Human Gene Set: GSE40685_NAIVE_CD4_TCELL_VS_FOXP3_KO_TREG_PRECURSOR_DN


Standard name GSE40685_NAIVE_CD4_TCELL_VS_FOXP3_KO_TREG_PRECURSOR_DN
Systematic name M9309
Brief description Genes down-regulated in CD4: naïve versus FOXP3 [GeneID=50943] knockout T reg precursors.
Full description or abstract Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis. It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape. Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to pre-accessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers inaccessible in Foxp3- CD4+ cells became accessible upon T cell receptor activation prior to Foxp3 expression with only a small subset associated with several functionally important genes being exclusively Treg cell-specific. Thus, in a late cellular differentiation process Foxp3 defines Treg cell functionality in an ?opportunistic? manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.
Collection C7: Immunologic Signature
      IMMUNESIGDB: ImmuneSigDB
Source publication Pubmed 23021222   Authors: Samstein RM,Arvey A,Josefowicz SZ,Peng X,Reynolds A,Sandstrom R,Neph S,Sabo P,Kim JM,Liao W,Li MO,Leslie C,Stamatoyannopoulos JA,Rudensky AY
Exact source GSE40685_2258_200_DN
Related gene sets (show 5 additional gene sets from the source publication)

(show 49 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Jernej Godec (Dana-Farber Cancer Institute)
Source platform or
identifier namespace
HUMAN_GENE_SYMBOL
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 195 genes
Gene families ? Categorize these 195 genes by gene family
Show members (show 200 source identifiers mapped to 195 genes)
Version history 7.3: Moved to ImmuneSigDB sub-collection.

See MSigDB license terms here. Please note that certain gene sets have special access terms.