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Additional file 1: of Immune oncology, immune responsiveness and the theory of everything

Tolga Turan (5343512)
Deepti Kannan (4677601)
Maulik Patel (5343515)
J. Matthew Barnes (118311)
Sonia Tanlimco (5343506)
Rongze Lu (173266)
Kyle Halliwill (3466961)
Sarah Kongpachith (5343509)
Douglas Kline (5343500)
Wouter Hendrickx (44559)
Alessandra Cesano (104314)
Lisa Butterfield (3455360)
Howard Kaufman (3526127)
Thomas Hudson (735427)
Davide Bedognetti (2632474)
Francesco Marincola (3441314)
Josue Samayoa (5343503)

Publication date

June 2018

DOI

10.6084/m9.figshare.6449102.v1

Abstract

List of individual genes and corresponding models related to immune suppression used for the Theory of Everything (TOE). (TXT 11 kb

Extracted data

Related items

Additional file 1: of Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes

Shouguo Gao (136403)
Nathaniel Wolanyk (3705835)
Ye Chen (241426)
Shuang Jia (21248)
Martin Hessner (261518)
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January 2017

Table S1. Innate & adaptive immunity genes. Table S2. Activated protein complexes. Table S3. GSEA re...

Additional file 3 of Expanding the potential genes of inborn errors of immunity through protein interactions

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August 2021

Additional file 3: Table S3. IEI Candidate Genes with Average in all Immune Cells > 0 TPM Filter

Additional file 6 of Time course study of the response to LPS targeting the pig immune gene networks

Elena Terenina (3459731)
ValĂŠrie Sautron (3459737)
Caroline Ydier (4715796)
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Laure Gress (3459734)
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Laurence Liaubet (90101)
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December 2017

Biological functions enriched by differentially expressed genes in list (List3) (n=30). Categories: ...

Additional file 1: of Widespread parainflammation in human cancer

Dvir Aran (1887838)
Audrey Lasry (3471737)
Adar Zinger (3471734)
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List of 840 inflammatory response genes based on three manually curated databases: inflammatory resp...

Additional file 5: of Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

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Full Table with numbers of transcripts per tissue for all populations and classes. (XLSX 18 kb

Additional file 1: of Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells

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September 2018

Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation o...

Additional file 7 of Expanding the potential genes of inborn errors of immunity through protein interactions

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Additional file 7: Table S7. IEI Candidate Genes with Average in NK Cells > 1 TPM Filter

Additional file 8: of Genes and functions from breast cancer signatures

Shujun Huang (4736610)
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Additional file 1: of Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer

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Additional file 2: of Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

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Oriol Pich (5327108)
Luis Serrano (5871)
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May 2018

This document contains the full list of genes with their respective significance and dN/dS values. (...

Additional file 6: of Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

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Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Matzaraki, Vasiliki
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Wijmenga, Cisca
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April 2017

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb

Additional file 6: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

Patrick Danaher (599741)
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SuFey Ong (6248810)
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Sean Ferree (3563423)

January 2019

Gene set enrichment results. For all KEGG, Reactome, and Biocarta gene sets, the proportion of genes...

Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Zapata, Luis
Pich, Oriol
Serrano, Luis
Kondrashov, Fyodor
Ossowski, Stephan
Schaefer, Martin

January 2018

This document contains the full list of genes with their respective significance and dN/dS values. (...

Additional file 1: of Identification and analysis of divergent immune gene families within the Tasmanian devil genome

Katrina Morris (184432)
Yuanyuan Cheng (159805)
Wesley Warren (225641)
Anthony Papenfuss (3436991)
Katherine Belov (14402)

November 2015

Accession numbers for all data used in this study. Description of data: Table including accession nu...

Additional file 1: of Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes

Shouguo Gao (136403)
Nathaniel Wolanyk (3705835)
Ye Chen (241426)
Shuang Jia (21248)
Martin Hessner (261518)
Xujing Wang (21247)

January 2017

Table S1. Innate & adaptive immunity genes. Table S2. Activated protein complexes. Table S3. GSEA re...

Additional file 3 of Expanding the potential genes of inborn errors of immunity through protein interactions

Humza A. Khan (7889852)
Manish J. Butte (154492)

August 2021

Additional file 3: Table S3. IEI Candidate Genes with Average in all Immune Cells > 0 TPM Filter

Additional file 6 of Time course study of the response to LPS targeting the pig immune gene networks

Elena Terenina (3459731)
ValĂŠrie Sautron (3459737)
Caroline Ydier (4715796)
Darya Bazovkina (4715799)
AmĂŠlie Sevin-Pujol (4715805)
Laure Gress (3459734)
Yannick Lippi (3459740)
Claire Naylies (480828)
Yvon Billon (522346)
Laurence Liaubet (90101)
Pierre Mormede (4715802)
Nathalie Villa-Vialaneix (131484)

December 2017

Biological functions enriched by differentially expressed genes in list (List3) (n=30). Categories: ...

