GRKC Resources
GENE REGULATION KNOWLEDGE COMMONS 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.
TOOLS
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
DATABASES AND DATASETS
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