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dc.contributor.authorHernández Sánchez, Luis Franciscoen_US
dc.contributor.authorBurger, Bramen_US
dc.contributor.authorHorro Marcos, Carlosen_US
dc.contributor.authorFabregat, Antonioen_US
dc.contributor.authorJohansson, Stefanen_US
dc.contributor.authorNjølstad, Pål Rasmusen_US
dc.contributor.authorBarsnes, Haralden_US
dc.contributor.authorHermjakob, Henningen_US
dc.contributor.authorVaudel, Marcen_US
dc.date.accessioned2020-06-12T13:56:03Z
dc.date.available2020-06-12T13:56:03Z
dc.date.issued2019-07-30
dc.PublishedHernández Sánchez LF, Burger B, Horro Marcos C, Fabregat, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping. GigaScience. 2019;8(8):giz088eng
dc.identifier.issn2047-217X
dc.identifier.urihttps://hdl.handle.net/1956/22570
dc.description.abstractBackground Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists. Findings Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, and pathways. Conclusions PathwayMatcher enables refining the network representation of pathways by including proteoforms defined as protein isoforms with posttranslational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity, and it becomes possible to distinguish interactions between different forms of the same protein.en_US
dc.language.isoengeng
dc.publisherOxford University Presseng
dc.rightsAttribution CC BYeng
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/eng
dc.titlePathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mappingen_US
dc.typePeer reviewed
dc.typeJournal article
dc.date.updated2020-02-05T14:15:27Z
dc.description.versionpublishedVersionen_US
dc.rights.holderCopyright 2019 The Author(s)
dc.identifier.doihttps://doi.org/10.1093/gigascience/giz088
dc.identifier.cristin1723777
dc.source.journalGigaScience
dc.relation.projectBergens forskningsstiftelse: BFS2016REK02
dc.relation.projectNorges forskningsråd: 251235


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