Martini: using literature keywords to compare gene sets
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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 journal › Journal article › peer-review
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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