MatrixDB

MatrixDB
Content
Description	extracellular matrix interactions database.
Data types; captured	Interactions DataBase, Biochemestry, Biacore, SPR
Organisms	All (Human only possible)
Contact
Laboratory	IBCP - UMR5086 CNRS / Univ Lyon1 - FRANCE
Authors	Emilie Chautard, Guillaume Launay, Nicolas Thierry-Mieg, Romain Salza, Franck Peysselon, Marie Fatoux-Ardore, Sofiane Badaoui, Sylvain Vallet, Lionel Ballut, Dorian Multedo, Sylvie Ricard-Blum.
Primary citation	PMID 20852260
Access
Standards	PSI-MI
Website	http://matrixdb.univ-lyon1.fr

Last updated July 28, 2019

MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides.^[1] MatrixDB takes into account the multimeric nature of the extracellular proteins (for example, collagens, laminins and thrombospondins are multimers). The database was initially released in 2009^[2] and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1.

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.

In cell biology, molecular biology and related fields, the word extracellular means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid. The term is used in contrast to intracellular.

The Université Claude Bernard Lyon 1, is one of the three public universities of Lyon, France. The dominant areas of study covered by the university are science and medicine. The main administrative, teaching and research facilities are located in Villeurbanne. Other campus are the domains of Gerland, Rockefeller and Laennec. Attached to the University are the Hospices civils de Lyon including the "Centre hospitalier Lyon Sud", which is the largest teaching hospital in the Rhône-Alpes region and second largest in France.

MatrixDB is linked with UniGene and the Human Protein Atlas. It also allows users to build customised tissue- and disease-specific interaction networks, which can be further analysed and visualised using Cytoscape or Medusa.^[1]

UniGene is a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that appear to stem from the same transcription locus. Information on protein similarities, gene expression, cDNA clones, and genomic location is included with each entry.

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. The version 18 consists of three separate parts, each focusing on a particular aspect of the genome-wide analysis of the human proteins; the Tissue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Cell Atlas showing the subcellular localization of proteins in single cells, and finally the new Pathology Atlas showing the impact of protein levels for survival of patients with cancer. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it was recently selected by the organization ELIXIR as a European core resource due to its fundamental importance for a wider life science community. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation.

Cytoscape open source software platform for visualizing molecular interaction networks and biological pathways

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript-centric sister project named Cytoscape.js that can be used to analyse and visualise graphs in JavaScript environments, like a browser.

MatrixDB is an active member of the International Molecular Exchange Consortium (IMEx),^[3] a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND),^[4] IntAct,^[5] the Molecular Interaction Database (MINT),^[6] MIPS,^[7] MPact, and BioGRID.^[3] The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the HUPO-PSI-MI XML standard format for annotating and exchanging interaction data.^[3]^[8] MatrixDB includes interaction data extracted from the literature by manual curation and offers access to relevant data involving extracellular proteins provided by IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital. It strives to provide a comprehensive curated resource for all major model organism species while attempting to remove redundancy to create a single mapping of data. Users of The BioGRID can search for their protein or publication of interest and retrieve annotation, as well as curated data as reported, by the primary literature and compiled by in house large-scale curation efforts. The BioGRID is hosted in Toronto, Ontario, Canada and Dallas, Texas, United States and is partnered with the Saccharomyces Genome Database. The BioGRID is funded by the BBSRC, NIH, and CIHR. BioGRID is a member of the International Molecular Exchange Consortium.

The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. The organization was founded in June 2001 and it promotes the development and awareness of proteomics research, advocates on behalf of proteomics researchers throughout the world, and facilitates scientific collaborations between members and initiatives. Ultimately, it is organized to gain a better and more complete understanding of the human proteome.

The Proteomics Standards Initiative (PSI) is a working group of Human Proteome Organization. It aims to define data standards for proteomics in order to facilitate data comparison, exchange and verification.

Related Research Articles

Protein–protein interactions (PPIs) are the physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by electrostatic forces including the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.

In academia, computational immunology is a field of science that encompasses high-throughput genomic and bioinformatics approaches to immunology. The field's main aim is to convert immunological data into computational problems, solve these problems using mathematical and computational approaches and then convert these results into immunologically meaningful interpretations.

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug data with comprehensive drug target information. DrugBank uses a fair bit of content from Wikipedia. Wikipedia also often links to Drugbank.

KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.

Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.

Fiona Brinkman is a Professor in Bioinformatics and Genomics in the Department of Molecular Biology and Biochemistry at Simon Fraser University in British Columbia, Canada, and is a leader in the area of microbial bioinformatics. She is interested in developing "more sustainable, holistic approaches for infectious disease control and conservation of microbiomes".

The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within DIP have been curated, both manually, by expert curators, and automatically, using computational approaches that utilize the knowledge about the protein–protein interaction networks extracted from the most reliable, core subset of the DIP data. The database was initially released in 2002. As of 2014, DIP is curated by the research group of David Eisenberg at UCLA.

