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Tablet S1. Transcription Factors Induced at Least Two Fold by OHT

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Tablet S1. Transcription factors induced at least two fold by OHT with p<0.01 Probe.Set.ID Gene Symbol Gene Title 207826_s_at ID3 inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 218839_at HEY1 hairy/enhancer-of-split related with YRPW motif 1 203574_at NFIL3 nuclear factor, interleukin 3 regulated 209291_at ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 44783_s_at HEY1 hairy/enhancer-of-split related with YRPW motif 1 220225_at IRX4 iroquois homeobox protein 4 220493_at DMRT1 doublesex and mab-3 related transcription factor 1 204194_at BACH1 BTB and CNC homology 1, basic leucine zipper transcription factor 1 204622_x_at NR4A2 nuclear receptor subfamily 4, group A, member 2 206140_at LHX2 LIM homeobox 2 212696_s_at RNF4 ring finger protein 4 207144_s_at CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 41037_at TEAD4 TEA domain family member 4 36711_at MAFF v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (avian) 216248_s_at NR4A2 nuclear receptor subfamily 4, group A, member 2 204131_s_at FOXO3A forkhead box O3A 204132_s_at FOXO3A forkhead box O3A 50221_at TFEB transcription factor EB 204281_at TEAD4 TEA domain family member 4 31845_at ELF4 E74-like factor 4 (ets domain transcription factor) 221558_s_at LEF1 lymphoid enhancer-binding factor 1 208502_s_at PITX1 paired-like homeodomain transcription factor 1 204249_s_at LMO2 LIM domain only 2 (rhombotin-like 1) 204798_at MYB v-myb myeloblastosis viral oncogene homolog (avian) 210319_x_at MSX2 msh homeobox homolog 2 (Drosophila) 221950_at EMX2 empty spiracles homolog 2 (Drosophila) 203408_s_at SATB1 special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA's) 206915_at NKX2-2 NK2 transcription factor related, locus 2 (Drosophila) 216417_x_at HOXB9 homeobox B9 202692_s_at UBTF upstream binding transcription factor, RNA polymerase I 207978_s_at NR4A3 nuclear receptor subfamily 4, group A, member 3 213150_at HOXA10 homeobox A10 209587_at PITX1 paired-like homeodomain transcription factor 1 210655_s_at FOXO3A forkhead box O3A 208157_at SIM2 single-minded homolog 2 (Drosophila) 204082_at PBX3 pre-B-cell leukemia transcription factor 3 214651_s_at HOXA9 homeobox A9 210649_s_at ARID1A AT rich interactive domain 1A (SWI- like) 213147_at HOXA10 homeobox A10 210016_at MYT1L myelin transcription factor 1-like 203973_s_at CEBPD CCAAT/enhancer binding protein (C/EBP), delta 220392_at EBF2 early B-cell factor 2 206289_at HOXA4 homeobox A4 210162_s_at NFATC1 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 209905_at HOXA9 homeobox A9 205935_at FOXF1 forkhead box F1 203358_s_at EZH2 enhancer of zeste homolog 2 (Drosophila) 218284_at SMAD3 SMAD, mothers against DPP homolog 3 (Drosophila) 209292_at ID4 Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 204621_s_at NR4A2 nuclear receptor subfamily 4, group A, member 2 204039_at CEBPA CCAAT/enhancer binding protein (C/EBP), alpha 219884_at LHX6 LIM homeobox 6 218128_at NFYB nuclear transcription factor Y, beta 215152_at MYB v-myb myeloblastosis viral oncogene homolog (avian) 209454_s_at TEAD3 TEA domain family member 3 202724_s_at FOXO1A forkhead box O1A (rhabdomyosarcoma) 205193_at MAFF v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (avian) 209205_s_at LMO4 LIM domain only 4 205906_at FOXJ1 forkhead