ppiTrim statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ppiTrim

Tool usage distribution map

This map represents all the scientific publications referring to ppiTrim per scientific context
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Associated diseases


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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


No version available


  • person_outline Yi-Kuo Yu

Publication for ppiTrim

ppiTrim citations


iCTNet2: integrating heterogeneous biological interactions to understand complex traits

PMCID: 4706053
PMID: 26834985
DOI: 10.5256/f1000research.7350.r9869

[…] tions (PPI) (n=98,228). PPIs are among the most studied interactions in network biology, although the known interactions may present only one tenth of the entire interactions. PPIs are collected from ppiTrim , which further curates iRefIndex , a master database consolidating interactions from 15 different sources (including BIND, HPRD, etc). miRNA-gene (n=2,457). MicroRNAs (miRNAs) are short RNA s […]


DeCoaD: determining correlations among diseases using protein interaction networks

BMC Res Notes
PMCID: 4467632
PMID: 26047952
DOI: 10.1186/s13104-015-1211-z

[…] on data from the Comparative Toxicogenomics Database (CTD) [], North Carolina State University, Raleigh, NC and Mount Desert Island Biological Laboratory, Salisbury Cove, Maine (http://ctdbase.org/). ppiTrim processes iRefindex [], which incorporates entries from all major protein interaction databases. Our protein–disease network will be periodically updated to reflect changes in the protein–prot […]


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 in a c […]


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

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

[…] 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 of interaction […]


Identification of core T cell network based on immunome interactome

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

[…] stem pathways from the KEGG pathways database [].Experimentally verified and consolidated PPI data for the human immunome proteins was retrieved from the iRefIndex database version 9.0 []. First, the ppiTrim version 1.2.1 [] was used to filter the iRefIndex dataset. This algorithm maps protein interactants to NCBI gene identifiers and removes undesired raw interactions, deflates potentially expand […]


Digenic inheritance in medical genetics

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

[…] change 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 at ftp://ftp.ncbi.nih.gov/pub/qmbpmn/ […]

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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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