Human Gene Set: RAO_BOUND_BY_SALL4_ISOFORM_B

For the Mouse gene set with the same name, see RAO_BOUND_BY_SALL4_ISOFORM_B

Standard name RAO_BOUND_BY_SALL4_ISOFORM_B
Systematic name M2520
Brief description Loci bound exclusively by SALL4 [GeneID=57167] isoform b in ES cells (embryonic stem).
Full description or abstract Murine embryonic stem (ES) cells are defined by continuous self-renewal and pluripotency. A diverse repertoire of protein isoforms arising from alternative splicing is expressed in ES cells without defined biological roles. Sall4, a transcription factor essential for pluripotency, exists as two isoforms (Sall4a and Sall4b). Both isoforms can form homodimers and a heterodimer with each other, and each can interact with Nanog. By genomewide location analysis, we determined that Sall4a and Sall4b have overlapping, but not identical binding sites within the ES cell genome. In addition, Sall4b, but not Sall4a, binds preferentially to highly expressed loci in ES cells. Sall4a and Sall4b binding sites are distinguished by both epigenetic marks at target loci and their clustering with binding sites of other pluripotency factors. When ES cells expressing a single isoform of Sall4 are generated, Sall4b alone could maintain the pluripotent state, although it could not completely suppress all differentiation markers. Sall4a and Sall4b collaborate in maintenance of the pluripotent state but play distinct roles. Our work is novel in establishing such isoform-specific differences in ES cells.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 20837710   Authors: Rao S,Zhen S,Roumiantsev S,McDonald LT,Yuan GC,Orkin SH
Exact source Table 1S, 2S: bound by Sall4b but not by Sall4a
Related gene sets (show 2 additional gene sets from the source publication)

(show 10 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Arthur Liberzon (MSigDB Team)
Source platform or
identifier namespace
Mouse_RefSeq
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 526 genes
Gene families ? Categorize these 526 genes by gene family
Show members (show 568 source identifiers mapped to 526 genes)
Version history 3.1: First introduced

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