box J1 213906_at MYBL1 v-myb myeloblastosis viral oncogene homolog (avian)-like 1 206283_s_at TAL1 T-cell acute lymphocytic leukemia 1 206510_at SIX2 sine oculis homeobox homolog 2 (Drosophila) 219990_at E2F8 E2F transcription factor 8 202449_s_at RXRA retinoid X receptor, alpha 200878_at EPAS1 endothelial PAS domain protein 1 206657_s_at MYOD1 myogenic differentiation 1 206363_at MAF v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) 212689_s_at JMJD1A jumonji domain containing 1A 205932_s_at MSX1 msh homeobox homolog 1 (Drosophila) 208510_s_at PPARG peroxisome proliferative activated receptor, gamma 213920_at CUTL2 cut-like 2 (Drosophila) 202672_s_at ATF3 activating transcription factor 3 210239_at IRX5 iroquois homeobox protein 5 211219_s_at LHX2 LIM homeobox 2 205555_s_at MSX2 msh homeobox homolog 2 (Drosophila) 210170_at PDLIM3 PDZ and LIM domain 3 209959_at NR4A3 nuclear receptor subfamily 4, group A, member 3 209293_x_at ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 218917_s_at ARID1A AT rich interactive domain 1A (SWI- like) 207069_s_at SMAD6 SMAD, mothers against DPP homolog 6 (Drosophila) 206558_at SIM2 single-minded homolog 2 (Drosophila) 207060_at EN2 engrailed homolog 2 210555_s_at NFATC3 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3 206377_at FOXF2 forkhead box F2 212612_at RCOR1 REST corepressor 1 209239_at NFKB1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 210948_s_at LEF1 lymphoid enhancer-binding factor 1 204668_at RNF24 ring finger protein 24 202340_x_at NR4A1 nuclear receptor subfamily 4, group A, member 1 218127_at NFYB nuclear transcription factor Y, beta 206511_s_at SIX2 sine oculis homeobox homolog 2 (Drosophila) 211467_s_at NFIB nuclear factor I/B 209347_s_at MAF v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) 215264_at EMX1 empty spiracles homolog 1 (Drosophila) 206589_at GFI1 growth factor independent 1 221016_s_at TCF7L1 transcription factor 7-like 1 (T-cell specific, HMG-box) /// transcription factor 7-like 1 (T-cell specific, HMG-box) 205817_at SIX1 sine oculis homeobox homolog 1 (Drosophila) 205604_at HOXD9 homeobox D9 214881_s_at UBTF upstream binding transcription factor, RNA polymerase I 204529_s_at TOX thymus high mobility group box protein TOX 213844_at HOXA5 homeobox A5 208216_at DLX4 distal-less homeobox 4 204188_s_at RARG retinoic acid receptor, gamma 206645_s_at NR0B1 nuclear receptor subfamily 0, group B, member 1 209262_s_at NR2F6 nuclear receptor subfamily 2, group F, member 6 218129_s_at NFYB nuclear transcription factor Y, beta 202531_at IRF1 interferon regulatory factor 1 40284_at FOXA2 forkhead box A2 202723_s_at FOXO1A forkhead box O1A (rhabdomyosarcoma) 211771_s_at POU2F2 POU domain, class 2, transcription factor 2 /// POU domain, class 2, transcription factor 2 210818_s_at BACH1 BTB and CNC homology 1, basic leucine zipper transcription factor 1 203490_at ELF4 E74-like factor 4 (ets domain transcription factor) 216925_s_at TAL1 T-cell acute lymphocytic leukemia 1 205259_at NR3C2 nuclear receptor subfamily 3, group C, member 2 209664_x_at NFATC1 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 207725_at POU4F2 POU domain, class 4, transcription factor 2 208978_at CRIP2 cysteine-rich protein 2 218344_s_at RCOR3 REST corepressor 3 206387_at CDX2 caudal type homeobox transcription factor 2 206847_s_at HOXA7 homeobox A7 218850_s_at LIMD1 LIM domains containing 1 210271_at NEUROD2 neurogenic differentiation 