ppiTrim statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Protein-protein interaction prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

ppiTrim specifications

Information


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

Versioning


Add your version

Maintainer


  • person_outline Yi-Kuo Yu <>

Publication for ppiTrim

ppiTrim in publications

 (4)
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 […]

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 […]

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 […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

ppiTrim reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ppiTrim