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MetaPath specifications

Information


Unique identifier OMICS_02624
Name MetaPath
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mihai Pop

Publication for MetaPath

MetaPath citations

 (15)
library_books

Feature genes in metastatic breast cancer identified by MetaDE and SVM classifier methods

2018
PMCID: 5802200
PMID: 29328377
DOI: 10.3892/mmr.2018.8398

[…] ding of metastasis progression is very important for identifying novel therapeutic strategies to prevent metastatic disease.The MetaOmics software in R language is comprised of the MetaDE, MetaQC and MetaPath packages. The MetaDE package primarily contains 12 state-of-the-art genomic meta-analysis methods to detect differentially expressed genes (). The MetaQC package is the quantitative and objec […]

library_books

Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide

2017
Genes
PMCID: 5748668
PMID: 29182580
DOI: 10.3390/genes8120350

[…] or contig abundance estimation and annotation, and Prodigal [] for structural gene prediction. KEGG orthology (KO) assignment was performed using KAAS [], and differential KO genes were identified by MetaPath []. Operational taxonomic unit (OTU)-based network analysis was performed with Cytoscape, using an organic yFile layout. Sequence data used in this study were deposited to the Short Read Arch […]

library_books

Prediction of Possible Biomarkers and Novel Pathways Conferring Risk to Post Traumatic Stress Disorder

2016
PLoS One
PMCID: 5172609
PMID: 27997584
DOI: 10.1371/journal.pone.0168404

[…] lustered samples were then subjected to meta-analysis.MetaOmics is a software suite for a systematic microarray meta-analysis pipeline containing three integrated R packages namely MetaQC, MetaDE and MetaPath. MetaQC determines the inclusion/exclusion criteria for meta-analysis, MetaDE provides many state-of-the-art genomic meta-analysis methods to detect differentially expressed genes and MetaPat […]

library_books

Meta analysis of gene expression and integrin associated signaling pathways in papillary renal cell carcinoma subtypes

2016
Oncotarget
PMCID: 5356653
PMID: 27705936
DOI: 10.18632/oncotarget.12390

[…] DE genes than the other two and was thus selected for further analysis. All the 1758 DE genes obtained with maxP criteria were analyzed by using meta-analysis for pathway enrichment (MAPE) within the MetaPath package to reveal cellular pathways differentially regulated between PRCC1 and PRCC2 []. MAPE analysis identified 115 enriched pathways when the MAPE_I method (threshold set to 0.2) which int […]

library_books

Overcoming the matched sample bottleneck: an orthogonal approach to integrate omic data

2016
Sci Rep
PMCID: 4941544
PMID: 27403564
DOI: 10.1038/srep29251

[…] The data analysis was done on a personal MacBook Pro that has 8 GB 1600 MHz DDR3 RAM, 2.9 GHz Intel Core i7. Since MetaPath cannot exploit multiple processors, we run all the analysis using a single core. The time needed to run MetaPath was 39 minutes for Colorectal cancer and 47 minutes for Pancreatic cancer.For […]

library_books

Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery

2016
PMCID: 5626454
PMID: 28983419
DOI: 10.4236/iim.2016.83006

[…] inger [] provided a predicate oriented path finding approach to do fact checking in a large knowledge graph. VEPath Cluster [] proposed a combination of a vertex-centric and edge-centric approach for metapath graph analysis to enhance the clustering quality of cross domain datasets. In addition, pattern analysis was also widely used in data mining and knowledge discovery. In paper [], the author p […]

Citations

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MetaPath institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA

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