GenomicKB

Genomic Knowledgebase (GenomicKB) is a database that uses a knowledge graph to consolidate genomic datasets and annotations. GenomicKB integrates data from more than 30 consortia, in which the genomic entities and relationships are represented as diverse nodes and edges with properties.

Learn more from the original GenomicKB article >>

  • I am interested in type 2 diabetes - find the GWAS variants of diabetes (including sub-types of diabetes), and find all genes that have eQTL relationships with these variants.

    first sample query image

  • I am interested in a tissue (e.g., transverse colon) - find all genes that express in the tissue with an FPKM > 10.

    second sample query image

  • I would like to find all GWAS variants of T2D that are located in enhancers and identify the associated genes of these enhancers.
    I'm curious whether the genes and the variants are connected with a chromatin loop.

    third sample query image

  • Chromatin loops are often formed between two CTCF binding sites, especially when the CTCF orientations are convergent. Among all loops of K562, find how many of them are between convergent CTCF sites.

    forth sample query image
DB dump of GKB database

2.1K+

Active Users

Since Jan.25.2023

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68

Countries

30

Data Dump Downloads

Since Sep.1.2023

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14

Countries

318 Million

Nodes

1.13 Billion

Edges

3.90 Billion

Attributes