Human Gene Set: BHATTACHARYA_EMBRYONIC_STEM_CELL


Standard name BHATTACHARYA_EMBRYONIC_STEM_CELL
Systematic name M4282
Brief description The 'stemnes' signature: genes up-regulated and common to 6 human embryonic stem cell lines tested.
Full description or abstract Human embryonic stem (huES) cells have the ability to differentiate into a variety of cell lineages and potentially provide a source of differentiated cells for many therapeutic uses. However, little is known about the mechanism of differentiation of huES cells and factors regulating cell development. We have used high-quality microarrays containing 16 659 seventy-base pair oligonucleotides to examine gene expression in 6 of the 11 available huES cell lines. Expression was compared against pooled RNA from multiple tissues (universal RNA) and genes enriched in huES cells were identified. All 6 cell lines expressed multiple markers of the undifferentiated state and shared significant homology in gene expression (overall similarity coefficient > 0.85).A common subset of 92 genes was identified that included Nanog, GTCM-1, connexin 43 (GJA1), oct-4, and TDGF1 (cripto). Gene expression was confirmed by a variety of techniques including comparison with databases, reverse transcriptase-polymerase chain reaction, focused cDNA microarrays, and immunocytochemistry. Comparison with published stemness genes revealed a limited overlap, suggesting little similarity with other stem cell populations. Several novel ES cell-specific expressed sequence tags were identified and mapped to the human genome. These results represent the first detailed characterization of undifferentiated huES cells and provide a unique set of markers to profile and better understand the biology of huES cells.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 15070671   Authors: Bhattacharya B,Miura T,Brandenberger R,Mejido J,Luo Y,Yang AX,Joshi BH,Ginis I,Thies RS,Amit M,Lyons I,Condie BG,Itskovitz-Eldor J,Rao MS,Puri RK
Exact source Table 2S
Related gene sets (show 1 gene sets from any of these authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Kate Stafford (MSigDB Team)
Source platform or
identifier namespace		 HUMAN_SEQ_ACCESSION
Dataset references  
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 84 genes
Gene families ? Categorize these 84 genes by gene family
Show members (show 92 source identifiers mapped to 84 genes)
Version history 3.0: Renamed from BHATTACHARYA_ESC_UP

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