Martini: using literature keywords to compare gene sets

Research output: Contribution to journalJournal articlepeer-review

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Martini : using literature keywords to compare gene sets. / Soldatos, Theodoros G; O'Donoghue, Seán I; Satagopam, Venkata P; Jensen, Lars J; Brown, Nigel P; Barbosa-Silva, Adriano; Schneider, Reinhard.

In: Nucleic Acids Research, Vol. 38, No. 1, 2010, p. 26-38.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Soldatos, TG, O'Donoghue, SI, Satagopam, VP, Jensen, LJ, Brown, NP, Barbosa-Silva, A & Schneider, R 2010, 'Martini: using literature keywords to compare gene sets', Nucleic Acids Research, vol. 38, no. 1, pp. 26-38. https://doi.org/10.1093/nar/gkp876

APA

Soldatos, T. G., O'Donoghue, S. I., Satagopam, V. P., Jensen, L. J., Brown, N. P., Barbosa-Silva, A., & Schneider, R. (2010). Martini: using literature keywords to compare gene sets. Nucleic Acids Research, 38(1), 26-38. https://doi.org/10.1093/nar/gkp876

Vancouver

Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A et al. Martini: using literature keywords to compare gene sets. Nucleic Acids Research. 2010;38(1):26-38. https://doi.org/10.1093/nar/gkp876

Author

Soldatos, Theodoros G ; O'Donoghue, Seán I ; Satagopam, Venkata P ; Jensen, Lars J ; Brown, Nigel P ; Barbosa-Silva, Adriano ; Schneider, Reinhard. / Martini : using literature keywords to compare gene sets. In: Nucleic Acids Research. 2010 ; Vol. 38, No. 1. pp. 26-38.

Bibtex

@article{e2aa944102f84a2389767ef46a1e5f76,
title = "Martini: using literature keywords to compare gene sets",
abstract = "Life scientists are often interested to compare two gene sets to gain insight into differences between two distinct, but related, phenotypes or conditions. Several tools have been developed for comparing gene sets, most of which find Gene Ontology (GO) terms that are significantly over-represented in one gene set. However, such tools often return GO terms that are too generic or too few to be informative. Here, we present Martini, an easy-to-use tool for comparing gene sets. Martini is based, not on GO, but on keywords extracted from Medline abstracts; Martini also supports a much wider range of species than comparable tools. To evaluate Martini we created a benchmark based on the human cell cycle, and we tested several comparable tools (CoPub, FatiGO, Marmite and ProfCom). Martini had the best benchmark performance, delivering a more detailed and accurate description of function. Martini also gave best or equal performance with three other datasets (related to Arabidopsis, melanoma and ovarian cancer), suggesting that Martini represents an advance in the automated comparison of gene sets. In agreement with previous studies, our results further suggest that literature-derived keywords are a richer source of gene-function information than GO annotations. Martini is freely available at http://martini.embl.de.",
keywords = "Arabidopsis, Cell Cycle, Dictionaries as Topic, Genes, Genes, Neoplasm, Genes, Plant, Humans, MEDLINE, Melanoma, Software, Terminology as Topic",
author = "Soldatos, {Theodoros G} and O'Donoghue, {Se{\'a}n I} and Satagopam, {Venkata P} and Jensen, {Lars J} and Brown, {Nigel P} and Adriano Barbosa-Silva and Reinhard Schneider",
year = "2010",
doi = "10.1093/nar/gkp876",
language = "English",
volume = "38",
pages = "26--38",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "1",

}

RIS

TY - JOUR

T1 - Martini

T2 - using literature keywords to compare gene sets

AU - Soldatos, Theodoros G

AU - O'Donoghue, Seán I

AU - Satagopam, Venkata P

AU - Jensen, Lars J

AU - Brown, Nigel P

AU - Barbosa-Silva, Adriano

AU - Schneider, Reinhard

PY - 2010

Y1 - 2010

N2 - Life scientists are often interested to compare two gene sets to gain insight into differences between two distinct, but related, phenotypes or conditions. Several tools have been developed for comparing gene sets, most of which find Gene Ontology (GO) terms that are significantly over-represented in one gene set. However, such tools often return GO terms that are too generic or too few to be informative. Here, we present Martini, an easy-to-use tool for comparing gene sets. Martini is based, not on GO, but on keywords extracted from Medline abstracts; Martini also supports a much wider range of species than comparable tools. To evaluate Martini we created a benchmark based on the human cell cycle, and we tested several comparable tools (CoPub, FatiGO, Marmite and ProfCom). Martini had the best benchmark performance, delivering a more detailed and accurate description of function. Martini also gave best or equal performance with three other datasets (related to Arabidopsis, melanoma and ovarian cancer), suggesting that Martini represents an advance in the automated comparison of gene sets. In agreement with previous studies, our results further suggest that literature-derived keywords are a richer source of gene-function information than GO annotations. Martini is freely available at http://martini.embl.de.

AB - Life scientists are often interested to compare two gene sets to gain insight into differences between two distinct, but related, phenotypes or conditions. Several tools have been developed for comparing gene sets, most of which find Gene Ontology (GO) terms that are significantly over-represented in one gene set. However, such tools often return GO terms that are too generic or too few to be informative. Here, we present Martini, an easy-to-use tool for comparing gene sets. Martini is based, not on GO, but on keywords extracted from Medline abstracts; Martini also supports a much wider range of species than comparable tools. To evaluate Martini we created a benchmark based on the human cell cycle, and we tested several comparable tools (CoPub, FatiGO, Marmite and ProfCom). Martini had the best benchmark performance, delivering a more detailed and accurate description of function. Martini also gave best or equal performance with three other datasets (related to Arabidopsis, melanoma and ovarian cancer), suggesting that Martini represents an advance in the automated comparison of gene sets. In agreement with previous studies, our results further suggest that literature-derived keywords are a richer source of gene-function information than GO annotations. Martini is freely available at http://martini.embl.de.

KW - Arabidopsis

KW - Cell Cycle

KW - Dictionaries as Topic

KW - Genes

KW - Genes, Neoplasm

KW - Genes, Plant

KW - Humans

KW - MEDLINE

KW - Melanoma

KW - Software

KW - Terminology as Topic

U2 - 10.1093/nar/gkp876

DO - 10.1093/nar/gkp876

M3 - Journal article

C2 - 19858102

VL - 38

SP - 26

EP - 38

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 1

ER -

ID: 40748847