AlleleDB is a repository, providing genomic annotation of cis-regulatory single nucleotide variants (SNVs) associated with allele-specific binding (ASB) and expression (ASE). We uniformly re-processed and analysed DNA sequences, RNA-seq and ChIP-seq data of 383 individuals from the 1000 Genomes Project: we first construct a personal genome for each individual, then overlap it with the reads from the individual's RNA-seq or ChIP-seq datasets to detect regions of allelic imbalance. Some details can be found at the AlleleSeq
website. For a list of RNA-seq and ChIP-seq data sources, please check 'Documentation
Start with 'Query
'. AlleleDB allows querying by genomic region/gene name/search terms, using the UCSC Genome Browser machinery on the human genome (hg19).
' gives a description of the querying process and the output of AlleleDB. For ASB, we provide the indvidual ID, the transcription factor name and the SNP position (hg19) in BED format. For ASE, we have the individual ID and the SNV position. We also provide the read counts from the RNA-seq and ChIP-seq datasets, and the 'winning' allele for each sample and SNV position.
' allows alternative data mining via individual IDs and TFs. The full dataset and sample information are also provided here for further bioinformatics manipulation.
Please contact J. Chen
(jieming dot chen at yale dot edu) for questions, comments or feedback on AlleleDB.