List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was CD4:CD8 lymphocyte ratio. The EFO term CD4:CD8 lymphocyte ratio was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
MA Ferreira, M Mangino, CJ Brumme, ZZ Zhao, SE Medland, MJ Wright, DR Nyholt, S Gordon, M Campbell, BP McEvoy, A Henders, DM Evans, JS Lanchbury, F Pereyra, BD Walker, DW Haas, N Soranzo, TD Spector, PI de Bakker, IH Frazer, GW Montgomery, NG Martin
55-kDa antigens found on HELPER-INDUCER T-LYMPHOCYTES and on a variety of other immune cell types. CD4 antigens are members of the immunoglobulin supergene family and are implicated as associative recognition elements in MAJOR HISTOCOMPATIBILITY COMPLEX class II-restricted immune responses. On T-lymphocytes they define the helper/inducer subset. CD4 antigens also serve as INTERLEUKIN-15 receptors and bind to the HIV receptors, binding directly to the HIV ENVELOPE PROTEIN GP120.
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Genes that are suppressed by THC in CD4 cells in C57BL/6J mice. Gene expression was evaluated via RNA-seq. Values presented are "1" for effect presence. Data taken from Supplemental Data 1.
Authors:
Xiaoming Yang, Marpe Bam, Prakash S Nagarkatti, Mitzi Nagarkatti
Genes that are induced by THC in CD4 cells in C57BL/6J mice. Gene expression was evaluated via RNA-seq. Values presented are "1" for effect presence. Data taken from Supplemental Data 1.
Authors:
Xiaoming Yang, Marpe Bam, Prakash S Nagarkatti, Mitzi Nagarkatti
Genes that are suppressed by THC in both CD4+ cells and total lymph node (LN) cells in C57BL/6J mice. Gene expression was evaluated via RNA-seq. Values presented are "1" for effect presence. Data taken from Supplemental Data 1.
Authors:
Xiaoming Yang, Marpe Bam, Prakash S Nagarkatti, Mitzi Nagarkatti
Genes that are induced by THC in both CD4+ cells and total lymph node (LN) cells in C57BL/6J mice. Gene expression was evaluated via RNA-seq. Values presented are "1" for effect presence. Data taken from Supplemental Data 1.
Authors:
Xiaoming Yang, Marpe Bam, Prakash S Nagarkatti, Mitzi Nagarkatti
"lack of the set of single-positive T cells that express CD4 on their surface" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
abnormal CD4-positive, alpha-beta T cell physiology (MP)
Description:
"any functional anomaly of the subset of T lymphocytes that carry the CD4 marker, recognize intravesicular peptides bound to MHC class-II molecules, and turn on antibody production" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
abnormal CD4-positive, alpha beta T cell morphology (MP)
Description:
"any structural anomaly of the subset of T lymphocytes that carry the CD4 marker, recognize intravesicular peptides bound to MHC class-II molecules, and turn on antibody production" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
abnormal CD4-positive, alpha beta T cell number (MP)
Description:
"anomaly in the number of the subset of T lymphocytes that carry the CD4 marker, recognize intravesicular peptides bound to MHC class-II molecules, and turn on antibody production" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
increased CD4-positive, alpha beta T cell number (MP)
Description:
"greater number of the subset of T lymphocytes that carry the CD4 marker, recognize intravesicular peptides bound to MHC class-II molecules, and turn on antibody production" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
decreased CD4-positive, alpha beta T cell number (MP)
Description:
"reduced number of the subset of T lymphocytes that carry the CD4 marker, recognize intravesicular peptides bound to MHC class-II molecules, and turn on antibody production" Data derived from MGI_GenePheno.rpt and the MP OBO tree dated 2016-11-07
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "TCR signaling in nave CD4+ T cells" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is pid.
gene2pc v. 0.1.0
Last updated 2015.08.31
A critical subpopulation of T-lymphocytes involved in the induction of most immunological functions. The HIV virus has selective tropism for the T4 cell which expresses the CD4 phenotypic marker, a receptor for HIV. In fact, the key element in the profound immunosuppression seen in HIV infection is the depletion of this subset of T-lymphocytes.
Generated by gene2mesh v. 1.1.1
QTL associated with T cell ratio modifier QTL 1. This interval was obtained by using a fixed interval width of 25 Mbp around the peak marker (146377508)
Authors:
Myrick C, DiGuisto R, DeWolfe J, Bowen E, Kappler J, Marrack P, Wakeland EK
Real-time RT-PCR measurements of gene expression were carried out with a set of 14 genes (Table 1) on three separate T-cell cultures. Polarized (day 14 cells) CD4+ Th1 or Th2 cells were triggered with antibodies for CD3 and CD28 for 2, 6 or 24 hours and gene expression was quantitated (Figure ​(Figure3).3Figure 3). During the time course of activation a general trend of downregulation of transcription was observed in the genes studied. The expression of a housekeeping gene, however, was unaffect
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment", which is defined as "The process in which a CD4-positive, alpha-beta T cell becomes committed to becoming a CD4-positive, CD25-positive, alpha-beta regulatory T cell." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response", which is defined as "The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of a CD4-positive, CD25-positive, alpha-beta regulatory T cell as part of an immune response." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment", which is defined as "The process in which a CD4-positive, alpha-beta T cell becomes committed to becoming a CD4-positive, CD25-positive, alpha-beta regulatory T cell." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.12.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "negative regulation of CD4 biosynthetic process", which is defined as "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "regulation of CD4 biosynthetic process", which is defined as "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CD4 biosynthetic process", which is defined as "The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CD4-positive, alpha-beta T cell lineage commitment", which is defined as "The process in which an immature T cell becomes committed to becoming a CD4-positive, alpha-beta T cell." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response", which is defined as "Any process that activates or increases the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response", which is defined as "Any process that modulates the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
GeneWeaver