

ADCK2 221893_s_at aarF domain containing kinase 2 0.0319699 0.9913072 1.5787645

MIF4GD 231727_s_at MIF4G domain containing 0.0319818 0.9913072 1.6253789

CPEB4 224829_at cytoplasmic polyadenylation element 0.0320158 0.9913072 0.4907696 binding protein 4

MDM4 235589_s_at Mdm4 binding protein homolog 0.0320206 0.9913072 0.5655264 (mouse)

C18orf34 1558820_a_at chromosome 18 open reading frame 34 0.0320752 0.9913072 0.5598032

LOC150763 235557_at hypothetical protein LOC150763 0.0323058 0.9913072 0.6106757

DOCK4 205003_at dedicator of cytokinesis 4 0.0324413 0.9913072 0.5900478

PTP4A1 200730_s_at protein tyrosine phosphatase type IVA, 0.0324679 0.9913072 0.6176361 member 1

MEOX1 205619_s_at mesenchyme 1 0.0324777 0.9913072 0.5369893

ACO2 200793_s_at aconitase 2, mitochondrial 0.0326536 0.9913072 1.5495539

ATP6V0E1 214149_s_at ATPase, H+ transporting, lysosomal 9kDa, 0.0326782 0.9913072 0.5724628 V0 subunit e1

ACTG2 202274_at , gamma 2, smooth muscle, enteric 0.0327458 0.9913072 1.3264769

CAD 202715_at carbamoyl-phosphate synthetase 2, aspartate 0.032894 0.9913072 1.5010691 transcarbamylase, and

MCTP1 220122_at multiple C2 domains, transmembrane 1 0.0330027 0.9913072 0.3887517

ERICH1 236467_at glutamate-rich 1 0.0331126 0.9913072 0.7317152

ZFHX3 208033_s_at zinc finger homeobox 3 0.0331824 0.9913072 1.7281588

RNF41 201962_s_at ring finger protein 41 0.0332017 0.9913072 1.4761121

OLAH 219975_x_at oleoyl-ACP 0.033212 0.9913072 0.7328481

ARHGAP29 1560318_at Rho GTPase activating protein 29 0.033264 0.9913072 0.6532639

LGALS3BP 200923_at lectin, galactoside-binding, soluble, 3 0.0334781 0.9913072 1.59621 binding protein

PCDH7 205534_at protocadherin 7 0.0336074 0.9913072 1.7837042

NR1H2 218215_s_at subfamily 1, group H, 0.0336155 0.9913072 1.638592 member 2

KIAA1958 230166_at KIAA1958 0.0336722 0.9913072 1.585602 GARNL3 238227_at GTPase activating Rap/RanGAP domain- 0.0342648 0.9913072 1.6950519 like 3

NTRK3 206462_s_at neurotrophic tyrosine kinase, receptor, type 0.0344753 0.9913072 2.0971952 3

TNFRSF1B 203508_at tumor necrosis factor receptor superfamily, 0.0346906 0.9913072 0.6081538 member 1B

RECQL 212917_x_at RecQ protein-like (DNA helicase Q1-like) 0.0346991 0.9913072 0.5801468

GADD45B 213560_at growth arrest and DNA-damage-inducible, 0.0347505 0.9913072 0.595008 beta

RFC5 213734_at replication factor C (activator 1) 5, 36.5kDa 0.034856 0.9913072 0.5563099

THOC4 226320_at THO complex 4 0.0350443 0.9913072 0.5958045

PRKXP1 235987_at protein kinase, X-linked, pseudogene 1 0.0351117 0.9913072 0.4946252

LOC493754 1569296_a_at RAB guanine nucleotide exchange factor 0.0351305 0.9913072 1.3983095 (GEF) 1 pseudogene

C21orf86 228908_s_at chromosome 21 open reading frame 86 0.0352102 0.9913072 0.668137

LOC100130744 236228_at hypothetical LOC100130744 0.0352346 0.9913072 1.3862272

NA 240468_at NA 0.0353902 0.9913072 0.6072184

PPP2R1A 200695_at protein phosphatase 2 (formerly 2A), 0.0355115 0.9913072 1.6895654 regulatory subunit A, alpha isoform

COCH 1554241_at coagulation factor C homolog, cochlin 0.0355522 0.9913072 0.5594512 (Limulus polyphemus)

GADD45G 204121_at growth arrest and DNA-damage-inducible, 0.03557 0.9913072 2.0429815 gamma

NA 1565913_at NA 0.0356106 0.9913072 0.6139082

DUS3L 224966_s_at dihydrouridine synthase 3-like (S. 0.0356301 0.9913072 1.5627469 cerevisiae)

NA 234180_at NA 0.0358165 0.9913072 0.5040408

PTOV1 212032_s_at prostate tumor overexpressed 1 0.0358366 0.9913072 1.6513896

ARGLU1 228477_at arginine and glutamate rich 1 0.0359185 0.9913072 0.5249957

NA 224549_x_at NA 0.0359571 0.9913072 0.4920339

NUMB 236930_at numb homolog (Drosophila) 0.0359621 0.9913072 0.556978

MAP2K2 202424_at mitogen-activated protein kinase kinase 2 0.0361286 0.9913072 1.6675538

NA 222249_at NA 0.036287 0.9913072 0.69545

NA 230391_at NA 0.0363445 0.9913072 0.4741369

TAGLN 1555724_s_at transgelin 0.0365789 0.9913072 1.5400386

NA 241506_at NA 0.0367993 0.9913072 1.8747083

NA 241508_at NA 0.0368527 0.9913072 0.5353355

STARD10 223103_at StAR-related lipid transfer (START) domain 0.0369791 0.9913072 1.7408359 containing 10

NA 221127_s_at NA 0.0370486 0.9913072 0.6513508

KAT5 206689_x_at K(lysine) acetyltransferase 5 0.0375591 0.9913072 1.6782307

NR1D2 225768_at nuclear receptor subfamily 1, group D, 0.037615 0.9913072 2.6985247 member 2

IL7R 205798_at interleukin 7 receptor 0.0376746 0.9913072 0.366342

NA 214316_x_at NA 0.0377636 0.9913072 0.6041321

TRAM1 210733_at translocation associated membrane protein 1 0.0377642 0.9913072 0.601157

NA 227210_at NA 0.0378013 0.9913072 0.5470259

NGEF 227240_at neuronal guanine nucleotide exchange factor 0.0378199 0.9913072 1.532969 COG1 227784_s_at component of oligomeric golgi complex 1 0.0379177 0.9913072 1.5924982

OSGIN2 1554414_a_at oxidative stress induced growth inhibitor 0.0379238 0.9913072 1.4698503 family member 2

ZNF326 227680_at zinc finger protein 326 0.0382734 0.9913072 0.641007

RNF216 218425_at ring finger protein 216 0.0383246 0.9913072 1.6845438

NA 1560706_at NA 0.0384409 0.9913072 0.5697766

C17orf42 238295_at open reading frame 42 0.0385303 0.9913072 0.554735

NA 240238_at NA 0.038594 0.9913072 0.6202789

MYO1D 212338_at ID 0.0390421 0.9913072 1.7009093

ILK 201234_at integrin-linked kinase 0.0391429 0.9913072 1.5020875

NA 244267_at NA 0.0391933 0.9913072 0.5181673

IGFBP3 210095_s_at insulin-like growth factor binding protein 3 0.039295 0.9913072 0.5736228

