Detailed Information on Publication Record
2015
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
IHNATOVÁ, Ivana and Eva BUDINSKÁBasic information
Original name
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Authors
IHNATOVÁ, Ivana (703 Slovakia, belonging to the institution) and Eva BUDINSKÁ (703 Slovakia, guarantor, belonging to the institution)
Edition
BMC Bioinformatics, London, BioMed Central, 2015, 1471-2105
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10103 Statistics and probability
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.435
RIV identification code
RIV/00216224:14110/15:00085197
Organization unit
Faculty of Medicine
UT WoS
000363616800001
Keywords in English
Topology; Pathway analysis; Microarray; RNA-Seq; Packages
Tags
International impact, Reviewed
Změněno: 11/12/2015 10:20, Ing. Mgr. Věra Pospíšilíková
Abstract
V originále
Background: Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses. The last generation of pathway analysis methods takes into account the topological structure of a pathway, which helps to increase both specificity and sensitivity of the findings. Simultaneously, the RNA-Seq technology is gaining popularity and becomes widely used for gene expression profiling. Unfortunately, majority of topological pathway analysis methods remains without implementation and if an implementation exists, it is limited in various factors. Results: We developed a new R/Bioconductor package ToPASeq offering uniform interface to seven distinct topology-based pathway analysis methods, of which three we implemented de-novo and four were adjusted from existing implementations. Apart this, ToPASeq offers a set of tailored visualization functions and functions for importing and manipulating pathways and their topologies, facilitating the application of the methods on different species. The package can be used to compare the differential expression of pathways between two conditions on both gene expression microarray and RNA-Seq data. The package is written in R and is available from Bioconductor 3.2 using AGPL-3 license. Conclusion: ToPASeq is a novel package that offers seven distinct methods for topology-based pathway analysis, which are easily applicable on microarray as well as RNA-Seq data, both in human and other species. At the same time, it provides specific tools for visualization of the results.
Links
| ED1.1.00/02.0068, research and development project |
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| LM2011028, research and development project |
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| LO1214, research and development project |
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