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ppiTrim specifications


Unique identifier OMICS_23686
Name ppiTrim
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Yi-Kuo Yu

Publication for ppiTrim

ppiTrim citations


Relating Diseases by Integrating Gene Associations and Information Flow through Protein Interaction Network

PLoS One
PMCID: 4216010
PMID: 25360770
DOI: 10.1371/journal.pone.0110936

[…] to uncover how gene groups associated with different diseases are related to one another in the context of protein-protein interactions, a protein-protein interaction database is needed. we used ppitrim to create such a database. by processing irefindex , which incorporates entries from all major protein interaction databases, ppitrim can produce a protein-protein interaction database […]


Building a Hierarchical Organization of Protein Complexes Out of Protein Association Data

PLoS One
PMCID: 4076247
PMID: 24978199
DOI: 10.1371/journal.pone.0100098

[…] most similar complexes., we obtained the evidences for protein complexes (associations) and protein-protein interactions in yeast (saccharomyces cerevisiae) and human (homo sapiens) by running the ppitrim script (version 1.3) with the irefindex database (candidate for release 10.0, dated nov 23rd 2012) as input (see and ). the ppitrim script outputs evidences for three classes […]


Identification of core T cell network based on immunome interactome

BMC Syst Biol
PMCID: 3937033
PMID: 24528953
DOI: 10.1186/1752-0509-8-17

[…] ppi network was reconstructed for the immunome proteins (see workflow in figure ). ppi data were retrieved from irefindex database (version 9.0) which compiles ppis from the major repositories []. ppitrim (version 1.2.1) was used for general filtering according to stojmirovic et al. []. only experimentally verified and binary ppis were retained. moreover, multiple binary ppis encoded […]


Digenic inheritance in medical genetics

J Med Genet
PMCID: 3778050
PMID: 23785127
DOI: 10.1136/jmedgenet-2013-101713

[…] over time and (2) when the same interaction is included in various sources, the duplicates are not necessarily consolidated. to address these limitations, stojmirović and yu developed a parser ppitrim whose results identify the genes according to their more stable integer identifiers in ncbi's entrez gene database. the ppitrim output files are available […]

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ppiTrim institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
ppiTrim funding source(s)
Supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health.

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