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Symbol Entrez Gene Name Group S

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Table S1, SDC. Common deregulated genes between WS and S (L1 vs. L2) S WS Group S Group WS Symbol Entrez Gene Name (Fold- (Fold- (Probesets) (Probesets) change) change) ATP-binding cassette, sub- ABCA1 203504_s_at -1.4 203505_at -1.3 family A (ABC1), member 1 ATP-binding cassette, sub- ABCC4 family C (CFTR/MRP), 203196_at -1.4 203196_at -1.5 member 4 ATP-binding cassette, sub- ABCD3 202850_at -1.4 202850_at -1.2 family D (ALD), member 3 ADCY1 adenylate cyclase 1 (brain) 213245_at -2.0 213245_at -2.1 ADM adrenomedullin 202912_at 2.4 202912_at 2.0 ADORA3 adenosine A3 receptor 206171_at -1.6 206171_at -1.4 ADRB2 adrenoceptor beta 2, surface 206170_at 2.4 206170_at 2.2 argonaute RISC catalytic AGO1 218287_s_at -1.3 218287_s_at -1.3 component 1 anaphase promoting complex ANAPC5 208722_s_at -1.3 211036_x_at -1.3 subunit 5 apolipoprotein L domain APOLD1 221031_s_at 2.8 221031_s_at 3.2 containing 1 AREG amphiregulin 205239_at 4.7 205239_at 4.7 ADP-ribosylation factor ARFGEF2 guanine nucleotide-exchange 218098_at -1.7 218098_at -1.4 factor 2 (brefeldin A-inhibited) ariadne RBR E3 ubiquitin ARIH1 201878_at 1.4 201878_at 1.3 protein ligase 1 ARL2 ADP-ribosylation factor-like 2 202564_x_at -1.2 202564_x_at -1.3 ADP-ribosylation factor-like ARL4C 202207_at 1.5 202207_at 1.7 4C ARMC8 armadillo repeat containing 8 203486_s_at -1.2 203486_s_at -1.3 ARRB1 arrestin, beta 1 43511_s_at -1.2 221861_at -1.1 ATF3 activating transcription factor 3 202672_s_at 11.9 202672_s_at 10.8 ATXN1 ataxin 1 203232_s_at -1.4 203232_s_at-1.5 AVL9 AVL9 homolog (S. cerevisiase) 212474_at -1.5 212474_at -1.4 BAG3 BCL2-associated athanogene 3 217911_s_at 3.3 217911_s_at 3.0 BCL2A1 BCL2-related protein A1 205681_at 4.5 205681_at 2.9 BCL3 B-cell CLL/lymphoma 3 204908_s_at 2.2 204908_s_at 1.8 basic helix-loop-helix family, BHLHE40 201170_s_at 3.0 201170_s_at 2.9 member e40 baculoviral IAP repeat BIRC3 210538_s_at 7.3 210538_s_at 4.6 containing 3 BMP2 bone morphogenetic protein 2 205290_s_at 2.1 205289_at 2.0 BTG2 BTG family, member 2 201236_s_at 2.5 201235_s_at 1.6 BTG3 BTG family, member 3 205548_s_at 1.9 205548_s_at 1.6 chromosome 14 open reading C14orf132 218820_at -1.6 218820_at -1.7 frame 132 carbamoyl-phosphate synthetase 2, aspartate CAD 202715_at -1.2 202715_at -1.5 transcarbamylase, and dihydroorotase CBX5 chromobox homolog 5 212126_at -1.6 212126_at -1.5 coiled-coil domain containing CCDC121 220321_s_at -1.3 220321_s_at -1.3 121 coiled-coil domain containing CCDC93 209688_s_at -1.5 209688_s_at -1.9 93 chemokine (C-C motif) ligand CCL20 205476_at 10.8 205476_at 5.6 20 chemokine (C-C motif) ligand CCL3 205114_s_at 4.5 205114_s_at 5.2 3 chemokine (C-C motif) ligand CCL4 204103_at 7.5 204103_at 7.2 4 CD160 CD160 molecule 207840_at -1.5 207840_at -1.3 CD55 molecule, decay accelerating factor for CD55 201925_s_at 2.2 201925_s_at 1.5 complement (Cromer blood group) CD59 molecule, complement CD59 212463_at -1.3 212463_at -1.4 regulatory protein CD83 CD83 molecule 204440_at 3.0 204440_at 2.6 cyclin-dependent kinase CDKN1A 202284_s_at 2.7 202284_s_at 2.0 inhibitor 1A (p21, Cip1) CCAAT/enhancer binding CEBPB 212501_at 1.5 212501_at 1.4 protein (C/EBP), beta CCAAT/enhancer binding CEBPD 203973_s_at 2.0 203973_s_at 1.9 protein (C/EBP), delta Cbp/p300-interacting transactivator, with Glu/Asp- CITED2 207980_s_at 2.2 207980_s_at 2.9 rich carboxy-terminal domain, 2 CDC28 protein kinase CKS2 204170_s_at 2.7 204170_s_at 3.1 regulatory subunit 2 chloride channel, voltage- CLCN3 201732_s_at -1.5 201735_s_at -1.5 sensitive 3 calmin (calponin-like, CLMN 213839_at -2.4 213839_at -2.4 transmembrane) CLTC clathrin, heavy chain (Hc) 200614_at -1.5 200614_at -1.4 COPB1 coatomer protein complex, 201359_at -1.4 