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.
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.
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).
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.
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.
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.
A database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions.
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.
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.
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