regulatory_interactions: Regulatory interactions from OmniPath and TRRUST

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This matrix contains a set of human regulatory interactions compiled from two literature-curated resources: OmniPath (directed protein-protein and signaling interactions reported in databases with an appropiate licence) and TRRUST (transcription factor-target interactions). For each interaction, both literature references and primary database references are reported. The users are responsible for respecting the terms of their licences and for citing them when required. This matrix can be edited or updated by the users if required.

Usage

regulatory_interactions

Format

Matrix

Value

Matrix

References

Ceol, A., et al. (2007). DOMINO: a database of domain-peptide interactions. Nucleic Acid Research, 35, D557-60.

Cui, Q., et al. (2007). A map of human cancer signaling. Molecular Systems Biology, 3:152.

Diella, F., et al. (2004). Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics, 22, 5:79.

Dinkel, H., et al. (2012). ELM–the database of eukaryotic linear motifs. Nucleic Acid Research, 40, D242-51.

Han, H., et al. (2015). TRRUST: a reference database of human transcriptional regulatory interactions. Scientific Reports, 15, 11432.

Hornbeck, P.V., et al. (2012). PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acid Research, 40, D261-70.

Korcsmaros, T., et al. (2010). Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics, 26, 2042:2050.

Lynn, D.J., et al. (2008). InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology, 4, 218.

Orchard, S., et al. (2014). The MIntAct project–IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acid Research, 242, D358-63.

Pagel, P., et al. (2005). The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.

Papp, D., et al. (2012). The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. FEBS Letters, 586, 1795-802.

Pawson, A.J., et al. (2014). The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Research, 42, D1098-106.

Peri, S., et al. (2003). Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research, 13, 2363-2371.

Turei, D., et al. (2015). Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. Autophagy, 11, 155-165.

Turei, D., et al. (2016). OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nature methods, 13, 966-967.

Sarkar, D., et al. (2015). LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database(Oxford), pii: bav014.

Shin, Y.C., et al. (2011). TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. Nucleic Acids Research, 39, D356-61.

Snel, B., et al. (2000). STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research, 28, 3442-3444.

Xenarios, I., et al. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research, 30, 303-305.

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.