1. Introduction of CCSI

CCSI is an integrated database for the collection, interpretation and analysis of chromatin interaction data. It contains 91 sets of chromosomal 3D (three-dimensional) data collected from published literature, UCSC database and NCBI GEO database, resulting in a total of 3,017,962 pairwise interactions. The search engine is the most remarkable feature for information acquisition. All involved data along with analysis pipeline are released for download.

4. Search method

1). Search page


2). Search result


With regard to hidden features, clicking 'plus' button will give details.


Browser page (Browser is fast for mm10, while a bit slow for hg38 owing to its larger genome size.)


5. Download method

1). Part1-1: Interaction pairs with annotation

The source and description about each dataset refer to the right columns. Click the filename, user can download complete interaction datasets with annotation. Take “3c-1” for example,

Part1-2: Interaction pairs without annotation

Similar to part1-1, they are interaction datasets without annotation.

2). Part2: Genome annotation file, enhancer positions and SNPs

Click the filename for download.
Notice: As for SNP information, we provide the website links instead of data owing to its big size.

3). Part3: Analysis pipeline

To run the "pipeline.py", user just need to prepare config file and input files, and "readme" file provides the detailed instruction.