Detection of gene orthology from gene co-expression and protein interaction networks

Fadi Towfic, Susan VanderPIas, Casey A. OIiver, OIiver Couture, Christopher K. TuggIe, M. Heather West GreenIee, Vasant Honavar

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. . Results: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms.Conclusions: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.

Original languageEnglish (US)
Article numberS7
JournalBMC bioinformatics
Volume11
Issue numberSUPPL. 3
DOIs
StatePublished - Apr 29 2010

Fingerprint

Protein Interaction Maps
Protein Interaction Networks
Gene Networks
Genes
Gene Regulatory Networks
Protein-protein Interaction
Gene
Proteins
Gene Expression
Alignment
Biological Phenomena
Sus scrofa
Decision Trees
Naive Bayes
Drosophilidae
Saccharomyces Cerevisiae
Classification Algorithm
Drosophila melanogaster
Hits
Decision tree

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Towfic, F., VanderPIas, S., OIiver, C. A., Couture, OI., TuggIe, C. K., West GreenIee, M. H., & Honavar, V. (2010). Detection of gene orthology from gene co-expression and protein interaction networks. BMC bioinformatics, 11(SUPPL. 3), [S7]. https://doi.org/10.1186/1471-2105-11-S3-S7
Towfic, Fadi ; VanderPIas, Susan ; OIiver, Casey A. ; Couture, OIiver ; TuggIe, Christopher K. ; West GreenIee, M. Heather ; Honavar, Vasant. / Detection of gene orthology from gene co-expression and protein interaction networks. In: BMC bioinformatics. 2010 ; Vol. 11, No. SUPPL. 3.
@article{4302fc184d8a4e30b9e50db2a11490de,
title = "Detection of gene orthology from gene co-expression and protein interaction networks",
abstract = "Background: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. . Results: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms.Conclusions: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.",
author = "Fadi Towfic and Susan VanderPIas and OIiver, {Casey A.} and OIiver Couture and TuggIe, {Christopher K.} and {West GreenIee}, {M. Heather} and Vasant Honavar",
year = "2010",
month = "4",
day = "29",
doi = "10.1186/1471-2105-11-S3-S7",
language = "English (US)",
volume = "11",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
number = "SUPPL. 3",

}

Towfic, F, VanderPIas, S, OIiver, CA, Couture, OI, TuggIe, CK, West GreenIee, MH & Honavar, V 2010, 'Detection of gene orthology from gene co-expression and protein interaction networks', BMC bioinformatics, vol. 11, no. SUPPL. 3, S7. https://doi.org/10.1186/1471-2105-11-S3-S7

Detection of gene orthology from gene co-expression and protein interaction networks. / Towfic, Fadi; VanderPIas, Susan; OIiver, Casey A.; Couture, OIiver; TuggIe, Christopher K.; West GreenIee, M. Heather; Honavar, Vasant.

In: BMC bioinformatics, Vol. 11, No. SUPPL. 3, S7, 29.04.2010.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Detection of gene orthology from gene co-expression and protein interaction networks

AU - Towfic, Fadi

AU - VanderPIas, Susan

AU - OIiver, Casey A.

AU - Couture, OIiver

AU - TuggIe, Christopher K.

AU - West GreenIee, M. Heather

AU - Honavar, Vasant

PY - 2010/4/29

Y1 - 2010/4/29

N2 - Background: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. . Results: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms.Conclusions: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.

AB - Background: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. . Results: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms.Conclusions: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.

UR - http://www.scopus.com/inward/record.url?scp=77952278454&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77952278454&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-11-S3-S7

DO - 10.1186/1471-2105-11-S3-S7

M3 - Article

C2 - 20438654

AN - SCOPUS:77952278454

VL - 11

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - SUPPL. 3

M1 - S7

ER -

Towfic F, VanderPIas S, OIiver CA, Couture OI, TuggIe CK, West GreenIee MH et al. Detection of gene orthology from gene co-expression and protein interaction networks. BMC bioinformatics. 2010 Apr 29;11(SUPPL. 3). S7. https://doi.org/10.1186/1471-2105-11-S3-S7