GO-Elite: a flexible solution for pathway and ontology over-representation.

A. C. Zambon; S. Gaj; I. Ho; K. Hanspers; K. Vranizan; C.T.A. Evelo; B.R. Conklin; A.R. Pico; N. Salomonis

doi:10.1093/bioinformatics/bts366

GO-Elite: a flexible solution for pathway and ontology over-representation.

A. C. Zambon, S. Gaj, I. Ho, K. Hanspers, K. Vranizan, C.T.A. Evelo, B.R. Conklin, A.R. Pico, N. Salomonis^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

SUMMARY: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis (ORA) on any structured ontology annotations, pathway database or biological IDs (e.g., gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. Results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application. AVAILABILITY: http://www.genmapp.org/go_elite CONTACT: nsalomonis@gladstone.ucsf.edu.

Original language	English
Pages (from-to)	2209-2210
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/bts366
Publication status	Published - 15 Aug 2012

Keywords

MICROARRAY DATA
GENE-ONTOLOGY
PROFILE

Access to Document

10.1093/bioinformatics/bts366Licence: CC BY-NC

Cite this

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title = "GO-Elite: a flexible solution for pathway and ontology over-representation.",

abstract = "SUMMARY: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis (ORA) on any structured ontology annotations, pathway database or biological IDs (e.g., gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. Results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application. AVAILABILITY: http://www.genmapp.org/go_elite CONTACT: nsalomonis@gladstone.ucsf.edu.",

keywords = "MICROARRAY DATA, GENE-ONTOLOGY, PROFILE",

author = "Zambon, {A. C.} and S. Gaj and I. Ho and K. Hanspers and K. Vranizan and C.T.A. Evelo and B.R. Conklin and A.R. Pico and N. Salomonis",

year = "2012",

month = aug,

day = "15",

doi = "10.1093/bioinformatics/bts366",

language = "English",

volume = "28",

pages = "2209--2210",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "16",

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TY - JOUR

T1 - GO-Elite: a flexible solution for pathway and ontology over-representation.

AU - Zambon, A. C.

AU - Gaj, S.

AU - Ho, I.

AU - Hanspers, K.

AU - Vranizan, K.

AU - Evelo, C.T.A.

AU - Conklin, B.R.

AU - Pico, A.R.

AU - Salomonis, N.

PY - 2012/8/15

Y1 - 2012/8/15

N2 - SUMMARY: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis (ORA) on any structured ontology annotations, pathway database or biological IDs (e.g., gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. Results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application. AVAILABILITY: http://www.genmapp.org/go_elite CONTACT: nsalomonis@gladstone.ucsf.edu.

AB - SUMMARY: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis (ORA) on any structured ontology annotations, pathway database or biological IDs (e.g., gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. Results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application. AVAILABILITY: http://www.genmapp.org/go_elite CONTACT: nsalomonis@gladstone.ucsf.edu.

KW - MICROARRAY DATA

KW - GENE-ONTOLOGY

KW - PROFILE

U2 - 10.1093/bioinformatics/bts366

DO - 10.1093/bioinformatics/bts366

M3 - Article

C2 - 22743224

SN - 1367-4803

VL - 28

SP - 2209

EP - 2210

JO - Bioinformatics

JF - Bioinformatics

IS - 16

ER -