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hmChIP was created by the Johns Hopkins School of Public Health Department of Biostatistics.
Software Copyright (c) The Johns Hopkins School of Public Health Department of Biostatistics All rights reserved.
Query Samples
Species PlatformType GSE or Lab ChIP Type
SortResultsBy Protein Name Cell or Tissue Type Overlap With Regions Below
Retrieve Data from Selected Samples
Parameter Upload Region Email

Introduction to hmChIP

 

Motivation
hmChIP is a database of genome-wide chromatin immu-noprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions.

Analysis Procedure
1. Query available experiments and samples
1.1 Choose "species", "platform type", "GSE or Lab" and "ChIP type".
1.2 Provide protein names (e.g., Sox17) and cell or tissue types (e.g., stem cell). If no key words are provided, all experiments in the database will be returned.
1.3 (Optional) In the box titled "Overlap With Regions Below", provide a list of query genomic regions as a bait. The regions should be stored in a COD file (e.g., Sox17_peak_2rep.cod) or a BED file (e.g., UTA_cMyc_Combined.bed). Use the "Browse" button to choose the file. If a list of query genomic regions is provided, the returned experiments will be rank ordered based on the degree of overlap with the query genomic regions.
1.4 Click the "Query" button. Experiments matching the search criteria will be returned.


2. Retrieve data
2.1 From the query results, check all samples you want to study.
2.2 Go to the section titled "Retrieve Data from Selected Samples". Provide a list of genomic regions for which you want to retrieve data. The regions should be stored in a COD file (e.g., Sox17_peak_2rep.cod) or a BED file (e.g., UTA_cMyc_Combined.bed). Choose this file using the "Browse" button next to the box titled "Upload Region".
2.3 Provide an email address. If no email address is provided, results will be returned on a webpage.
2.4 Click "Run". Data for input genomic regions will be retrieved from the selected samples.
Note: If the number of your input regions is more than 3000 lines or the number of selected samples is more than 60, we will not return the PDF file with the heat map, since the clustering may take significant amount of computational resource and may affect other users/jobs. We recommend you to do your own clustering using dChip.

How to interpret analysis results is explained in user manual.

If you encountered bugs, or if you want us to add new data sets you wish to use, please contact:
Li Chen lichen1@jhsph.edu
Hongkai Ji hji@jhsph.edu

[Citation]
Li Chen, George Wu, and Hongkai Ji (2011) hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. Bioinformatics, doi: 10.1093/bioinformatics/btr156

ArrayType

Mouse_mm8ChIPchip_AffyPromoterGPL5811[Mm_PromPR] Affymetrix Mouse_mm8 Promoter 1.0R Array
Mouse_mm8ChIPchip_AffyGenomeGPL6444[Mm35b_P01R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 1
GPL6445[Mm35b_P02R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 2
GPL6446[Mm35b_P03R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 3
GPL6447[Mm35b_P04R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 4
GPL6448[Mm35b_P05R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 5
GPL6449[Mm35b_P06R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 6
GPL6450[Mm35b_P07R] Affymetrix Mouse_mm8 Tiling 2.0R Set, Array 7
Mouse_mm8ChIPseqGPL9185Illumina Genome Analyzer(Mus musculus)
GPL9250Illumina Genome Analyzer II (Mus musculus)
Human_hg18ChIPchip_AffyPromoterGPL5082[Hs_PromPR] Affymetrix Human_hg18 Promoter 1.0R Array
Human_hg18ChIPchip_AffyGenomeGPL4910[Hs35b_P01R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 1
GPL4911[Hs35b_P02R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 2
GPL4912[Hs35b_P03R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 3
GPL4913[Hs35b_P04R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 4
GPL4914[Hs35b_P05R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 5
GPL4915[Hs35b_P06R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 6
GPL4916[Hs35b_P07R] Affymetrix Human_hg18 Tiling 2.0R Set, Array 7
Human_hg18ChIPseqGPL9052Illumina Genome Analyzer(Homo sapiens)
GPL9115Illumina Genome Analyzer II (Homo sapiens)