About 4DGenome
4DGenome is a public database that archives and disseminates chromatin interaction data.
Currently, 4DGenome contains over 8,038,248 interactions curated from both experimental studies (high throughput and individual studies) and computational predictions.
It covers five organisms, Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
The database is continuously updated by a dedicated team of curators.
4DGenome web interface offers search functions for quick queries with your genomic regions or genes of interest. Users can also download records in the database in a number of ways.
4DGenome web interface offers search functions for quick queries with your genomic regions or genes of interest. Users can also download records in the database in a number of ways.
- Search by genomic regions
The genomic coordinates of the region can be inputted in the query box, using the same format as that used in the UCSC genome browser, e.g. chr1:1000-20000. Then choose the organism, cell type and method and submit the query. A specific organism must be selected. For cell type and method the default is all. Up to 10 genomic regions are allowed for each query. - Search by genes
RefSeq gene symbols or Ensembl gene IDs can be used. Wild card is accepted in this query mode. For example, inputting ATF* will search with gene names starting with ATF, e.g. ATF2, ATF3 etc. The search is not case sensitive. The user can specify organism, cell type and method, otherwise the default is all organism/cell/method in this query mode. Up to 10 genes are allowed for each query. - Batch search
Upload a tab-delimited text file. Each row of the file contains a genomic region or a gene of interest. For query by genomic regions, the first three columns of the file (chromosome number, left genomic coordinate, right genomic coordinate) are required. Additional columns are allowed in the file but are not used during the search. For query by genes, the first column of the file (gene symbol or ID) is required. Additional columns are allowed but are not used during the search. Up to 100 genomic regions/genes are allowed in each query file.
File Format of Interaction Records
Records for chromatin interactions are documented in a standardized format. Each record contains 14 tab-delimited columns, which are described below.
- InteractorAChr, InteractorAStart, InteractorAEnd:
Genomic coordinates of the left interacting region. - InteractorBChr, InteractorBStart, InteractorBEnd:
Genomic coordinates of the right interacting region. - Agene, Bgene:
Genes that overlap with the interacting regions. - Organism:
Organism in which the interaction was detected. - Cell/Tissue:
Cell or tissue type in which the interaction was detected. - Detection Method
3C: Chromosome conformation capture
4C: Circularized Chromosome Conformation Capture
5C: Carbon-Copy Chromosome Conformation Capture
Hi-C: Hi-C
ChIA-PET: Chromatin Interaction Analysis by Paired-End Tag Sequencing
Capture-C: Capture-C
IM-PET: Integrated Method for Predicting Enhancer Targets [software] - Confidence Score1
3C: NA
4C,5C,Hi-C,ChIA-PET,IM-PET: p-value or False Discovery Rate (FDR)
Capture-C: confidence interval cutoff - Confidence Score2
Hi-C: result of Fit-Hi-C
Others: as Confidence Score1 if it's available, otherwise set to contact frequency - Contact Frequency
3C,IM-PET: NA
4C,5C,Hi-C,ChIA-PET: Normalized count of sequencing reads
Capture-C: normalized reads density - Pubmed ID
ID of the publication in which the interaction was reported.
Terms and Conditions
Files are published under a Creative Commons Attribution 3.0 License or a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License