Additional file 1: of Widespread parainflammation in human cancer

Dvir Aran (1887838)
Audrey Lasry (3471737)
Adar Zinger (3471734)
Moshe Biton (648180)
Eli Pikarsky (103960)
Asaf Hellman (1887835)
Atul Butte (2581003)
Yinon Ben-Neriah (131442)

July 2016

List of 840 inflammatory response genes based on three manually curated databases: inflammatory resp...

Additional file 5: of Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

Cemalettin Bekpen (12735)
Chen Xie (114508)
Diethard Tautz (17015)

August 2018

Full Table with numbers of transcripts per tissue for all populations and classes. (XLSX 18 kb

Additional file 1: of Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells

Cherry Leung (5776427)
Kevin Yang (243588)
Xisheng Li (2902387)
Vicken Chan (5776433)
Manching Ku (235604)
Herman Waldmann (369067)
Shohei Hori (5776436)
Jason Tsang (3565154)
Yuk Lo (5776442)
Kathy Lui (5776445)

September 2018

Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation o...

Additional file 7 of Expanding the potential genes of inborn errors of immunity through protein interactions

Humza A. Khan (7889852)
Manish J. Butte (154492)

August 2021

Additional file 7: Table S7. IEI Candidate Genes with Average in NK Cells > 1 TPM Filter

Additional file 8: of Genes and functions from breast cancer signatures

Shujun Huang (4736610)
Leigh Murphy (4736604)
Wayne Xu (139880)

April 2018

Figure S1. Genes and function terms among signatures. A. Common genes discovered in signatures (uppe...

Additional file 1: of Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer

Sriganesh Srihari (3542939)
Jitin Singla (3542936)
Limsoon Wong (54603)
Mark Ragan (3542933)

October 2015

âInferring synthetic lethal interactions from mutual exclusivity of genetic events in cancerâ Ad...

Additional file 2: of Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Luis Zapata (5327111)
Oriol Pich (5327108)
Luis Serrano (5871)
Fyodor Kondrashov (5327114)
Stephan Ossowski (209903)
Martin Schaefer (64096)

May 2018

This document contains the full list of genes with their respective significance and dN/dS values. (...

Additional file 6: of Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

Cemalettin Bekpen (12735)
Chen Xie (114508)
Diethard Tautz (17015)

August 2018

Gains of expression from single tissues in IRA to additional tissues in GER or FRA. The Table includ...

Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Matzaraki, Vasiliki
Magadi Gopalaiah, Vinod Kumar
Wijmenga, Cisca
Zhernakova, Sasha
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Translational Immunology Groningen (TRIGR)

April 2017

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb

Additional file 6: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

Patrick Danaher (599741)
Sarah Warren (5437160)
SuFey Ong (6248810)
Nathan Elliott (306622)
Alessandra Cesano (104314)
Sean Ferree (3563423)

January 2019

Gene set enrichment results. For all KEGG, Reactome, and Biocarta gene sets, the proportion of genes...

Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Zapata, Luis
Pich, Oriol
Serrano, Luis
Kondrashov, Fyodor
Ossowski, Stephan
Schaefer, Martin

January 2018

This document contains the full list of genes with their respective significance and dN/dS values. (...

Additional file 1: of Identification and analysis of divergent immune gene families within the Tasmanian devil genome

Katrina Morris (184432)
Yuanyuan Cheng (159805)
Wesley Warren (225641)
Anthony Papenfuss (3436991)
Katherine Belov (14402)

November 2015

Accession numbers for all data used in this study. Description of data: Table including accession nu...

Additional file 1: of Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes

Shouguo Gao (136403)
Nathaniel Wolanyk (3705835)
Ye Chen (241426)
Shuang Jia (21248)
Martin Hessner (261518)
Xujing Wang (21247)

January 2017

Table S1. Innate & adaptive immunity genes. Table S2. Activated protein complexes. Table S3. GSEA re...

Additional file 3 of Expanding the potential genes of inborn errors of immunity through protein interactions

Humza A. Khan (7889852)
Manish J. Butte (154492)

August 2021

Additional file 3: Table S3. IEI Candidate Genes with Average in all Immune Cells > 0 TPM Filter

Additional file 6 of Time course study of the response to LPS targeting the pig immune gene networks

Elena Terenina (3459731)
ValĂŠrie Sautron (3459737)
Caroline Ydier (4715796)
Darya Bazovkina (4715799)
AmĂŠlie Sevin-Pujol (4715805)
Laure Gress (3459734)
Yannick Lippi (3459740)
Claire Naylies (480828)
Yvon Billon (522346)
Laurence Liaubet (90101)
Pierre Mormede (4715802)
Nathalie Villa-Vialaneix (131484)

December 2017

Biological functions enriched by differentially expressed genes in list (List3) (n=30). Categories: ...