The 3D structure of the genome plays a critical role in regulating gene expression. Recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this kind of interaction data.
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).
Collects experimentally validated IncRNA-chromatin interactions. LnChrom includes more than 382000 interaction pairs in up to 260 cell types/tissues in human and mouse. Users can access, for each interaction, to manually-curated metadata, including associated proteins/complexes, chromatin modifying factors and epigenetic modifications and diseases from original publications.
Compiles ChIP-seq, DNase-seq and transposase-accessible chromatin assay (ATAC-seq) information with their related annotations and metadata. TFmapper starts from a user-defined biological sample to highlight trans-acting factors or histone modifications with peaks at a targeted gene or a genomic region. Searches can be made by gene or by position across multiple datasets and the application includes links to visualize peaks.
Gathers a list of long-range chromatin interaction partners of any queried locus. 3DIV allows exploration of long-range chromatin interaction patterns surrounding the target of interest and comparison of multiple samples with synchronized modes. It employs transcriptional start site (TSS) of the corresponding gene as the queried genomic coordinate. This database offers a dynamic browsing system and session manager to save and load the result.
Allows for high resolution analysis of spatial DNA sequence co-occurrence frequencies at the single allele level. Multicontactchromatin is an online resource that assists users in the calculation of the significance of such three-way interactions. It permits statistically distinguishing cooperative from random and competitive interactions, for chosen genomic regions. It also can identify and analyze relevant structures.
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.
Manages Hi-C genomic interaction data. GITAR is a resource that provides two modules to process and visualize Hi-C data, including topologically associating domains (TADs) analysis. The first one, HiCtool, is a Python library that leads the user step-by-step through a pipeline which goes from the source data to the computation, visualization and storage of intra-chromosomal contact maps and topological domain coordinates. The second one is “Processed data”, a large collection of human and mouse datasets.