Download core data of CohesinDB

!! The processed data of each study can be download via Data page

All cohesin binding sites with annotations

751,590 cohesin binding sites identified from ChIP-seq samples in CohesinDB, with annotations of epigenome, 3D genome, transcriptome, and cis-regulatory modules.

Click to download 660 Mb (108 Mb compressed) file in .tsv format: allcohesin.final.tsv.gz

Click to show the description of file header.

  1. Basic-Chrom: Chromosome of cohesin binding sites.
  2. Basic-Start: Start genomic loci of cohesin binding sites (hg38).
  3. Basic-End: End genomic loci of cohesin binding sites (hg38).
  4. Basic-Study: The studies that are used to identify a cohesin site (Encode, 4DN or GEO.)
  5. Basic-CellType: The cell types that are used to identify this cohesin site.
  6. Category-CellSpecificity: A score that measures the cell specificity.
  7. Category-Subunit: The involved cohesin subunits.
  8. Category-CTCF: Whether this cohesin site have overlaps with CTCF.
  9. Category-Location: (Ensembl) Intra: Intragenic; Inter: Intergenic; TSS: transcription start sites; TES: transcription end sites.
  10. 3Dgenome-Boundary: Whether this cohesin site overlaps with TAD boundary.
  11. 3Dgenome-Hub: Whether this cohesin site overlap with chromatin hubs.
  12. 3Dgenome-HiCloop: Whether this cohesin site overlap with Hi-C loops.
  13. 3Dgenome-HiChIPloop: Whether this cohesin site overlap with Hi-ChIP loops.
  14. 3Dgenome-ChIAloop: Whether this cohesin site overlap with ChIA-PET loops.
  15. Cis-Enhancer: Whether this cohesin site overlap with Enhancers (defined in Fantom5 database).
  16. Cis-CobindTF: The possible transcription factors that are located at this cohesin sites. TFs information is from ReMAP2020 database
  17. Cis-TargetGeneName: The candidate cohesin regulated gene names that are evidenced by both "cohesin DEGs" and "cohesin loops".
  18. Cis-TargetGeneID: The candidate cohesin regulated gene IDs that are evidenced by both "cohesin DEGs" and "cohesin loops".
  19. Function-SNP: The SNPs (from GWAS catalog) on this cohesin sites. "." represent no SNPs on this site.
  20. Function-CodeMutation: Number of mutation events that are defined in COSMIC database.
  21. Function-NoncodeMutation: Number of noncoding mutation events that are defined in COSMIC database.
  22. Addition-CTCFmotif: Whether this cohesin site have CTCF motif.
  23. Addition-SuperEnhancer: Whether this cohesin site overlap with Super Enhancers (defined in SEdb database).
  24. Addition-CompartA: Percentage of Hi-C samples shows Compartment A.
  25. Addition-top1HMMname: The name of most overlaped chromatin states (Roadmap ChromHMM project).
  26. Addition-top1HMMper: The percentage of most overlaped chromatin states (Roadmap ChromHMM project).
  27. More information on help page

All cohesin-mediated chromatin loops with annotations

957,868 cohesin-mediated interactions identified from ChIA-PET, Hi-ChIP and Hi-C.

Click to download 101 Mb (19 Mb compressed) file in .tsv format: allloop.final.tsv.gz

Click to show the description of file header.

  1. Chrom1: Chromosome of cohesin loop anchor 1.
  2. Start1: Start genomic loci of cohesin loop anchor 1 (hg38).
  3. End1: End genomic loci of cohesin loop anchor 1 (hg38).
  4. Chrom2: Chromosome of cohesin loop anchor 2.
  5. Start2: Start genomic loci of cohesin loop anchor 2 (hg38).
  6. End2: End genomic loci of cohesin loop anchor 2 (hg38).
  7. Assay: The assay type (Hi-C, Hi-ChIP or ChIA-PET) involved.
  8. Subunit: The cohesin subunits involved.
  9. Celltype: The cell type involved.
  10. Study: The studies that are used to identify a cohesin loop (Encode, 4DN or GEO.)
  11. Looplength: The genomic length of a loop (kb).
  12. More information on help page

All genes annotated by cohesin and CRMs

60,607 genes with the annotations of cohesin and cis-regulatory modules

Click to download 110 Mb (27 Mb compressed) file in .tsv format: allgene.final.tsv.gz

Click to show the description of file header.

  1. ID: Ensembl gene ID.
  2. Symbol: HUGO gene Symbol.
  3. Chrom: Chromosome of the gene.
  4. Start: Start genomic loci of the gene (hg38).
  5. End: End genomic loci of the gene (hg38).
  6. Strand: Strand of the gene, i.e., + or -.
  7. GeneType: Protein coding genes or other genes.
  8. Double-Whether: Whether a gene is regulated by cohesin as evidenced by cohesin loop and cohesin DEG.
  9. Double-RegulatoryCohesin: Regulatory cohesin sites for this gene. "." if the gene is not related to cohesin CRM.
  10. Interaction-Whether: Whether a gene is connected to cohesin sites via chromatin loops.
  11. Interaction-Type: The types of loops (e.g., Hi-C or ChIA-PET). Direct means cohesin sites are located on gene body.
  12. Interaction-Study: The studies involved in the cohesin-loop evidence.
  13. Interaction-Subunit: The cohesin subunits involved in the cohesin-loop evidence.
  14. DEG-Whether: Whether a gene is related to cohesin-DEG evidence.
  15. DEG-NunmerOfStudy: Number of studies have identified this gene as cohesin DEGs.
  16. DEG-Study: The studies involved in the cohesin-DEG evidence.
  17. DEG-Subunit: The cohesin subunits involved in the cohesin-DEG evidence.
  18. Corraltion-Whether: (Deprecated) Whether a gene is co-expressed with cohesin genes.
  19. Correlation-Rho: (Deprecated) Rho of corresion with cohesin genes.
  20. Correlation-FDR: (Deprecated) FDR of corresion with cohesin genes.
  21. Correlation-Subunit: (Deprecated) Cohesin subunits that co-express with a gene.
  22. CelltypeInvolvedLoop: Cell types involed in the cohesin loop evidence.
  23. CelltypeInvolvedDEG: Cell types involed in the cohesin DEG evidence.
  24. More information on help page

All CRMs (cohesin-gene pairs)

2,229,500 double-evidenced cis-regulatory modules (cohesin-gene pairs) annotated with cell types.

Click to download 727 Mb (138 Mb compressed) file in .tsv format: double-evidenced.pair.tsv.gz

Click to show the description of file header.

  1. GeneName: HUGO gene symbol of a gene involved in double evidenced cohesin CRMs.
  2. GeneID: Ensembl gene ID of a gene involved in double evidenced cohesin CRMs.
  3. RegulatorySite: Regulatory cohesin sites in 'chromosome-start-end' style.
  4. CelltypeInvolvedAll: Cell types (combine the following three columns) involved in double evidenced cohesin CRMs.
  5. CelltypeInvolvedCohesin: Cell types involved in the cohesin binding sites.
  6. CelltypeInvolvedLoop: Cell types involved in the cohesin-loop evidence.
  7. CelltypeInvolvedDEG: Cell types involved in the cohesin-DEG evidence.

All cohesin ChIP-seq peaks

776 cohesin related ChIP-seq peak file at bed3 format

Click to download 1.01 Gb (352 MB compressed) file in .bed3 format: : allpeak3col.tar.gz

Click to show the description of file header.

  1. Chrom: Chromosome of the site.
  2. Start: Start genomic loci of the site (hg38).
  3. End: End genomic loci of the site (hg38).