Human Gene Set: FERNANDEZ_BOUND_BY_MYC


Standard name FERNANDEZ_BOUND_BY_MYC
Systematic name M3456
Brief description Genes identified by ChIP within the high-affinity group of MYC [GeneID=4609] targets.
Full description or abstract The transcription factor Myc is induced by mitogenic signals and regulates downstream cellular responses. If overexpressed, Myc promotes malignant transformation. Myc modulates expression of diverse genes in experimental systems, but few are proven direct targets. Here, we present a large-scale screen for genomic Myc-binding sites in live human cells. We used bioinformatics to select consensus DNA elements (CACGTG or E-boxes) situated in the 5' regulatory region of genes and measured Myc binding to those sequences in vivo by quantitative chromatin immunoprecipitation. Strikingly, most promoter-associated E-boxes showed selective recovery with Myc, unlike non-E-box promoters or E-boxes in bulk genomic DNA. Promoter E-boxes were distributed in two groups bound by Myc at distinct frequencies. The high-affinity group included an estimated 11% of all cellular loci, was highly conserved among different cells, and was bound independently of Myc expression levels. Overexpressed Myc associated at increased frequency with low-affinity targets and, at extreme levels, also with other sequences, suggesting that some binding was not sequence-specific. The strongest DNA-sequence parameter defining high-affinity targets was the location of E-boxes within CpG islands, correlating with an open, preacetylated state of chromatin. Myc further enhanced histone acetylation, with or without accompanying induction of mRNA expression. Our findings point to a high regulatory and biological diversity among Myc-target genes.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 12695333   Authors: Fernandez PC,Frank SR,Wang L,Schroeder M,Liu S,Greene J,Cocito A,Amati B
Exact source Table 1
Related gene sets (show 60 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Yujin Hoshida (Broad Institute)
Source platform or
identifier namespace		 HUMAN_GENE_SYMBOL
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 181 genes
Gene families ? Categorize these 181 genes by gene family
Show members (show 182 source identifiers mapped to 181 genes)
Version history 3.0: Renamed from FERNANDEZ_MYC_TARGETS

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