Help index


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.


2. Data resource

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3. Framework of construction

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4. Search method

1). Search page

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2). Search result

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

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

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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,
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Part1-2: Interaction pairs without annotation

Similar to part1-1, they are interaction datasets without annotation.
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2). Part2: Genome annotation file, enhancer positions and SNPs

Click the filename for download.
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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.