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Protocols

pathDIP specifications

Information


Unique identifier OMICS_14022
Name pathDIP
Alternative name pathway Data Integration Portal
Restrictions to use None
Database management system Other
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.5.0.0
Maintained Yes

Maintainer


  • person_outline Igor Jurisica

Publication for pathway Data Integration Portal

pathDIP citations

 (4)
library_books

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes

2018
Oncotarget
PMCID: 5823624
PMID: 29507679
DOI: 10.18632/oncotarget.24070

[…] Using Pathway Data Integration Portal v2.5.1.2 (http://ophid.utoronto.ca/pathDIP), we performed comprehensive pathway enrichment analysis across 20 major pathway databases []. We considered literature curat […]

library_books

HABP2 p.G534E variant in patients with family history of thyroid and breast cancer

2017
Oncotarget
PMCID: 5522276
PMID: 28402931
DOI: 10.18632/oncotarget.16639

[…] as visualized in NAViGaTOR v3 [] (http://ophid.utoronto.ca/navigator).To elucidate biological functions of the protein network (Figure ), we performed a comprehensive pathway enrichment analysis. The Pathway Data Integration Portal (pathDIP) was used to perform enrichment analysis across pathways from 20 major pathway databases (pathDIP ver. 2.5; []). We considered literature curated gene: pathway […]

call_split

Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific

2016
PMCID: 4989508
PMID: 27534398
DOI: 10.1186/s13058-016-0739-8
call_split See protocol

[…] nes expressed differentially between BRCA1 mutation carriers and non-carriers by testing for differences in mean gene expression levels with a Benjamini-Hochberg false discovery rate of P < 0.05. The PathDIP database (http://ophid.utoronto.ca/pathDIP) was used to identify over-represented signaling pathways using data from significantly upregulated and downregulated genes through functional enrich […]

library_books

Quantification of angiotensin II regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring

2016
PMCID: 4974759
PMID: 27499720
DOI: 10.1186/s12014-016-9117-x

[…] 3 (http://ophid.utoronto.ca/navigator) (1937718), and the corresponding XML file can be found at: http://www.cs.utoronto.ca/~juris/data/ClinProteom16/.Considering the proteins in the network, we used pathDIP v1.0 (http://ophid.utoronto.ca/pathDIP) to perform pathway enrichment analysis across pathway variants gathered from major public pathways databases. List of 60 most enriched pathways were vis […]

Citations

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pathDIP institution(s)
Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, TMDT, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
pathDIP funding source(s)
This work was supported by the Ontario Research Fund (GL2-01-030), the Canada Research Chair Program (CRC 203373, 225404), the Ontario Research Fund (RE-03-020), the Natural Sciences Research Council (NSERC 203475), the Canada Foundation for Innovation (CFI 12301, 203373, 29272, 225404, 30865), the US Army (DOD W81XWH-1-1-0501) and IBM.

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