SERAC1 1569864_at serine containing 1 0.0395327 0.9913072 0.7530155

EIF3C 200647_x_at eukaryotic translation initiation factor 3, 0.0396325 0.9913072 1.5111996 subunit C

SLC25A37 242335_at solute carrier family 25, member 37 0.0396424 0.9913072 0.7436605

C7orf20 223811_s_at open reading frame 20 0.0396862 0.9913072 1.5759804

MFAP4 212713_at microfibrillar-associated protein 4 0.0397409 0.9913072 1.7074267

NLRC3 236295_s_at NLR family, CARD domain containing 3 0.0398175 0.9913072 0.5146997

NA 242733_at NA 0.040079 0.9913072 0.4503528

CPEB2 235479_at cytoplasmic polyadenylation element 0.0401216 0.9913072 0.606548 binding protein 2

NA 235147_at NA 0.0401984 0.9913072 0.569471

SLC44A1 228486_at solute carrier family 44, member 1 0.0402113 0.9913072 0.5922104

TMEM106A 1552302_at transmembrane protein 106A 0.040255 0.9913072 0.5441975

RECQL 205091_x_at RecQ protein-like (DNA helicase Q1-like) 0.0402619 0.9913072 0.6691216

C21orf86 228909_at chromosome 21 open reading frame 86 0.0403629 0.9913072 0.7418999

PMM1 203467_at phosphomannomutase 1 0.0404209 0.9913072 1.555309

RASGRP2 208206_s_at RAS guanyl releasing protein 2 (calcium and 0.040695 0.9913072 1.4033935 DAG-regulated)

NA 224348_s_at NA 0.0407304 0.9913072 0.4716678

ENC1 201340_s_at ectodermal-neural cortex (with BTB-like 0.0408764 0.9913072 0.4186858 domain)

NA 240608_at NA 0.0409799 0.9913072 1.7215056

PYGM 205577_at phosphorylase, glycogen, muscle 0.0415504 0.9913072 1.6113174

S100A8 214370_at S100 calcium binding protein A8 0.0417665 0.9913072 0.7296157

NA 238378_at NA 0.0419639 0.9913072 0.643291

SFRS1 201742_x_at splicing factor, arginine/serine-rich 1 0.0419885 0.9913072 1.5986172

NA 235385_at NA 0.0420757 0.9913072 0.5552315

OAZ2 201365_at ornithine decarboxylase antizyme 2 0.0421055 0.9913072 1.6592326

FAM48A 216682_s_at family with sequence similarity 48, member 0.0421196 0.9913072 0.5791548 A

ABCB1 243951_at ATP-binding cassette, sub-family B 0.0421514 0.9913072 0.62377 (MDR/TAP), member 1

SMC4 201663_s_at structural maintenance of 4 0.0422707 0.9913072 0.6430737

ROR1 211057_at receptor tyrosine kinase-like orphan receptor 0.0422737 0.9913072 1.5944933 1

NA 243178_at NA 0.0423387 0.9913072 0.5850629 VRK3 221999_at vaccinia related kinase 3 0.0423653 0.9913072 1.4339991

NA 242500_at NA 0.0424612 0.9913072 0.5107641

MYO1G 244654_at myosin IG 0.042498 0.9913072 0.5600867

TRIM28 200990_at tripartite motif-containing 28 0.042608 0.9913072 1.5760361

PIM1 209193_at pim-1 oncogene 0.0426514 0.9913072 0.6857046

SLC25A6 212085_at solute carrier family 25 (mitochondrial 0.0427641 0.9913072 1.8981591 carrier; adenine nucleotide translocator), member 6

NA 240248_at NA 0.0430073 0.9913072 0.6003525

SDK1 229407_at sidekick homolog 1, cell adhesion molecule 0.0434576 0.9913072 1.6241467 (chicken)

ENPEP 204844_at glutamyl aminopeptidase (aminopeptidase 0.0435709 0.9913072 0.4481421 A)

IFNAR2 204786_s_at interferon (alpha, beta and omega) receptor 2 0.0436631 0.9913072 0.5598719

ELOVL5 214153_at ELOVL family member 5, elongation of 0.0437349 0.9913072 0.5387797 long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)

BMP2K 219546_at BMP2 inducible kinase 0.0437999 0.9913072 0.6240758

TCEA3 226388_at transcription elongation factor A (SII), 3 0.0439879 0.9913072 1.4164564

CBFA2T3 208056_s_at core-binding factor, runt domain, alpha 0.0440404 0.9913072 0.6039146 subunit 2; translocated to, 3

NA 242384_at NA 0.0442564 0.9913072 0.6189114

PDIA4 211048_s_at protein disulfide isomerase family A, 0.0443587 0.9913072 0.6279341 member 4

EIF3C 210949_s_at eukaryotic translation initiation factor 3, 0.0443695 0.9913072 1.5911918 subunit C

C7orf27 225437_s_at chromosome 7 open reading frame 27 0.0444146 0.9913072 1.5101133

HEMK1 218621_at HemK methyltransferase family member 1 0.0445085 0.9913072 1.3418424

TSHZ2 238577_s_at teashirt zinc finger homeobox 2 0.0445276 0.9913072 0.6478851

LOX 215446_s_at lysyl oxidase 0.0446001 0.9913072 0.6324715

MORC2 216863_s_at MORC family CW-type zinc finger 2 0.0446275 0.9913072 1.6478407

LOC100131043 244029_at hypothetical LOC100131043 0.0447069 0.9913072 0.6243744

NA 238915_at NA 0.044718 0.9913072 0.7240266

LOC728153 233204_at similar to FAM133B protein 0.044776 0.9913072 0.7306897

TIA1 201450_s_at TIA1 cytotoxic granule-associated RNA 0.0450618 0.9913072 0.7051485 binding protein

SOX17 230943_at SRY (sex determining region Y)-box 17 0.0451049 0.9913072 0.480573

PPP1R11 1566303_s_at protein phosphatase 1, regulatory (inhibitor) 0.0453266 0.9913072 1.7172406 subunit 11

MYOT 219728_at myotilin 0.0453855 0.9913072 0.728225

BCL11B 222895_s_at B-cell CLL/lymphoma 11B (zinc finger 0.045464 0.9913072 0.4804431 protein)

CAPNS1 200001_at calpain, small subunit 1 0.0455275 0.9913072 1.6266201

NA 1558444_at NA 0.0455294 0.9913072 0.471299

SYK 207540_s_at spleen tyrosine kinase 0.0458156 0.9913072 0.6457768

C1QTNF1 224197_s_at C1q and tumor necrosis factor related 0.0458647 0.9913072 1.4422943 protein 1

NR1D1 31637_s_at nuclear receptor subfamily 1, group D, 0.0461021 0.9913072 1.5998896 member 1 C16orf14 1553715_s_at open reading frame 14 0.0461127 0.9913072 1.6165114

SMPD2 205622_at sphingomyelin phosphodiesterase 2, neutral 0.0461326 0.9913072 1.7112235 membrane (neutral sphingomyelinase)

ARHGAP26 205068_s_at Rho GTPase activating protein 26 0.0461746 0.9913072 0.6831768

ITIH4 37201_at inter-alpha (globulin) inhibitor H4 (plasma 0.0462772 0.9913072 1.6423832 Kallikrein-sensitive glycoprotein)