201359_at -1.3 subunit beta 1 CPD carboxypeptidase D 201941_at -1.3 201941_at -1.3 CUL3 cullin 3 201370_s_at -1.4 201371_s_at-1.4 chemokine (C-X-C motif) CXCL1 ligand 1 (melanoma growth 204470_at 4.6 204470_at 2.9 stimulating activity, alpha) chemokine (C-X-C motif) CXCL3 207850_at 5.0 207850_at 3.6 ligand 3 chemokine (C-X-C motif) CXCL8 202859_x_at 12.2 202859_x_at 7.5 ligand 8 chemokine (C-X-C motif) CXCR4 217028_at 2.4 209201_x_at 1.6 receptor 4 cysteine-rich, angiogenic CYR61 201289_at 3.1 201289_at 3.6 inducer, 61 DCP2 decapping mRNA 2 212919_at -1.7 212919_at -2.0 DEAH (Asp-Glu-Ala-His) box DHX32 218198_at -1.2 218198_at -1.2 polypeptide 32 DnaJ (Hsp40) homolog, DNAJB1 200666_s_at 3.8 200666_s_at 4.3 subfamily B, member 1 DPH5 diphthamide biosynthesis 5 222360_at -1.2 219590_x_at -1.2 DUSP10 dual specificity phosphatase 10 215501_s_at 2.0 215501_s_at 2.6 DUSP2 dual specificity phosphatase 2 204794_at 2.1 204794_at 1.8 DUSP3 dual specificity phosphatase 3 201536_at -1.3 201536_at -1.3 DUSP5 dual specificity phosphatase 5 209457_at 3.4 209457_at 4.0 EGR1 early growth response 1 201693_s_at 3.6 201693_s_at 3.6 EGR2 early growth response 2 205249_at 4.6 205249_at 4.5 eukaryotic translation initiation EIF1 212130_x_at 1.3 212227_x_at 1.3 factor 1 E74-like factor 3 (ets domain ELF3 transcription factor, epithelial- 210827_s_at 2.4 210827_s_at 2.2 specific ) elongation factor RNA ELL 204096_s_at 1.2 204096_s_at 1.2 polymerase II elongation factor, RNA ELL2 214446_at 1.7 214446_at 1.5 polymerase II, 2 v-ets avian erythroblastosis ETS2 201329_s_at 2.3 201329_s_at 2.1 virus E26 oncogene homolog 2 family with sequence similarity FAM172A 212936_at -1.7 212936_at -1.7 172, member A family with sequence similarity FAM178A 203482_at -1.5 203482_at -1.5 178, member A family with sequence similarity FAM46A 221766_s_at 2.6 221766_s_at 1.8 46, member A FAM46C family with sequence similarity 220306_at 1.7 220306_at 1.6 46, member C Fanconi anemia, FANCC 205189_s_at -1.4 205189_s_at -1.4 complementation group C FEM1C fem-1 homolog c (C. elegans) 213341_at 1.6 213341_at 1.8 FBJ murine osteosarcoma viral FOS 209189_at 5.6 209189_at 5.5 oncogene homolog FOSL2 FOS-like antigen 2 218880_at 2.8 218880_at 2.5 FZD4 frizzled class receptor 4 218665_at -1.5 218665_at -1.3 growth arrest and DNA- GADD45A 203725_at 1.9 203725_at 1.7 damage-inducible, alpha growth arrest and DNA- GADD45B 209305_s_at 4.4 209305_s_at 4.5 damage-inducible, beta polypeptide N- GALNT10 acetylgalactosaminyltransferase 212256_at -1.4 207357_s_at -1.2 10 glutamate-cysteine ligase, GCLM 203925_at 1.2 203925_at 1.3 modifier subunit GCN1 general control of GCN1L1 amino-acid synthesis 1-like 1 212139_at -1.5 212139_at -1.5 (yeast) golgi-associated, gamma GGA2 adaptin ear containing, ARF 208914_at -1.4 208914_at -1.3 binding protein 2 GLUL glutamate-ammonia ligase 200648_s_at1.5 200648_s_at1.5 GPR183 G protein-coupled receptor 183 205419_at 3.3 205419_at 2.8 glycosyltransferase-like GTDC1 219770_at -1.2 219770_at -1.2 domain containing 1 granzyme B (granzyme 2, GZMB cytotoxic T-lymphocyte- 210164_at 1.8 210164_at 1.7 associated serine esterase 1) granzyme K (granzyme 3; GZMK 206666_at -1.6 206666_at -1.3 tryptase II) HBA1/HBA2 hemoglobin, alpha 1 217414_x_at 2.4 217414_x_at 2.7 heparin-binding EGF-like HBEGF 203821_at 2.5 203821_at 2.2 growth factor hydroxycarboxylic acid HCAR3 205220_at 3.3 205220_at 2.8 receptor 3 HDAC4 histone deacetylase 4 204225_at -1.3 204225_at -1.7 hypoxia inducible lipid droplet- HILPDA 218507_at 1.6 218507_at 1.4 associated HSPA1A/HSPA1B heat shock 70kDa protein 1A 202581_at 12.6 202581_at 11.4 heat shock 105kDa/110kDa HSPH1 206976_s_at 2.7 208744_x_at 2.4 protein 1 HTT huntingtin 202389_s_at -1.2 202390_s_at-1.2 ICAM1 intercellular adhesion molecule 202638_s_at4.5 202638_s_at3.1 1 IER2 immediate early response 2 202081_at 