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GRKC Resources


The Gene Regulation Knowledge Commons is defined as  “The collection of freely accessible gene regulation information resources, containing information that is well annotated with unambiguous descriptors according to quality criteria and standards that allow seamless integration and interoperability as well as automated computational access with third-party software” (Kuiper et al., 2022). Albeit still largely incomplete, an overview of available tools and resources is given below.


Author: Saez-Rodriguez. Type: TF-TG

Author: Califano. Type: TF-TG

Author: van Nimwegen. Type: TF-TG

Author: Saez-Rodriguez. Type: TF-TG

Author: Bradley. Type: TF-TG

Author: Saez-Rodriguez. Type: TF-TG

Author: Saez-Rodriguez. Type: TF-TG

Author: Barillot. Type: TF-TG

Author: Van Helden. Type: TF-TG


Author: Brazma. Type: gene expression data

Author: CCLE project. Type: cell line data

Author: The FANTOM project. Type: patient data

Author: Kulakovskiy. Type: transcription factor binding models database

Author: Orchard. Type: Molecular interaction database

Author: Kanehisa Laboratories. Type: database of genes and genomes

Author: Honing. Type: Drosophila melanogaster TF database

Author: The Reactome group. Type: pathway database

Author: Korcsmaros Group. Type: signaling pathway, TF, miRNAs, and regulatory enzymes database

Author: The de Duve Institute. Type: annotated TF-TG database

Author: Lee. Type: transcriptional regulatory networks database

Author: Brazma. Type: gene expression data

Type: tumor data

Author: National Center for Biotechnology Information. Type: gene expression data

Author: The Human Tumor Atlas Network Center. Type: tumor data

Author: Baitaluk. Type: search engine based on the Semantic Web technologies

Author: The Wistar Institute. Type: gene promoters database

Author: Stein Aerts. Type: curated regulatory annotation database

Author:  Halfon lab. Type: Regulatory element database for Drosophila 

Author: Perfetto, Licata. Type: Causal networks database

Author: Kuiper. Type: TF database

Author: Monteiro. Type: Saccharomyces cerevisiae TF database

Author: Kuiper. Type: tfact2gene graph

Author: Saez-Rodriguez. Type: TF-drug in cancer database

Author: Huang. Type: Gene expression database

Author: Lemke. Type: Human TF regulation interaction database

Author: Janky & Hulselmans. Type: TF-target subnetworks

Author: Hermjakob – ELIXIR infrastructure. Type: gene expression data

Author: Portales-Casamar. Type: TF and regulatory sequence database

Author: Santos-Zavaleta, Type: transcriptional regulation in Escherichia coli K-12 database

Author: The Cancer Genome Atlas Program. Type: Cancer genomics datasets and database

Author: Wingender. Type: classification of eukaryotic TF database

Author: Brazma. Type: gene expression data

Author: Laegreid. Type: TF-TG datasets

Author: O’Donovan. Type: GO annotation database

Author: ICGC ARGO DCC Team. Type: Cancer genomics data sets

Author: Mathelier. Type: eukaryotes TF binding profiles

Author: Saez-Rodriguez. Type: database of molecular biology prior knowledge

Author: Bioinformatics Solutions Inc. Type: protein identification database

Author: Ballester. Type: regulatory regions database

Author: Schmeier . Type: transcription co-factors and TF database

Author: Wingender. Type: eukaryotic TF databases

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