hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

(a) Query all mouse transcription factor data. Here we choose species = mouse_mm8, platform type =ChIPchip_or_ChIPseq, GSE or lab = All, ChIP Type = TF or DNA-binding proteins. We then choose a file in the box titled "Overlap With Regions Below" using the "Browse button. For this example, we choose the file "Sox17_peak_2rep.cod which contains Sox17 binding regions in XEN cells. Next, click the "Query button. Now the Sox17 binding regions will be used as a bait to search the database.
(b) In the query results, all mouse TF ChIP-chip and ChIP-seq experiments are listed. These experiments are rank ordered based on the degree of overlap between their peak lists and the Sox17 binding regions. The "Ranking Statistics column shows the enrichment ratios when comparing the observed overlap to the expected overlap. A p-value is computed for each experiment to test if the observed overlap is significantly different from the expected overlap. P-values are adjusted for multiple testing using the Benjamini-Hochberg procedure. The p-values and adjusted p-values (i.e. FDR) are shown as well. The results show that, other than Sox17 itself, the two TFs that overlap most with Sox17 binding sites are Sox2 and Nanog. From the query results, select samples from the experiments ranked at top 1 (Sox17 in XEN cells), top 4 (Sox2 in mESC), and top 5 (Nanog in mESC). These samples are all generated using the same platform (Affymetrix mouse promoter arrays) and can be meaningfully compared.
(c) Go to the "Retrieve Data from Selected Samples section. Provide genomic coordinates of Sox17 binding regions, but do not provide an email address. Click "Run Note: in general, the bait regions provided for database query in step (a) and the genomic regions provided for data retrieval in step (c) do not necessary need to be the same. Users can use one set of regions as bait to query the database, and retrieve data for another set of regions.
(d) Since no email address is provided, the data will be returned by hmChIP through a web page.
(e) The returned heat map again shows that a significant fraction of Sox17 binding sites in XEN cells are bound by Sox2 and Nanog in mESC.