2.9 202081_at 2.1 IER3 immediate early response 3 201631_s_at 3.5 201631_s_at 2.2 IER5 immediate early response 5 218611_at 2.6 218611_at 2.1 IL1B interleukin 1, beta 39402_at 3.3 39402_at 3.1 interleukin 1 receptor IL1RN 212657_s_at 5.4 212657_s_at 5.0 antagonist IL6 interleukin 6 205207_at 2.8 205207_at 2.0 INHBA inhibin, beta A 210511_s_at 1.5 210511_s_at 1.5 IPO5 importin 5 211954_s_at -1.5 211954_s_at-1.4 inositol-trisphosphate 3-kinase ITPKC 213076_at 1.9 213076_at 1.4 C influenza virus NS1A binding IVNS1ABP 206245_s_at 1.6 206245_s_at 1.8 protein JMJD6 jumonji domain containing 6 212723_at 1.8 212722_s_at 1.6 JUN jun proto-oncogene 201466_s_at 5.4 201466_s_at6.1 JUNB jun B proto-oncogene 201473_at 2.5 201473_at 2.1 JUND jun D proto-oncogene 203752_s_at 2.8 203752_s_at 3.4 potassium voltage-gated KCNE4 channel, Isk-related family, 222379_at 2.1 222379_at 1.6 member 4 KH and NYN domain KHNYN 212356_at -1.4 212356_at -1.6 containing KIAA0100 KIAA0100 201729_s_at -1.8 201728_s_at-1.5 KLF2 Kruppel-like factor 2 219371_s_at 2.3 219371_s_at 2.2 KLF4 Kruppel-like factor 4 (gut) 221841_s_at 3.4 221841_s_at 3.1 KLF6 Kruppel-like factor 6 208961_s_at 4.0 208961_s_at 4.6 KLF9 Kruppel-like factor 9 203542_s_at 1.6 203542_s_at 1.7 KLHDC10 kelch domain containing 10 209256_s_at -1.8 209256_s_at -1.5 Kirsten rat sarcoma viral KRAS 214352_s_at 1.3 214352_s_at 1.3 oncogene homolog lymphocyte cytosolic protein 2 LCP2 (SH2 domain containing 205269_at 1.7 205270_s_at 1.3 leukocyte protein of 76kDa) long intergenic non-protein LINC00341 219563_at -1.9 219563_at -2.1 coding RNA 341 LOC102724428/SIK1 salt-inducible kinase 1 208078_s_at 3.4 208078_s_at 4.2 uncharacterized LOC103344931 213739_at -1.2 213739_at -1.3 LOC103344931 leucine-rich pentatricopeptide LRPPRC 211615_s_at -1.3 211615_s_at -1.3 repeat containing LRRC37A3 (includes leucine rich repeat containing 221740_x_at -1.4 221740_x_at -1.6 others) 37, member A3 MAFF v-maf avian 36711_at 8.0 36711_at 5.0 musculoaponeurotic fibrosarcoma oncogene homolog
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    © 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 128, 3197-3209 doi:10.1242/jcs.165233 RESEARCH ARTICLE The miR-199–dynamin regulatory axis controls receptor-mediated endocytosis Juan F. Aranda1,2, Alberto Canfrán-Duque1,2, Leigh Goedeke1,2, Yajaira Suárez1,2 and Carlos Fernández-Hernando1,2,* ABSTRACT mechanism for the selective uptake of essential nutrients such as Small non-coding RNAs (microRNAs) are important regulators of low-density lipoprotein (LDL), through the LDL receptor (LDLR) gene expression that modulate many physiological processes; (Brown and Goldstein, 1986), or iron, through transferrin receptor however, their role in regulating intracellular transport remains (TfR) (Harding et al., 1983). Thus, factors that affect RME have a largely unknown. Intriguingly, we found that the dynamin (DNM) direct effect on these receptors, and, in the case of LDLR, to regulate genes, a GTPase family of proteins responsible for endocytosis in intracellular cholesterol levels. In both the LDLR and TfR eukaryotic cells, encode the conserved miR-199a and miR-199b internalization processes, clathrin plays a key role during the family of miRNAs within their intronic sequences. Here, we formation of coated vesicles (Moore et al., 1987). Once vesicles are demonstrate that miR-199a and miR-199b regulate endocytic internalized, their passage through a broad endosomal compartment transport by controlling the expression of important mediators of system is required; first they are rapidly transported into early endocytosis such as clathrin heavy chain (CLTC), Rab5A, low- endosomes, where Rab5A is a key regulator (Nielsen et al., 1999), density lipoprotein receptor (LDLR) and caveolin-1 (Cav-1).
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses

    Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses

    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
  • Download Author Version (PDF)

    Download Author Version (PDF)

    Molecular BioSystems Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/molecularbiosystems Page 1 of 29 Molecular BioSystems Mutated Genes and Driver Pathways Involved in Myelodysplastic Syndromes—A Transcriptome Sequencing Based Approach Liang Liu1*, Hongyan Wang1*, Jianguo Wen2*, Chih-En Tseng2,3*, Youli Zu2, Chung-che Chang4§, Xiaobo Zhou1§ 1 Center for Bioinformatics and Systems Biology, Division of Radiologic Sciences, Wake Forest University Baptist Medical Center, Winston-Salem, NC 27157, USA. 2 Department of Pathology, the Methodist Hospital Research Institute,
  • Integrative Genomics Discoveries and Development at the Center for Applied Genomics at CHOP

    Integrative Genomics Discoveries and Development at the Center for Applied Genomics at CHOP

    The Children’s Hospital of Philadelphia Integrative Genomics Discoveries and Development at The Center for Applied Genomics at CHOP Novel Genome-based Therapeutic Approaches Hakon Hakonarson, MD, PhD, Professor of Pediatrics CHOP’s Endowed Chair in Genetic Research Director, Center for Applied Genomics The Children’s Hospital of Philadelphia University of Pennsylvania, School of Medicine Duke Center for Applied Genomics and Precision Medicine 2019 Genomic and Precision Medicine Forum Nov 07, 2019 Genomics in the 21st Century Disclosures Dr. Hakonarson and CHOP own stock in Aevi Genomic Medicine Inc. developing anti-LIGHT therapy for IBD. Dr. Hakonarson is an inventor of technology involving therapeutic development of ADHD, GLA and HCCAA Novel Therapeutic Stem Cell/Gene Editing Approaches § iPS and stem cell therapy shows early promise § Gene therapy for LCA (RPE65) at CHOP via AAV § Targeted T cell therapy for cancer (UPENN/CHOP) § CRISPR-cas9 gene editing § Single cell sequencing The Center for Applied Genomics (CAG) at CHOP u Founded in June 2006 u Staff of 70 u Over 100 active disease projects with CHOP/Penn collaborators u TARGET: Genotype 100,000 children u ~450k GWAS samples >130k kids u IC - participation in future studies >85% u Database u Electronic Health Records u extensive information on each child u >1.2 million visits per year to Population Genomics Research CHOP Recruitment of CHOP/PENN HealthCare Network Patients u High-level of automation ADHD, Autism, Diabetes, IBD, Autoimmunity, Asthma/Atopy, Cancer, RDs - all high priority