MAFIP 227330_x_at MAFF interacting protein 0.0463202 0.9913072 1.7388838

SCAND1 218206_x_at SCAN domain containing 1 0.0465237 0.9913072 1.6870916

NA 243170_at NA 0.0465502 0.9913072 1.6743349

CAMK2N1 229163_at calcium/calmodulin-dependent protein 0.0465644 0.9913072 0.6305586 kinase II inhibitor 1

SNTA1 203516_at syntrophin, alpha 1 (-associated 0.0465937 0.9913072 1.4154642 protein A1, 59kDa, acidic component)

NA 1564840_at NA 0.0466575 0.9913072 0.6370277

NA 1559391_s_at NA 0.0467343 0.9913072 0.4011513

BANF1 210125_s_at barrier to autointegration factor 1 0.0467727 0.9913072 1.5115369

PSMD7 244515_at proteasome (prosome, macropain) 26S 0.0467919 0.9913072 0.6783723 subunit, non-ATPase, 7

LOC284837 1563088_a_at hypothetical LOC284837 0.0467987 0.9913072 0.701128

HSPB1 201841_s_at heat shock 27kDa protein 1 0.0468021 0.9913072 1.5023169

TMEM35 219685_at transmembrane protein 35 0.0468183 0.9913072 1.849308

SIVA1 203489_at SIVA1, apoptosis-inducing factor 0.0469258 0.9913072 1.4132856

AGPAT9 224480_s_at 1-acylglycerol-3-phosphate O- 0.0469299 0.9913072 0.4928686 acyltransferase 9

NA 232687_at NA 0.0469653 0.9913072 0.5291294

HBS1L 209315_at HBS1-like (S. cerevisiae) 0.0470293 0.9913072 1.7298753

TCF4 212386_at transcription factor 4 0.0471246 0.9913072 0.6578932

SELE 206211_at selectin E 0.0472654 0.9913072 0.3024285

SUPT6H 208420_x_at suppressor of Ty 6 homolog (S. cerevisiae) 0.0473592 0.9913072 1.5209362

NA 239154_at NA 0.0474537 0.9913072 0.6464278

C19orf39 227352_at chromosome 19 open reading frame 39 0.0474577 0.9913072 1.3341774

LOC284757 236846_at hypothetical protein LOC284757 0.0475462 0.9913072 0.6604561

NECAB3 210720_s_at N-terminal EF-hand calcium binding protein 0.0476027 0.9913072 1.5064902 3

SEPP1 201427_s_at selenoprotein P, plasma, 1 0.0477609 0.9913072 0.6900388

SLC25A1 210010_s_at solute carrier family 25 (mitochondrial 0.0479595 0.9913072 1.5470635 carrier; citrate transporter), member 1

SLC25A11 207088_s_at solute carrier family 25 (mitochondrial 0.0480774 0.9913072 1.6554813 carrier; oxoglutarate carrier), member 11

NA 229226_at NA 0.048088 0.9913072 1.4870073

DDAH2 202262_x_at dimethylarginine dimethylaminohydrolase 2 0.0482862 0.9913072 1.5235071

ABHD14A 210006_at abhydrolase domain containing 14A 0.0484736 0.9913072 1.376815

SPP1 209875_s_at secreted phosphoprotein 1 0.0485659 0.9913072 0.3063859

PLAGL1 207002_s_at pleiomorphic adenoma gene-like 1 0.0486636 0.9913072 0.6720035

TMEM38B 222735_at transmembrane protein 38B 0.0487074 0.9913072 0.5473235 LOC81691 208107_s_at exonuclease NEF-sp 0.0487612 0.9913072 1.5895986

TPD52L1 210372_s_at tumor protein D52-like 1 0.0491161 0.9913072 1.5740724

GLB1L2 213713_s_at galactosidase, beta 1-like 2 0.0492667 0.9913072 1.7033326

PSAT1 223062_s_at phosphoserine aminotransferase 1 0.0492709 0.9913072 0.5751788

UBAC1 202151_s_at UBA domain containing 1 0.0493026 0.9913072 1.5977257

CCRK 205271_s_at cell cycle related kinase 0.0495276 0.9913072 1.6928404

CAB39L 225915_at calcium binding protein 39-like 0.0495726 0.9913072 1.8008354

NA 232583_at NA 0.0496993 0.9913072 0.6610002

NRXN3 205795_at neurexin 3 0.0497163 0.9913072 2.0798767

ADM 202912_at adrenomedullin 0.0497483 0.9913072 0.5025873

SH2D1A 210116_at SH2 domain protein 1A 0.0497674 0.9913072 0.6013336

NA 244219_at NA 0.0499168 0.9913072 0.7895493

IL1R1 202948_at interleukin 1 receptor, type I 0.0499373 0.9913072 0.5724628

SMTN 207390_s_at smoothelin 0.0499743 0.9913072 1.9910083

Supplemental Table E3: Univariate analysis comparing gene expression in NPH-IPF vs. Control arterioles

