Single nucleotide polymorphisms (SNPs) represent the most common type of sequence variation. SNPs in the coding region are most intensively studied since they are relatively easy interpretable with well-annotated protein-coding sequences of human genome. Some SNPs are the polymorphisms localized to the binding sites of various transcription factors (TFBSs). Such SNPs may alter the regulation of gene transcription and exert a functional effect. iCHIPS integrated the experiment results of ChIP-seq (hmChIP, ENCODE, and ROADMAP Epigenomics), SNP information of populations (1000 Genomes Project), disease association information of GWAS (NHGRI), and gene annotation (ENCODE). Users not only could search the relationship between TFs and target genes, but also could explore the relevant genome variants and diseases. If users have their own genomic data mapping to specific genomic regions, ePIANNO could help to annotate genes and SNPs located in upstream or downstream.
ePIANNO was constructed by combining the ChIP-seq data part and the annotation part. In the ChIP-seq data part, there were 393 ChIP-seq experiments of human including 129 chromatin modification (CM) and 263 transcription factor binding site (TFBS) experiments downloaded from hmChIP database, 489 CM and 1165 TFBS experiments from ENCODE, and 1069 CM experiments from Roadmap Epigenomics Project. We collect the peak data results of those ChIP-seq experiments without any further filtering. Each peak data only contained DNA-binding locations and its specific cellular context. Totally, the database contained potential 253,000,853 DNA binding sites in various cell types or experiments. Genomic variant data from 1000 Genomes Project, GWAS Catalog of NHGRI, and gene annotation of ENCODE were included in the annotation part.
Efficiency of query system is improved.
Rename iCHIPs to ePIANNO.
New Dataset: ENCODE and ROADMAP Epigenomics.
ChipSeq Query System is now officially online.