2 209261_s_at NR2F6 nuclear receptor subfamily 2, group F, member 6 218881_s_at FOSL2 FOS-like antigen 2 218724_s_at TGIF2 TGFB-induced factor 2 (TALE family homeobox) 208492_at RFXAP regulatory factor X-associated protein 214614_at HLXB9 homeobox HB9 214457_at HOXA2 homeobox A2 214401_at PAX1 paired box gene 1 215006_at EZH2 Enhancer of zeste homolog 2 (Drosophila) 204189_at RARG retinoic acid receptor, gamma 206228_at PAX2 paired box gene 2 205225_at ESR1 estrogen receptor 1 210103_s_at FOXA2 forkhead box A2 209710_at GATA2 GATA binding protein 2 209189_at FOS v-fos FBJ murine osteosarcoma viral oncogene homolog 221866_at TFEB transcription factor EB 205286_at TFAP2C transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) 207260_at FEV FEV (ETS oncogene family) 216161_at SBNO1 Sno, strawberry notch homolog 1 (Drosophila) 208487_at LMX1B LIM homeobox transcription factor 1, beta 217399_s_at FOXO3A forkhead box O3A 210745_at ONECUT1 one cut domain, family member 1 220804_s_at TP73 tumor protein p73 219568_x_at SOX18 SRY (sex determining region Y)-box 18 214326_x_at JUND jun D proto-oncogene 216928_at TAL1 T-cell acute lymphocytic leukemia 1 220480_at HAND2 heart and neural crest derivatives expressed 2 211466_at NFIB nuclear factor I/B 203393_at HES1 hairy and enhancer of split 1, (Drosophila) 204530_s_at TOX thymus high mobility group box protein TOX 210556_at NFATC3 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3 fold by OHT TTEST OHT 113 unique TFs 9.0 3.02267E-12 ARID1A 100.7 3.30322E-11 ATF3 2.7 3.41166E-11 BACH1 27.4 3.42266E-11 CDX2 66.9 1.96087E-10 CEBPA 12.1 2.33272E-10 CEBPD 11.2 4.1045E-10 CITED1 3.7 9.00757E-10 CRIP2 18.1 1.93485E-09 CUTL2 8.1 2.01815E-09 DLX4 2.8 2.20603E-09 DMRT1 23.3 3.27527E-09 E2F8 5.0 3.27765E-09 EBF2 2.3 3.41224E-09 ELF4 27.0 4.6143E-09 EMX1 4.0 5.09799E-09 EMX2 3.2 5.55042E-09 EN2 4.2 7.83035E-09 EPAS1 3.6 1.01405E-08 ESR1 3.3 1.16226E-08 EZH2 5.7 1.20024E-08 FEV 5.1 1.29333E-08 FOS 6.2 1.63506E-08 FOSL2 23.9 1.73649E-08 FOXA2 4.3 2.02575E-08 FOXF1 4.7 2.09327E-08 FOXF2 2.3 2.3856E-08 FOXJ1 2.9 2.47067E-08 FOXO1A 2.7 2.47876E-08 FOXO3A 2.8 2.51846E-08 GATA2 11.4 2.87736E-08 GFI1 4.5 2.95973E-08 HAND2 5.9 3.04831E-08 HES1 2.7 3.05259E-08 HEY1 14.4 3.47266E-08 HLXB9 2.6 3.70825E-08 HOXA10 6.2 4.21138E-08 HOXA2 2.8 4.43601E-08 HOXA4 5.8 4.81339E-08 HOXA5 3.7 4.94957E-08 HOXA7 5.5 5.08813E-08 HOXA9 15.2 5.86654E-08 HOXB9 7.1 5.94509E-08 HOXD9 11.3 7.26726E-08 ID3 6.5 7.80711E-08 ID4 9.4 1.0584E-07 IRF1 3.6 1.12827E-07 IRX4 2.9 1.1679E-07 IRX5 16.3 1.193E-07 JMJD1A 21.0 1.22548E-07 JUND 21.1 1.39176E-07
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    Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press The E–Id protein axis modulates the activities of the PI3K–AKT–mTORC1– Hif1a and c-myc/p19Arf pathways to suppress innate variant TFH cell development, thymocyte expansion, and lymphomagenesis Masaki Miyazaki,1,8 Kazuko Miyazaki,1,8 Shuwen Chen,1 Vivek Chandra,1 Keisuke Wagatsuma,2 Yasutoshi Agata,2 Hans-Reimer Rodewald,3 Rintaro Saito,4 Aaron N. Chang,5 Nissi Varki,6 Hiroshi Kawamoto,7 and Cornelis Murre1 1Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; 2Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan; 3Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany; 4Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA; 5Center for Computational Biology, Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA; 6Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA; 7Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan It is now well established that the E and Id protein axis regulates multiple steps in lymphocyte development. However, it remains unknown how E and Id proteins mechanistically enforce and maintain the naı¨ve T-cell fate. Here we show that Id2 and Id3 suppressed the development and expansion of innate variant follicular helper T (TFH) cells. Innate variant TFH cells required major histocompatibility complex (MHC) class I-like signaling and were associated with germinal center B cells.
  • A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

    A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

    A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Supplementary Information Supplementary Discussion All SARS-CoV-2 protein and gene functions described in the subnetwork appendices, including the text below and the text found in the individual bait subnetworks, are based on the functions of homologous genes from other coronavirus species. These are mainly from SARS-CoV and MERS-CoV, but when available and applicable other related viruses were used to provide insight into function. The SARS-CoV-2 proteins and genes listed here were designed and researched based on the gene alignments provided by Chan et. al. 1 2020 .​ Though we are reasonably sure the genes here are well annotated, we want to note that not every ​ protein has been verified to be expressed or functional during SARS-CoV-2 infections, either in vitro or in vivo. ​ ​ In an effort to be as comprehensive and transparent as possible, we are reporting the sub-networks of these functionally unverified proteins along with the other SARS-CoV-2 proteins. In such cases, we have made notes within the text below, and on the corresponding subnetwork figures, and would advise that more caution be taken when examining these proteins and their molecular interactions. Due to practical limits in our sample preparation and data collection process, we were unable to generate data for proteins corresponding to Nsp3, Orf7b, and Nsp16. Therefore these three genes have been left out of the following literature review of the SARS-CoV-2 proteins and the protein-protein interactions (PPIs) identified in this study.
  • Core Binding Factor Β Is Required for Group 2 Innate Lymphoid Cell Activation

    Core Binding Factor Β Is Required for Group 2 Innate Lymphoid Cell Activation

    Cutting Edge: Core Binding Factor β Is Required for Group 2 Innate Lymphoid Cell Activation This information is current as Xiaofei Shen, Mingwei Liang, Xiangyu Chen, Muhammad of September 24, 2021. Asghar Pasha, Shanti S. D'Souza, Kelsi Hidde, Jennifer Howard, Dil Afroz Sultana, Ivan Ting Hin Fung, Longyun Ye, Jiexue Pan, Gang Liu, James R. Drake, Lisa A. Drake, Jinfang Zhu, Avinash Bhandoola and Qi Yang J Immunol 2019; 202:1669-1673; Prepublished online 6 Downloaded from February 2019; doi: 10.4049/jimmunol.1800852 http://www.jimmunol.org/content/202/6/1669 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2019/02/05/jimmunol.180085 Material 2.DCSupplemental References This article cites 20 articles, 10 of which you can access for free at: http://www.jimmunol.org/content/202/6/1669.full#ref-list-1 Why The JI? Submit online. by guest on September 24, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2019 by The American Association of Immunologists, Inc. All rights reserved.