Gene Symbol Probe Set ID Gene Description Parametric FDR Fold p-value Change MTUS1 212096_s_at mitochondrial tumor suppressor 0.0000022 0.0226348 0.543933022 1 ARHGAP26 226576_at Rho GTPase activating protein 0.0000037 0.0226348 0.321866964 26 HIPK2 225368_at homeodomain interacting 0.0000044 0.0226348 0.435704782 protein kinase 2 NA 235856_at NA 0.0000062 0.0226348 6.202464117 ARHGAP26 205068_s_at Rho GTPase activating protein 0.0000069 0.0226348 0.391954193 26 FRYL 212546_s_at FRY-like 0.0000219 0.0517835 0.543242694 SYTL4 227703_s_at synaptotagmin-like 4 0.0000221 0.0517835 0.353462636 C4A 214428_x_at complement component 4A 0.0000265 0.0543316 3.100435142 (Rodgers blood group) SMOC2 223235_s_at SPARC related modular 0.0000356 0.064879 2.606554839 calcium binding 2 NA 221590_s_at NA 0.0000457 0.0671851 0.451891557 AASS 210852_s_at aminoadipate-semialdehyde 0.0000501 0.0671851 0.376355373 synthase NA 231502_at NA 0.0000533 0.0671851 0.446944765 C4B 208451_s_at complement component 4B 0.000063 0.0671851 3.182037962 (Chido blood group) FHOD3 218980_at formin homology 2 domain 0.0000643 0.0671851 4.111181925 containing 3 CTH 217127_at cystathionase (cystathionine 0.000078 0.0671851 0.197283072 gamma-lyase) SERTAD4 230660_at SERTA domain containing 4 0.0000794 0.0671851 3.802836126 NA 232527_at NA 0.0000851 0.0671851 0.474070177 LOC100129406 240868_at hypothetical protein 0.0000896 0.0671851 0.34068647 LOC100129406 ITPR2 202662_s_at inositol 1,4,5-triphosphate 0.0000953 0.0671851 0.505553347 receptor, type 2 TIMP3 201148_s_at TIMP metallopeptidase 0.0000957 0.0671851 0.378062934 inhibitor 3 KLF6 224606_at Kruppel-like factor 6 0.0000999 0.0671851 0.517446427 SCRG1 205475_at scrapie responsive protein 1 0.0001017 0.0671851 5.325436828 NA 244447_at NA 0.0001047 0.0671851 0.145714264 GPD1L 212510_at glycerol-3-phosphate 0.0001048 0.0671851 0.532777791 dehydrogenase 1-like HNRPDL 1554678_s_at heterogeneous nuclear 0.0001056 0.0671851 0.438880369 ribonucleoprotein D-like IGFBP3 210095_s_at insulin-like growth factor 0.0001065 0.0671851 0.292445836 binding protein 3 NA 237798_at NA 0.0001128 0.0685239 0.503608691 RPS27A 242214_at ribosomal protein S27a 0.0001195 0.0700014 0.311562164 LOC145474 230505_at hypothetical protein 0.0001286 0.0727299 0.589009412 LOC145474 SULF1 212354_at sulfatase 1 0.0001431 0.0727299 2.242599238 DUSP5 209457_at dual specificity phosphatase 5 0.0001459 0.0727299 0.287057859 DDX3X 212515_s_at DEAD (Asp-Glu-Ala-Asp) box 0.0001518 0.0727299 0.316735139 polypeptide 3, X-linked KIAA0174 226095_s_at KIAA0174 0.000152 0.0727299 0.646349564 EIF1 202021_x_at eukaryotic translation initiation 0.000163 0.0727299 0.458262629 factor 1 MYLIP 228097_at myosin regulatory light chain 0.0001633 0.0727299 0.259834936 interacting protein ST6GALNAC3 235334_at ST6 (alpha-N-acetyl- 0.0001645 0.0727299 0.335761586 neuraminyl-2,3-beta-galactosyl- 1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 HIPK2 225097_at homeodomain interacting 0.0001669 0.0727299 0.480904228 protein kinase 2 YRDC 218647_s_at yrdC domain containing (E. 0.0001685 0.0727299 0.535296767 coli) MAOA 204388_s_at monoamine oxidase A 0.0001747 0.0734725 0.31491678 DDX50 1568815_a_at DEAD (Asp-Glu-Ala-Asp) box 0.000185 0.0757292 0.409882441 polypeptide 50 PSMD7 238738_at proteasome (prosome, 0.0001893 0.0757292 0.48650083 macropain) 26S subunit, non- ATPase, 7 PIGA 205281_s_at phosphatidylinositol glycan 0.0001962 0.0766208 0.29724814 anchor biosynthesis, class A INSR 213792_s_at insulin receptor 0.0002411 0.0881608 0.524772535 SHOC2 202777_at soc-2 suppressor of clear 0.0002526 0.0881608 0.46476867 homolog (C. elegans) NA 241321_at NA 0.0002548 0.0881608 0.420653578 TGFBI 201506_at transforming growth factor, 0.0002554 0.0881608 2.65443352 beta-induced, 68kDa HNRPDL 209067_s_at heterogeneous nuclear 0.000256 0.0881608 0.594860818 ribonucleoprotein D-like LRRC16A 219573_at leucine rich repeat containing 0.000258 0.0881608 0.38123205 16A KLF10 202393_s_at Kruppel-like factor 10 0.0002844 0.0882533 0.39098458 RLIM 225416_at ring finger protein, LIM domain 0.0002856 0.0882533 0.595945991 interacting FLJ35776 238432_at hypothetical LOC649446 0.0002958 0.0882533 1.572543513 EMP1 201325_s_at epithelial membrane protein 1 0.0003 0.0882533 0.282666539 BAG5 230427_s_at BCL2-associated athanogene 5 0.0003073 0.0882533 0.31441868 PIM1 209193_at pim-1 oncogene 0.0003104 0.0882533 0.25712953 GPX8 228141_at glutathione peroxidase 8 0.0003138 0.0882533 1.824527747 (putative) ABI1 209027_s_at abl-interactor 1 0.0003165 0.0882533 0.520753728 NA 238107_at NA 0.0003179 0.0882533 2.032853668 CHRDL2 223987_at -like 2 0.0003199 0.0882533 2.015840907 TMEM87A 212202_s_at transmembrane protein 87A 0.00032 0.0882533 0.615235853 NA 243509_at NA 0.0003293 0.0882533 0.306432061 MAOA 212741_at monoamine oxidase A 0.000333 0.0882533 0.420422281 YY1 224718_at YY1 transcription factor 0.0003336 0.0882533 0.595052645 EIF1 212227_x_at eukaryotic translation initiation 0.0003542 0.0897045 0.457718428 factor 1 TMEM61 230822_at transmembrane protein 61 0.0003561 0.0897045 2.150362622 DIDO1 227335_at death