Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Orchard, Sandra; Kerrien, Samuel; Abbani, Sara; Aranda, Bruno; Bhate, Jignesh; Bidwell, Shelby L.; Bridge, Alan; Briganti, Leonardo; Brinkman, Fiona S. L.; Cesareni, Gianni; Chatr‐aryamontri, Andrew; Chautard, Émilie; Chen, Carol; Dumousseau, Marine; Goll, Johannes; Hancock, Robert E. W.; Hannick, Linda I.; Jurišica, Igor; Khadake, Jyoti; Lynn, David J.; Mahadevan, Usha; Perfetto, Livia; Raghunath, Arathi; Ricard‐Blum, Sylvie; Roechert, Bernd; Salwiński, Łukasz; Stümpflen, Volker; Tyers, Mike; Uetz, Peter; Xenarios, Ioannis; Hermjakob, Henning

doi:10.1038/nmeth.1931

Cited by 496 publications

(414 citation statements)

References 34 publications

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“…This data set was next integrated with protein interaction information from three additional major PPI databases, IntAct, BioGRID and DIP [17][18][19]. These databases are part of the PSIMEx consortium [20] and adopt a common data model and common controlled vocabularies, thus facilitating data integration. Duplicated entries were merged and redundant interactions have been removed.…”

Section: Interaction Tabmentioning

confidence: 99%

HUPHO: the human phosphatase portal

et al. 2012

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Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in the cell. Phosphorylation is a key post-translational modification underlying the regulation of many cellular processes. Thus, a comprehensive picture of phosphatase function and the identification of their target substrates would aid a systematic approach to a mechanistic description of cell signalling. Here we present a website designed to facilitate the retrieval of information about human protein phosphatases. To this end we developed a search engine to recover and integrate information annotated in several publicly available web resources. In addition we present a text-mining-assisted annotation effort aimed at extracting phosphatase related data reported in the scientific literature. The HuPho (human phosphatases) website can be accessed at http://hupho.uniroma2.it.

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Section: Interaction Tabmentioning

confidence: 99%

HUPHO: the human phosphatase portal

et al. 2012

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“…The community standard data formats enable users to download interaction from multiple resources and readily combine these into a single data set. Members of the IMEx Consortium (Orchard et al 2012) have gone further than this, managing curation across multiple separately funded resources to give the user a single, consistently annotated data set and make optimum use of public funds by avoiding repetitive capture of the same papers and reducing parallel database and tool development. Members of the IMEx Consortium have already extended their activities into the capture of protein-small molecule data, and the IntAct database also collates transcription factor/transcribed gene interactions.…”

Section: Introductionmentioning

confidence: 99%

The yeast noncoding RNA interaction network

Panni

Prakash

Bateman

et al. 2017

RNA

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This article describes the creation of the first expert manually curated noncoding RNA interaction networks for S. cerevisiae. The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains. We also see an enrichment of WD40 domains suggesting their direct involvement in ncRNA interactions. We discuss the challenges in collecting noncoding RNA interaction data and the opportunities for worldwide collaboration to fill the unmet need for this data.

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“…The SDMN was generated by query-query protein-protein interaction (QQPPI) [29] and genetic interactions in Pathway Commons database [30] which collects BIND [31], BioGRID [32], CTD [33], DIP [34], HPRD [35], HumanCyc [36], IntAct [37], KEGG [38], NetPath [39], PANTHER [40], PhosphoSitePlus [41], PID [42], Reactome [43], SMPDB [44], TRANSFAC [45], MiRTarBase [46], DrugBank [47], Recon 2 [48], and WikiPathways databases [49] contain 34,661 molecular pathways.…”

Section: Epigenetics and Dna Methylation Proiles In Schizophreniamentioning

confidence: 99%

Transcriptome Analysis of Systems Biology for Schizophrenia

Huang¹,

Tsao²,

Wang³

et al. 2016

Schizophrenia Treatment - The New Facets

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Transcriptome analysis of postmortem brain samples provides more insights to evaluate biological dysfunctions by analysis of diferential expression and genetic interactions in schizophrenia. The growing development of new technologies such as next-generation sequencing (NGS) helps to explore detailed and underlying molecular changes from global perspective of view, not only focus in single SNP variants. It is implicated that schizophrenia genetic and protein interactions may give rise to biological dysfunction not only in dopamine dysfunction but also in immune, energy metabolism, mitochondrial dysfunction and hemostasis. Epigenetic investigation of schizophrenia provides important information on how the environmental factors afect the genetic architecture of the disease. DNA methylation plays a pivotal role in etiology for schizophrenia. The schizophrenia diferential methylation genes and diferential expression genes were analyzed to ind the potential protein complexes related to the etiology of schizophrenia from alteration of DNA methylation. The protein complexes and pathways involved in schizophrenia diferential methylation network may be responsible for the etiology and potential treatment targets. It is implicated that the interaction between diferential expression candidate genes and diferential methylation genes may describe the global view of disease mechanisms and it has important roles in the pathogenesis for schizophrenia.

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Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Cited by 496 publications

References 34 publications

HUPHO: the human phosphatase portal

HUPHO: the human phosphatase portal

The yeast noncoding RNA interaction network

Transcriptome Analysis of Systems Biology for Schizophrenia

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