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).

The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural models of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. 3did uses the Pfam database to define the position of protein domains in the protein structures. 3did was first published in 2005. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction 3did identifies and groups different binding modes by clustering similar interfaces into “interaction topologies”. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every six months and is available for bulk download and for browsing at http://3did.irbbarcelona.org.

The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada. One of the first dedicated metabolomics databases, the HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.

The Death Domain database is a secondary database of protein-protein interactions (PPI) of the death domain superfamily. Members of this superfamily are key players in apoptosis, inflammation, necrosis, and immune cell signaling pathways. Negative death domain superfamily-mediated signaling events result in various human diseases which include, cancers, neurodegenerative diseases, and immunological disorders. Creating death domain databases are of particular interest to researchers in the biomedical field as it enables a further understanding of the molecular mechanisms involved in death domain interactions while also providing easy access to tools such as an interaction map that illustrates the protein-protein interaction network and information. There is currently only one database that exclusively looks at death domains but there are other databases and resources that have information on this superfamily. According to PubMed, this database has been cited by seven peer-reviewed articles to date because of its extensive and specific information on the death domains and their PPI summaries.

Dehydrogenase/reductase member 7B is an enzyme encoded by the DHRS7B gene in humans, found on chromosome 17p11.2. DHRS7B encodes a protein that is predicted to function in steroid hormone regulation. A deletion in the chromosomal region 17p11.2 has been associated with Smith-Magenis Syndrome, a genetic developmental disorder.

In molecular biology the International Molecular Exchange Consortium (IMEx) is a group of the major public providers of molecular interaction data which collaborate to supply the user with a single, non-redundant set of molecular interactions, captured using a detailed curation model and made available in the PSI-MI standard formats. Participating databases include DIP, IntAct, the Molecular Interaction Database (MINT), MatrixDB, InnateDB, IID, HPIDB, UCL Cardiovascular Gene Annotation, MBInfo, Molecular Connections and UniProt. The group collates the interaction data and prevent duplicate entries in the various databases. The IMEx consortium also supports and contributes to the development of the HUPO-PSI-MI XML format, which is now widely implemented.

SHLD1 or shieldin complex subunit 1 is a gene on chromosome 20. The C20orf196 gene encodes an mRNA that is 1,763 base pairs long, and a protein that is 205 amino acids long.

Cytochrome c oxidase assembly factor 5 is a protein that in humans is encoded by the COA5 gene. This gene encodes an ortholog of yeast Pet191, which in yeast is a subunit of a large oligomeric complex associated with the mitochondrial inner membrane, and required for the assembly of the cytochrome c oxidase complex. Mutations in this gene are associated with mitochondrial complex IV deficiency.

Chromosome 1 open reading frame 198 (C1orf198) is a protein that in humans is encoded by the C1orf198 gene. This particular gene does not have any paralogs in Homo sapiens, but many orthologs have been found throughout the Eukarya domain. C1orf198 has high levels of expression in all tissues throughout the human body, but is most highly expressed in lung, brain, and spinal cord tissues. Its function is most likely involved in lung development and hypoxia-associated events in the mitochondria, which are major consumers of oxygen in cells and are severely affected by decreases in available cellular oxygen.