inducer-obliterator 1 0.0003587 0.0897045 0.517154343 TNFRSF10D 227345_at tumor necrosis factor receptor 0.0003646 0.0897045 0.309018898 superfamily, member 10d, decoy with truncated death domain RUFY2 241996_at RUN and FYVE domain 0.0003702 0.0897045 0.327788626 containing 2 EIF1 212130_x_at eukaryotic translation initiation 0.0003719 0.0897045 0.484775313 factor 1 LIN52 228583_at lin-52 homolog (C. elegans) 0.0003833 0.0907157 0.592874386 NA 230048_at NA 0.0003956 0.0907157 0.276648575 FBXO31 219785_s_at F-box protein 31 0.0003997 0.0907157 0.608202535 SFRS2B 238929_at splicing factor, arginine/serine- 0.0004031 0.0907157 0.493485263 rich 2B CDK9 236023_at cyclin-dependent kinase 9 0.0004148 0.0907157 0.607714329 TRIM32 203846_at tripartite motif-containing 32 0.0004276 0.0907157 1.90847751 GABARAPL1 208869_s_at GABA(A) receptor-associated 0.0004287 0.0907157 0.45645652 protein like 1 LOC100131015 244659_at hypothetical LOC100131015 0.0004297 0.0907157 0.509676887 CRY1 209674_at cryptochrome 1 (photolyase- 0.0004299 0.0907157 0.535929928 like) ZNF367 229551_x_at zinc finger protein 367 0.0004314 0.0907157 0.486850058 MIDN 225954_s_at midnolin 0.0004417 0.0910311 0.29323198 SYNE1 244144_at spectrin repeat containing, 0.000444 0.0910311 0.361183894 nuclear envelope 1 RAB7B 230266_at RAB7B, member RAS 0.0004567 0.0918174 3.803734599 oncogene family ALDH6A1 221589_s_at dehydrogenase 6 0.000472 0.0918174 0.389253885 family, member A1 PTGER3 213933_at prostaglandin E receptor 3 0.0004748 0.0918174 3.346234152 (subtype EP3) EMP1 201324_at epithelial membrane protein 1 0.0004806 0.0918174 0.361602539 AMD1 201197_at adenosylmethionine 0.0004893 0.0918174 0.316920691 decarboxylase 1 TMTC1 226322_at transmembrane and 0.0004906 0.0918174 0.474504028 tetratricopeptide repeat containing 1 NA 1565638_at NA 0.0005101 0.0918174 0.321051611 ZNF295 225539_at zinc finger protein 295 0.0005101 0.0918174 0.475019124 NA 243675_at NA 0.0005209 0.0918174 0.402864264 MXD1 226275_at MAX dimerization protein 1 0.000522 0.0918174 0.531164643 PTPRG 227126_at protein tyrosine phosphatase, 0.0005231 0.0918174 0.327763659 receptor type, G NA 1560342_at NA 0.0005295 0.0918174 0.392583919 NA 241887_at NA 0.0005327 0.0918174 0.517846846 GABARAPL1 208868_s_at GABA(A) receptor-associated 0.000535 0.0918174 0.520891724 protein like 1 ST7OT1 1555912_at ST7 overlapping transcript 1 0.0005407 0.0918174 0.456832852 (non-protein coding) NA 229011_at NA 0.0005416 0.0918174 0.337506182 INSR 226450_at insulin receptor 0.000543 0.0918174 0.537262667 SLC2A14 222088_s_at solute carrier family 2 0.000551 0.0922194 0.344044473 (facilitated glucose transporter), member 14 PCF11 203378_at PCF11, cleavage and 0.0005606 0.0928784 0.540278592 polyadenylation factor subunit, homolog (S. cerevisiae) ACTB AFFX- actin, beta 0.0005763 0.0945247 0.515205989 HSAC07/X00351_3_at CLCN4 214769_at chloride channel 4 0.0006138 0.0996787 0.495142817 NA 229849_at NA 0.0006385 0.1019153 2.449802562 MAOA 204389_at monoamine oxidase A 0.00064 0.1019153 0.332118912 EMP1 213895_at epithelial membrane protein 1 0.0006523 0.102614 0.214787518 MXD1 228846_at MAX dimerization protein 1 0.0006569 0.102614 0.451752829 NA 239808_at NA 0.0006887 0.1057239 0.429132348 FBXO9 1559094_at F-box protein 9 0.0006897 0.1057239 0.567403271 NA 231055_at NA 0.0007064 0.1069709 0.482091806 NA 1562528_at NA 0.0007143 0.1069709 0.422223407 NA 237626_at NA 0.0007174 0.1069709 0.387259583 ZBTB43 204182_s_at zinc finger and BTB domain 0.0007406 0.1094353 0.511311607 containing 43 TMEM22 219569_s_at transmembrane protein 22 0.0007658 0.1117223 0.561813815 NA 226397_s_at NA 0.0007697 0.1117223 0.477127012 CAPN5 226292_at calpain 5 0.0007984 0.1148716 1.90528787 CLIP1 242287_at CAP-GLY domain containing 0.0008426 0.1197063 0.54405106 linker protein 1 PEAR1 228618_at platelet endothelial aggregation 0.0008466 0.1197063 0.528646366 receptor 1 KLF13 225390_s_at Kruppel-like factor 13 0.0008694 0.1202768 0.576807035 INO80D 226555_at INO80 complex subunit D 0.000875 0.1202768 0.596761699 MCL1 214056_at myeloid cell leukemia sequence 0.0008804 0.1202768 0.442458592 1 (BCL2-related) LUC7L2 220099_s_at LUC7-like 2 (S. cerevisiae) 0.0008813 0.1202768 0.611669687 FAM43A 227410_at family with sequence similarity 0.0008873 0.1202768 0.325851727 43, member A ZBTB2 226284_at zinc finger and BTB domain 0.0009011 0.1211462 0.506391663 containing 2 FOSL2 225262_at FOS-like antigen 2 0.0009176 0.1221602 0.314004011 SNW1 215424_s_at SNW domain containing 1 0.0009341 0.1221602 0.602328192 LIFR 205876_at leukemia inhibitory factor 0.000937 0.1221602 0.329094392 receptor alpha NA 244028_at NA 0.0009525 0.1221602 0.538945822 NECAP1 209300_s_at NECAP endocytosis associated 0.0009701 0.1221602 0.694900198 1 COL1A1 202310_s_at collagen, type I, alpha 1 0.0009781 0.1221602 2.552579975 HELQ 228736_at helicase, POLQ-like 0.0009828 0.1221602 0.595516756 NA 239780_at NA 0.000988 0.1221602 0.43331543 PPM1K 235061_at protein phosphatase 1K (PP2C 0.000995 0.1221602 0.422646129 domain containing) THY1 208851_s_at Thy-1 cell surface antigen 0.0009991 0.1221602 2.56719376

