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LOGIQA / Long-range Genome Interactions Quality Assessment

A database for hosting quality scores dedicated to long-range chromatin interaction assay. LOGIQA provides a platform for visualizing genome interactions made available by the scientific community. Based on the concept applied by the NGS-QC Generator over ChIP-seq and related datasets, LOGIQA infers quality indicators by the comparison of multiple sequence reads random sampling assays. To facilitate the retrieval of datasets, LOGIQA provides a user-friendly query panel covering items like species, type of experiment (e.g. in situ HiC), use of restriction enzyme for chromatin fragmentation, target molecule for ChIA-PET assays, name of (an) author(s), minimal/ maximal PET counts to be retrieved, as well as a key-word search for the abstract of the corresponding publication(s).

4DGenome

Obsolete
A general repository for chromatin interaction data. Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies. All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

CCSI / Chromatin Chromatin Space Interaction

Obsolete
A database for the collection, interpretation and analysis of chromatin interaction data. CCSI was constructed by integrating and annotating 91 sets of chromatin interaction data derived from published literature, UCSC database and NCBI GEO database, resulting in a total of 3 017 962 pairwise interactions (false discovery rate < 0.05), covering human, mouse and yeast. A web interface has been designed to provide access to the chromatin interactions. The main features of CCSI are (i) showing chromatin interactions and corresponding genes, enhancers and SNPs within the regions in the search page; (ii) offering complete interaction datasets, enhancer and SNP information in the download page; and (iii) providing analysis pipeline for the annotation of interaction data. In conclusion, CCSI will facilitate exploring transcriptional regulatory mechanism in disease pathogenesis associated with spatial interactions among genes, regulatory regions and SNPs.

3CDB / Chromosome Conformation Capture

A database of 3C determined functional chromatin interactions. To construct 3CDB, we searched PubMed and Google Scholar with carefully designed keyword combinations and retrieved more than 5000 articles from which we manually extracted 3319 interactions in 17 species. Moreover, we proposed a systematic evaluation scheme for data reliability and classified the interactions into four categories. Contact frequencies are not directly comparable as a result of various modified 3C protocols employed among laboratories. Our evaluation scheme provides a plausible solution to this long-standing problem in the field. A user-friendly web interface was designed to assist quick searches in 3CDB. We believe that 3CDB will provide fundamental information for experimental design and phylogenetic analysis, as well as bridge the gap between molecular and systems biologists who must now contend with noisy high-throughput data.