References

1 2 Chautard, E.; Fatoux-Ardore, M.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (17 September 2010). "MatrixDB, the extracellular matrix interaction database". Nucleic Acids Research. 39 (Database): D235–D240. doi:10.1093/nar/gkq830. PMC 3013758 . PMID 20852260.
↑ Chautard, E.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (15 January 2009). "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions". Bioinformatics. 25 (5): 690–691. doi:10.1093/bioinformatics/btp025. PMC 2647840 . PMID 19147664.
1 2 3 Orchard, S.; Kerrien, S.; Abbani, S.; Aranda, B.; Bhate, J.; Bidwell, S.; Bridge, A.; Briganti, L.; Brinkman, F.; Cesareni, G.; Chatr-Aryamontri, A.; Chautard, E.; Chen, C.; Dumousseau, M.; Goll, J.; Hancock, R.; Hannick, L. I.; Jurisica, I.; Khadake, J.; Lynn, D. J.; Mahadevan, U.; Perfetto, L.; Raghunath, A.; Ricard-Blum, S.; Roechert, B.; Salwinski, L.; Stümpflen, V.; Tyers, M.; Uetz, P.; Xenarios, I. (2012). "Protein interaction data curation: The International Molecular Exchange (IMEx) consortium". Nature Methods. 9 (4): 345–350. doi:10.1038/nmeth.1931. PMC 3703241 . PMID 22453911.
↑ Alfarano, C. (17 December 2004). "The Biomolecular Interaction Network Database and related tools 2005 update". Nucleic Acids Research. 33 (Database issue): D418–D424. doi:10.1093/nar/gki051. PMC 540005 . PMID 15608229.
↑ Kerrien, S.; Aranda, B.; Breuza, L.; Bridge, A.; Broackes-Carter, F.; Chen, C.; Duesbury, M.; Dumousseau, M.; Feuermann, M.; Hinz, U.; Jandrasits, C.; Jimenez, R. C.; Khadake, J.; Mahadevan, U.; Masson, P.; Pedruzzi, I.; Pfeiffenberger, E.; Porras, P.; Raghunath, A.; Roechert, B.; Orchard, S.; Hermjakob, H. (24 November 2011). "The IntAct molecular interaction database in 2012". Nucleic Acids Research. 40 (D1): D841–D846. doi:10.1093/nar/gkr1088. PMC 3245075 . PMID 22121220.
↑ Zanzoni, A; Montecchi-Palazzi, L; Quondam, M; Ausiello, G; Helmer-Citterich, M; Cesareni, G (Feb 20, 2002). "MINT: a Molecular INTeraction database". FEBS Letters. 513 (1): 135–40. doi:10.1016/s0014-5793(01)03293-8. PMC 1751541 . PMID 11911893.
↑ Guldener, U. (1 January 2006). "MPact: the MIPS protein interaction resource on yeast". Nucleic Acids Research. 34 (90001): D436–D441. doi:10.1093/nar/gkj003. PMC 1347366 . PMID 16381906.
↑ Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf. "The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data". Nature Biotechnology. 22 (2): 177–183. doi:10.1038/nbt926. PMID 14755292.

External links

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.

[main-ref-1] 1 2 Chautard, E.; Fatoux-Ardore, M.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (17 September 2010). "MatrixDB, the extracellular matrix interaction database". Nucleic Acids Research. 39 (Database): D235–D240. doi:10.1093/nar/gkq830. PMC 3013758 . PMID 20852260.

[2] Chautard, E.; Ballut, L.; Thierry-Mieg, N.; Ricard-Blum, S. (15 January 2009). "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions". Bioinformatics. 25 (5): 690–691. doi:10.1093/bioinformatics/btp025. PMC 2647840 . PMID 19147664.

[imex-3] 1 2 3 Orchard, S.; Kerrien, S.; Abbani, S.; Aranda, B.; Bhate, J.; Bidwell, S.; Bridge, A.; Briganti, L.; Brinkman, F.; Cesareni, G.; Chatr-Aryamontri, A.; Chautard, E.; Chen, C.; Dumousseau, M.; Goll, J.; Hancock, R.; Hannick, L. I.; Jurisica, I.; Khadake, J.; Lynn, D. J.; Mahadevan, U.; Perfetto, L.; Raghunath, A.; Ricard-Blum, S.; Roechert, B.; Salwinski, L.; Stümpflen, V.; Tyers, M.; Uetz, P.; Xenarios, I. (2012). "Protein interaction data curation: The International Molecular Exchange (IMEx) consortium". Nature Methods. 9 (4): 345–350. doi:10.1038/nmeth.1931. PMC 3703241 . PMID 22453911.

[bind-4] Alfarano, C. (17 December 2004). "The Biomolecular Interaction Network Database and related tools 2005 update". Nucleic Acids Research. 33 (Database issue): D418–D424. doi:10.1093/nar/gki051. PMC 540005 . PMID 15608229.

[intact-5] Kerrien, S.; Aranda, B.; Breuza, L.; Bridge, A.; Broackes-Carter, F.; Chen, C.; Duesbury, M.; Dumousseau, M.; Feuermann, M.; Hinz, U.; Jandrasits, C.; Jimenez, R. C.; Khadake, J.; Mahadevan, U.; Masson, P.; Pedruzzi, I.; Pfeiffenberger, E.; Porras, P.; Raghunath, A.; Roechert, B.; Orchard, S.; Hermjakob, H. (24 November 2011). "The IntAct molecular interaction database in 2012". Nucleic Acids Research. 40 (D1): D841–D846. doi:10.1093/nar/gkr1088. PMC 3245075 . PMID 22121220.

[mint-6] Zanzoni, A; Montecchi-Palazzi, L; Quondam, M; Ausiello, G; Helmer-Citterich, M; Cesareni, G (Feb 20, 2002). "MINT: a Molecular INTeraction database". FEBS Letters. 513 (1): 135–40. doi:10.1016/s0014-5793(01)03293-8. PMC 1751541 . PMID 11911893.

[7] Guldener, U. (1 January 2006). "MPact: the MIPS protein interaction resource on yeast". Nucleic Acids Research. 34 (90001): D436–D441. doi:10.1093/nar/gkj003. PMC 1347366 . PMID 16381906.

[hupo-psi-8] Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf. "The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data". Nature Biotechnology. 22 (2): 177–183. doi:10.1038/nbt926. PMID 14755292.