Supplemental Table E4: Listing of all differentially expressed genes in IPF vessels compared to Normal vessels (p<0.001, q < 10)

Gene Probe set ID Gene Description Parametric FDR Fold- symbol p-value change SYTL4 227703_s_at synaptotagmin-like 4 6.00E-07 0.01 0.36 NA 235856_at NA 1.10E-06 0.01 5.08 SCRG1 205475_at scrapie responsive protein 1 1.40E-06 0.01 5.19 HNRPDL 1554678_s_at heterogeneous nuclear 2.40E-06 0.01 0.43 ribonucleoprotein D-like ST7OT1 1555912_at ST7 overlapping transcript 1 (non- 2.60E-06 0.01 0.45 protein coding) CTH 217127_at cystathionase (cystathionine 3.80E-06 0.01 0.24 gamma-lyase) ACTB AFFX-HSAC07/X00351_3_at actin, beta 4.50E-06 0.01 0.49 C4A 214428_x_at complement component 4A 5.80E-06 0.01 2.93 (Rodgers blood group) NA 230048_at NA 6.00E-06 0.01 0.3 AASS 210852_s_at aminoadipate-semialdehyde 6.40E-06 0.01 0.42 synthase MAOA 204388_s_at monoamine oxidase A 7.20E-06 0.01 0.34 NA 231055_at NA 1.05E-05 0.01 0.47 EIF1 202021_x_at eukaryotic translation initiation 1.18E-05 0.01 0.48 factor 1 ABI1 209027_s_at abl-interactor 1 1.26E-05 0.01 0.5 LRRC16A 219573_at leucine rich repeat containing 16A 1.26E-05 0.01 0.42 TGFBI 201506_at transforming growth factor, beta- 1.41E-05 0.01 2.41 induced, 68kDa NA 238107_at NA 1.54E-05 0.01 1.93 SULT1B1 207601_at sulfotransferase family, cytosolic, 1.57E-05 0.01 0.47 1B, member 1 MTUS1 212096_s_at mitochondrial tumor suppressor 1 1.58E-05 0.01 0.5 SMOC2 223235_s_at SPARC related modular calcium 1.83E-05 0.01 2.34 binding 2 TNFRSF10D 227345_at tumor necrosis factor receptor 1.84E-05 0.01 0.35 superfamily, member 10d, decoy with truncated death domain ADRA2C 206128_at adrenergic, alpha-2C-, receptor 2.03E-05 0.01 0.42 C4B 208451_s_at complement component 4B (Chido 2.07E-05 0.01 2.71 blood group) PIGA 205281_s_at phosphatidylinositol glycan anchor 2.07E-05 0.01 0.33 biosynthesis, class A GABARAPL1 208869_s_at GABA(A) receptor-associated 2.19E-05 0.01 0.47 protein like 1 NA 226397_s_at NA 2.22E-05 0.01 0.5 EIF1 212227_x_at eukaryotic translation initiation 2.31E-05 0.01 0.47 factor 1 ALDH6A1 221589_s_at 6 family, 2.40E-05 0.01 0.4 member A1 BAG5 230427_s_at BCL2-associated athanogene 5 2.42E-05 0.01 0.34 INSR 213792_s_at insulin receptor 2.91E-05 0.02 0.55 MAOA 204389_at monoamine oxidase A 3.14E-05 0.02 0.36 NA 244447_at NA 3.20E-05 0.02 0.18 STMN3 222557_at -like 3 3.36E-05 0.02 1.78 PTGFRN 224937_at prostaglandin F2 receptor negative 3.50E-05 0.02 2.36 regulator NA 237798_at NA 3.53E-05 0.02 0.56 TIMP3 201148_s_at TIMP metallopeptidase inhibitor 3 3.54E-05 0.02 0.44 KDELR3 204017_at KDEL (Lys-Asp-Glu-Leu) 3.60E-05 0.02 2.53 endoplasmic reticulum protein retention receptor 3 EIF1 212130_x_at eukaryotic translation initiation 3.64E-05 0.02 0.5 factor 1 CCT6B 206587_at chaperonin containing TCP1, 3.77E-05 0.02 0.41 subunit 6B (zeta 2) PIM1 209193_at pim-1 oncogene 4.39E-05 0.02 0.31 NAF1 244828_x_at nuclear assembly factor 1 homolog 4.72E-05 0.02 0.54 (S. cerevisiae) DUSP5 209457_at dual specificity phosphatase 5 4.79E-05 0.02 0.31 ARHGAP26 226576_at Rho GTPase activating protein 26 5.46E-05 0.02 0.34 NA 1556239_a_at NA 5.56E-05 0.02 0.52 NA 237143_at NA 5.84E-05 0.02 0.45 AMD1 201197_at adenosylmethionine decarboxylase 1 6.24E-05 0.02 0.36 CCNL1 1555411_a_at cyclin L1 6.32E-05 0.02 0.39 INSR 226450_at insulin receptor 6.46E-05 0.02 0.49 COL15A1 203477_at collagen, type XV, alpha 1 7.47E-05 0.02 2.52 MAOA 212741_at monoamine oxidase A 7.63E-05 0.02 0.44 CBS 212816_s_at cystathionine-beta-synthase 7.68E-05 0.02 0.4 THY1 208851_s_at Thy-1 cell surface antigen 7.97E-05 0.03 2.79 GPD1L 212510_at glycerol-3-phosphate dehydrogenase 8.34E-05 0.03 0.49 1-like PPIL4 226472_at peptidylprolyl isomerase 8.49E-05 0.03 0.53 (cyclophilin)-like 4 NA 242181_at NA 8.54E-05 0.03 0.4 ARHGAP26 205068_s_at Rho GTPase activating protein 26 8.69E-05 0.03 0.47 ARIH2 238068_at ariadne homolog 2 (Drosophila) 8.87E-05 0.03 0.53 MLLT10 238257_at myeloid/lymphoid or mixed-lineage 8.89E-05 0.03 0.42 leukemia (trithorax homolog, Drosophila); translocated to, 10 NA 232527_at NA 9.47E-05 0.03 0.46 SLC7A8 216092_s_at solute carrier family 7 (cationic 9.48E-05 0.03 0.53 amino acid transporter, y+ system), member 8 SLC25A25 225212_at solute carrier family 25 9.50E-05 0.03 0.41 (mitochondrial carrier; phosphate carrier), member 25 MUT 202959_at methylmalonyl Coenzyme A mutase 9.59E-05 0.03 0.54 EMP1 213895_at epithelial membrane protein 1 9.88E-05 0.03 0.24 KLF6 224606_at Kruppel-like factor 6 9.92E-05 0.03 0.53 IER5 218611_at immediate early response 5 9.99E-05 0.03 0.45 LIFR 205876_at leukemia inhibitory factor receptor 0.0001106 0.03 0.36 alpha SLC2A14 222088_s_at solute carrier family 2 (facilitated 0.0001131 0.03 0.39 glucose transporter), member 14 STAT1 200887_s_at signal transducer and activator of 0.0001192 0.03 1.8 transcription 1, 91kDa GPX8 228141_at glutathione peroxidase 8 (putative) 0.0001192 0.03 1.9 UNC84B 212144_at unc-84 homolog B (C. elegans) 0.0001239 0.03 0.54 RTP4 219684_at receptor (chemosensory) transporter 0.0001259 0.03 2.65 protein 4 LOH3CR2A 220244_at loss of heterozygosity, 3, 0.0001287 0.03 0.34 chromosomal region 2, gene A SFRS2B 238929_at splicing factor, arginine/serine-rich 0.0001332 0.03 0.43 2B S1PR1 239401_at sphingosine-1-phosphate receptor 1 0.000134 0.03 0.45 CCNB1IP1 217988_at cyclin B1 interacting protein 1 0.0001349 0.03 0.57 FBXW11 209455_at F-box and WD repeat domain 0.0001365 0.03 0.58 containing 11 ARG2 203946_s_at arginase, type II 0.000145 0.03 0.4 PPP2R1B 202883_s_at protein phosphatase 2 (formerly 0.0001475 0.03 0.56 2A), regulatory subunit A, beta isoform KIAA0174 226095_s_at KIAA0174 0.0001482 0.03 0.57 TBC1D1 212350_at TBC1 (tre-2/USP6, BUB2, cdc16) 0.0001544 0.03 0.52 domain family, member 1 NA 243675_at NA 0.000155 0.03 0.44 IGFBP3 212143_s_at insulin-like growth factor binding 0.0001555 0.03 0.29 protein 3 STAT1 AFFX- signal