This track shows putative binding loci of c-Myc and STAT1 as determined by Sequence Tag Analysis of Genomic Enrichment (STAGE). The c-Myc (cellular myelocytomatosis) protein is a transcription factor associated with cell proliferation, differentiation, and neoplastic disease. STAT1 is a signal transducer and transcription factor that binds to IFN-gamma activating sequence.
STAGE was performed in HeLa cells under normal growth conditions (10% Fetal Bovine Serum) with anti-Myc, or in IFN-gamma stimulated cells with anti-STAT1 antibody. Cloned STAGE tags were sequenced and mapped to the human genome as described in Kim et al. (2005), referenced below.
The Tags subtrack shows all STAGE tags within the ENCODE region and thus represents the raw data. The Peaks subtrack shows high confidence c-Myc binding regions derived from the STAGE tags.
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Each tag was assigned a probability of enrichment calculated from the frequency of occurrence of the tag in the STAGE sequencing pool and the number of times the tag is present in the genome, assuming a binomial distribution. Generally, tags that have a low frequency of occurence in the sequencing pool and a high genomic frequency were assigned low probabilities of enrichment.
Peaks were determined by using a 500 bp window to scan across each chromosome. Each window was assigned a probability based on the tags mapped within that window as described in Bhinge et al. referenced below.
For c-Myc, scores generated from the real data were compared to simulations where similar numbers of tags were randomly sampled from the genome. Calculating probabilities as above, a probability cut-off of 0.8 gave a false positive rate of less than 0.05.
For STAT1, scores generated from the real data were compared to simulations where similar numbers of tags were randomly sampled from the genome. Calculating probabilities as described, a probability cut-off of 0.95 gave a false positive rate of less than 0.01. Additionally, 10 STAGE-detected STAT1 binding sites were assayed by qPCR analysis and 9 out 10 were confirmed as true positives, so the false positive rate is estimated at 10%.
These data were contributed by Jonghwan Kim, Akshay Bhinge, and Vishy Iyer from the Iyer lab at the University of Texas at Austin, and by Ghia Euskirchen and Michael Snyder of the Snyder lab at Yale University
Kim, J., Bhinge, A., Morgan, X.C. and Iyer, V.R. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods 2, 47-53 (2005).
Bhinge A. et al. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research (accepted).