transducer and activator of 0.0001588 0.03 1.8 HUMISGF3A/M97935_3_at transcription 1, 91kDa PLAU 205479_s_at plasminogen activator, urokinase 0.0001612 0.03 2.29 ANXA1 233011_at annexin A1 0.0001624 0.03 0.21 PEAR1 228618_at platelet endothelial aggregation 0.0001624 0.03 0.52 receptor 1 KLF10 202393_s_at Kruppel-like factor 10 0.0001628 0.03 0.44 NA 228843_at NA 0.000171 0.03 2.13 NID1 202008_s_at nidogen 1 0.0001752 0.03 0.49 HCRP1 216176_at hepatocellular carcinoma-related 0.0001769 0.03 2.39 HCRP1 PLA2G4C 209785_s_at phospholipase A2, group IVC 0.0001831 0.03 2.23 (cytosolic, calcium-independent) RAB7B 230266_at RAB7B, member RAS oncogene 0.0001866 0.03 3.14 family TPP2 1569856_at tripeptidyl peptidase II 0.0001883 0.03 0.52 ZNF385B 1555801_s_at zinc finger protein 385B 0.000191 0.03 0.43 THY1 213869_x_at Thy-1 cell surface antigen 0.0001963 0.03 3.53 LOC100130744 236228_at hypothetical LOC100130744 0.0001977 0.03 0.48 CIRBP 200811_at cold inducible RNA binding protein 0.0002021 0.03 0.55 AKIRIN2 223144_s_at akirin 2 0.0002021 0.03 0.45 RBBP6 223802_s_at retinoblastoma binding protein 6 0.0002047 0.03 0.49 BTN3A3 204821_at butyrophilin, subfamily 3, member 0.0002063 0.03 1.92 A3 ALDH6A1 221588_x_at aldehyde dehydrogenase 6 family, 0.00021 0.03 0.45 member A1 MAFF 205193_at v- musculoaponeurotic 0.0002104 0.03 0.35 fibrosarcoma oncogene homolog F (avian) PPAPDC1B 223569_at phosphatidic acid phosphatase type 0.000222 0.04 1.87 2 domain containing 1B DDX3X 212515_s_at DEAD (Asp-Glu-Ala-Asp) box 0.0002293 0.04 0.36 polypeptide 3, X-linked LIN52 228583_at lin-52 homolog (C. elegans) 0.0002397 0.04 0.58 ST6GALNAC3 235334_at ST6 (alpha-N-acetyl-neuraminyl- 0.0002401 0.04 0.38 2,3-beta-galactosyl-1,3)-N- acetylgalactosaminide alpha-2,6- sialyltransferase 3 LOC441108 230405_at hypothetical gene supported by 0.0002479 0.04 1.77 AK128882 HIPK2 225368_at homeodomain interacting protein 0.0002484 0.04 0.44 kinase 2 ZBTB17 236127_at zinc finger and BTB domain 0.0002519 0.04 0.51 containing 17 MXRA5 209596_at matrix-remodelling associated 5 0.0002543 0.04 6.21 NA 240347_at NA 0.0002642 0.04 0.34 NA 239123_at NA 0.0002669 0.04 0.43 LNPEP 236728_at leucyl/cystinyl aminopeptidase 0.000269 0.04 0.4 NA 236521_at NA 0.0002717 0.04 2.78 CFH 213800_at complement factor H 0.0002801 0.04 3.61 SULF1 212354_at sulfatase 1 0.0002878 0.04 2.06 NA 242606_at NA 0.0002906 0.04 0.52 ZBTB16 205883_at zinc finger and BTB domain 0.0002941 0.04 0.26 containing 16 YRDC 218647_s_at yrdC domain containing (E. coli) 0.0002968 0.04 0.56 HNRPDL 209067_s_at heterogeneous nuclear 0.0002996 0.04 0.57 ribonucleoprotein D-like SERTAD4 230660_at SERTA domain containing 4 0.0003022 0.04 3.18 ADIPOR2 201346_at adiponectin receptor 2 0.0003054 0.04 0.58 NA 241321_at NA 0.0003154 0.04 0.4 MIDN 225954_s_at midnolin 0.0003176 0.04 0.37 HIPK2 225097_at homeodomain interacting protein 0.0003206 0.04 0.54 kinase 2 BCKDHB 210653_s_at branched chain keto acid 0.0003304 0.04 0.47 dehydrogenase E1, beta polypeptide ALDH6A1 204290_s_at aldehyde dehydrogenase 6 family, 0.0003313 0.04 0.4 member A1 TLE1 203222_s_at transducin-like enhancer of split 1 0.0003314 0.04 0.55 (E(sp1) homolog, Drosophila) LOC100129406 240868_at hypothetical protein LOC100129406 0.0003332 0.04 0.39 NA 221590_s_at NA 0.0003373 0.04 0.5 NA 229506_at NA 0.0003395 0.04 0.52 MSL2 218733_at male-specific lethal 2 homolog 0.0003408 0.04 0.58 (Drosophila) BCR 226602_s_at breakpoint cluster region 0.0003456 0.04 0.57 ZNF385B 229019_at zinc finger protein 385B 0.0003518 0.04 0.39 NA 243509_at NA 0.0003696 0.04 0.37 ARMC8 1555279_at armadillo repeat containing 8 0.0003707 0.04 0.42 ATP2A2 239996_x_at ATPase, Ca++ transporting, cardiac 0.0003739 0.04 1.7 muscle, slow twitch 2 THEM2 204565_at thioesterase superfamily member 2 0.0003778 0.04 1.77 GABARAPL1 208868_s_at GABA(A) receptor-associated 0.0003853 0.05 0.55 protein like 1 KLF15 231015_at Kruppel-like factor 15 0.0003885 0.05 0.48 LOC284837 1563088_a_at hypothetical LOC284837 0.0003934 0.05 1.84 YY1 224718_at YY1 transcription factor 0.0003999 0.05 0.58 FBXW7 218751_s_at F-box and WD repeat domain 0.0004028 0.05 0.56 containing 7 CAPN5 226292_at calpain 5 0.0004053 0.05 1.72 SFRP2 223122_s_at secreted -related protein 2 0.0004054 0.05 9 BTN3A1 209770_at butyrophilin, subfamily 3, member 0.000407 0.05 1.88 A1 NA 233976_at NA 0.0004074 0.05 0.55 RBMS2 225776_at RNA binding motif, single stranded 0.0004119 0.05 0.56 interacting protein 2 LAMP1 201552_at lysosomal-associated membrane 0.0004152 0.05 0.51 protein 1 FBXO9 1559094_at F-box protein 9 0.000418 0.05 0.57 C12orf73 226927_at open reading frame 0.0004197 0.05 1.81 73 ARFGEF2 215931_s_at ADP-ribosylation factor guanine 0.0004227 0.05 0.59 nucleotide-exchange factor 2 (brefeldin A-inhibited) OCA2 206498_at oculocutaneous albinism II 0.0004232 0.05 0.5 FMO3 40665_at flavin containing monooxygenase 3 0.0004325 0.05 3.05 INO80D 226555_at INO80 complex subunit D 0.0004341 0.05 0.57 ARMC8 1555281_x_at armadillo repeat containing 8 0.0004433 0.05 0.43 EMP1 201325_s_at epithelial membrane protein 1 0.0004502 0.05 0.31 DUSP8 206374_at dual specificity phosphatase 8 0.0004513 0.05 0.39 C5 205500_at complement component 5 0.0004613 0.05 0.46 PPM1D 204566_at protein phosphatase 1D magnesium- 0.000472 0.05 0.55 dependent, delta isoform DUSP16 224832_at dual specificity phosphatase 16 0.0004734 0.05 0.54 FMO3 206496_at flavin containing monooxygenase 3 0.0004742 0.05 2.77 ERI2 239648_at exoribonuclease 2 0.0004798 0.05 0.53 TMEM39A 241392_at transmembrane protein 39A 0.0004817 0.05 0.41 LOC100131015 244659_at hypothetical LOC100131015 0.0004863 0.05 0.5 RPS27A 242214_at ribosomal protein S27a 0.0005004 0.05 0.41 LIFR 227771_at leukemia inhibitory factor receptor 0.0005019 0.05 0.51 alpha NA 1556451_at NA 0.0005036 0.05 0.56 CLCN4 214769_at chloride channel 4 0.000506 0.05 0.52 C6orf114 1554486_a_at open reading frame 0.0005066 0.05 0.38 114 TSGA14 225485_at testis specific, 14 0.0005084 0.05 2.44 PLXNA4 228104_at plexin A4 0.0005111 0.05 1.89 RAPGEF6 1555247_a_at Rap guanine nucleotide exchange 0.0005244 0.05 0.5 factor (GEF) 6 CHD1 235791_x_at chromodomain helicase DNA 0.0005338 0.05 0.49 binding protein 1 ADA 216705_s_at adenosine deaminase 0.0005339 0.05 1.67 ZNF542 235121_at zinc finger protein 542 0.0005382 0.05 0.54 LOC100128501 229296_at hypothetical protein LOC100128501 0.0005396 0.05 1.89 NA 237626_at NA 0.0005425 0.05 0.45 ANKRD50 236189_at repeat domain 50 0.0005488 0.05 0.45 MIER3 231975_s_at mesoderm induction early response 0.0005517 0.05 0.53 1, family member 3 IRS2 209184_s_at insulin receptor substrate 2 0.0005537 0.05 0.46 NA 229011_at NA 0.0005564 0.05 0.41 NA 244647_at NA 0.0005606 0.05 0.46 RBM15 228455_at RNA binding motif protein 15 0.0005616 0.05 2.61 ZNF385B 1555800_at zinc finger protein 385B 0.0005652 0.05 0.4 NA 240405_at NA 0.00057 0.05 0.58 PPP1CB 201409_s_at protein phosphatase 1, catalytic 0.0005723 0.05 0.5 subunit, beta isoform GCDH 203500_at glutaryl-Coenzyme A 0.0005775 0.05 0.6 dehydrogenase NA 226345_at NA 0.000581 0.05 0.56 TNRC6C 222820_at trinucleotide repeat containing 6C 0.0005838 0.05 0.49 C1orf124 223511_at chromosome 1 open reading frame 0.0005861 0.05 0.59 124 MKNK2 223199_at MAP kinase interacting 0.0005916 0.05 0.53 serine/threonine kinase 2 HIF3A 219319_at hypoxia inducible factor 3, alpha 0.0006036 0.05 0.34 subunit SLC2A3 202498_s_at solute carrier family 2 (facilitated 0.0006064 0.05 0.49 glucose transporter), member 3 UBD 205890_s_at ubiquitin D 0.0006229 0.05 3.82 UQCC 229672_at ubiquinol-cytochrome c reductase 0.0006398 0.05 1.94 complex chaperone KCNMB4 219287_at potassium large conductance 0.0006496 0.05 0.52 calcium-activated channel, subfamily M, beta member 4 NA 1556216_s_at NA 0.00065 0.05 0.52 NA 239907_at NA 0.0006521 0.05 3.79 GALNT2 217787_s_at UDP-N-acetyl-alpha-D- 0.0006529 0.05 0.56 galactosamine:polypeptide N- acetylgalactosaminyltransferase 2 (GalNAc-T2) SLC35D2 213082_s_at solute carrier family 35, member D2 0.000655 0.05 0.54 IGFBP3 210095_s_at insulin-like growth factor binding 0.0006552 0.05 0.39 protein 3 ZBTB2 226284_at zinc finger and BTB domain 0.0006581 0.05 0.53 containing 2 TMEM87A 212202_s_at transmembrane protein 87A 0.0006594 0.05 0.58 PPM1K 235061_at protein phosphatase 1K (PP2C 0.0006724 0.05 0.38 domain containing) ZHX3 217367_s_at zinc fingers and 3 0.000691 0.05 0.48 SHOC2 202777_at soc-2 suppressor of clear homolog 0.0006926 0.05 0.52 (C. elegans) NA 244787_at NA 0.0007185 0.06 0.32 SULF1 212353_at sulfatase 1 0.0007414 0.06 2.16 AASS 214829_at aminoadipate-semialdehyde 0.0007534 0.06 0.35 synthase NA 232679_at NA 0.0007549 0.06 0.6 CHD2 225077_at chromodomain helicase DNA 0.0007636 0.06 0.55 binding protein 2 FRYL 212546_s_at FRY-like 0.0007703 0.06 0.56 PHLDB2 1557578_at pleckstrin homology-like domain, 0.0007725 0.06 0.42 family B, member 2 TMED5 239283_at transmembrane emp24 protein 0.0007734 0.06 0.47 transport domain containing 5 EARS2 227374_at glutamyl-tRNA synthetase 2, 0.0007744 0.06 1.74 mitochondrial (putative) RARRES3 204070_at responder 0.0007849 0.06 2.1 (tazarotene induced) 3 PIK3CA 235980_at phosphoinositide-3-kinase, catalytic, 0.000807 0.06 0.52 alpha polypeptide C12orf48 224147_at chromosome 12 open reading frame 0.000809 0.06 0.59 48 TBC1D1 1569566_at TBC1 (tre-2/USP6, BUB2, cdc16) 0.0008094 0.06 0.47 domain family, member 1 KCNMB4 222857_s_at potassium large conductance 0.0008154 0.06 0.42 calcium-activated channel, subfamily M, beta member 4 INTS7 218783_at integrator complex subunit 7 0.0008196 0.06 1.97 BTN3A3 204820_s_at butyrophilin, subfamily 3, member 0.0008372 0.06 2.08 A3 XYLT1 213725_x_at xylosyltransferase I 0.0008394 0.06 0.43 NA 228930_at NA 0.0008462 0.06 1.86 RLIM 244470_at ring finger protein, LIM domain 0.0008477 0.06 0.44 interacting ITPR2 202662_s_at inositol 1,4,5-triphosphate receptor, 0.0008513 0.06 0.53 type 2 GLUL 242281_at glutamate-ammonia 0.000871 0.06 0.34 (glutamine synthetase) SYNCRIP 1555427_s_at synaptotagmin binding, cytoplasmic 0.0008827 0.06 0.52 RNA interacting protein TMEM61 230822_at transmembrane protein 61 0.0008838 0.06 1.98 NA 240623_at NA 0.000892 0.06 0.51 ADHFE1 229430_at dehydrogenase, iron 0.0008952 0.06 0.46 containing, 1 ING1 209808_x_at inhibitor of growth family, member 0.0009092 0.06 0.48 1 EMP1 201324_at epithelial membrane protein 1 0.0009159 0.06 0.44 CSDA 201161_s_at cold shock domain protein A 0.0009208 0.06 0.58 ACADL 206069_s_at acyl-Coenzyme A dehydrogenase, 0.000921 0.06 0.28 long chain MYLIP 228097_at myosin regulatory light chain 0.0009286 0.06 0.29 interacting protein NA 244340_x_at NA 0.0009318 0.06 1.77 TMTC1 226322_at transmembrane and tetratricopeptide 0.0009369 0.06 0.53 repeat containing 1 ERG 222079_at v-ets erythroblastosis virus E26 0.0009396 0.06 0.54 oncogene homolog (avian) CTH 206085_s_at cystathionase (cystathionine 0.000947 0.06 0.58 gamma-lyase) CCND1 208711_s_at cyclin D1 0.0009515 0.06 2.14 DIDO1 227335_at death inducer-obliterator 1 0.0009539 0.06 0.51 AGTR2 207294_at angiotensin II receptor, type 2 0.0009539 0.06 0.59 TRIM32 203846_at tripartite motif-containing 32 0.0009562 0.06 1.68 NA 236699_at NA 0.0009562 0.06 0.5 GMPR 204187_at guanosine monophosphate reductase 0.0009624 0.06 0.55 IFRD1 202147_s_at interferon-related developmental 0.0009663 0.06 0.52 regulator 1 KBTBD2 223584_s_at kelch repeat and BTB (POZ) 0.0009679 0.06 0.44 domain containing 2 VAMP3 211749_s_at vesicle-associated membrane protein 0.0009754 0.06 0.56 3 (cellubrevin) NA 1563469_at NA 0.0009797 0.06 0.43 RPS20 216247_at ribosomal protein S20 0.0009815 0.06 0.61 NA 1565638_at NA 0.0009878 0.06 0.38 RPS6KA2 212912_at ribosomal protein S6 kinase, 90kDa, 0.0009893 0.06 0.44 polypeptide 2 NA 231057_at NA 0.0009987 0.06 0.5