Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

doi:10.1186/1471-2105-7-241

BMC Bioinformatics
Volume 7

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Aubry M
Monnier A
Chicault C
de Tayrac M
Galibert MD
Burgun A
Mosser J

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Monnier A
Chicault C
de Tayrac M
Galibert MD
Burgun A
Mosser J
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Methodology article

Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

Marc Aubry¹ , Annabelle Monnier² , Celine Chicault¹ , Marie de Tayrac¹ , Marie-Dominique Galibert¹ , Anita Burgun³ and Jean Mosser¹^,2

¹CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, Groupe Oncogénomique, IFR140 GFAS, Faculté de Médecine, 2 avenue du Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France

²OUEST-genopole^®Transcriptomic PF, IFR140 Génétique Fonctionnelle Agronomie et Santé, Université de Rennes 1, 35043 Rennes Cedex, France

³EA 3888 Modélisation Conceptuelle des Connaissances Biomédicales, Faculté de Médecine, Université de Rennes 1, 35043 Rennes Cedex, France

author email corresponding author email

BMC Bioinformatics 2006, 7:241doi:10.1186/1471-2105-7-241


Published:	4 May 2006

Additional files

Additional File 1:

GO terms associated with the Down cluster: Venn category, GO ID, Name, GOA Human annotation with evidence codes and genes, PubGene annotation with significant scores and genes.

Format: TXT Size: 24KB Download file

Additional File 2:

Up cluster. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

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Additional File 3:

Glioblastomas clusters. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

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Additional File 4:

Acute Lymphocyte Leukemias (ALL) clusters. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOA-PUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

Format: PDF Size: 31KB Download file

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Additional File 5:

Circadian cluster. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

Format: PDF Size: 12KB Download file

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Additional File 6:

Lung cluster. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

Format: PDF Size: 8KB Download file

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Additional File 7:

Retina clusters. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

Format: PDF Size: 14KB Download file

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Additional File 8:

Alzheimer's disease cluster. (A) Boxplots of the PQIs for the Evidence (GOA), Literature (PUB) and combination of both (GOAPUB). (B) Boxplots of the PQIs for the evidence and literature terms (GOAPUB), for the same set enriched with the associative relations (+Dep.) or a random term set of the same size (+Random).

Format: PDF Size: 12KB Download file

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Additional File 9:

Enriched GO Process terms (p < = 0.05) associated with at least 4 genes in the glioGBM cluster. Color: red = terms found in GOA and PubGene, green = terms only found in GOA, blue = terms only found in PubGene. Shape: rectangle = significantly enriched annotated terms (p < = 0.05) ; ellipse = non-significantly enri-ched annotated terms (p > 0.05).

Format: PDF Size: 21KB Download file

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Additional File 10:

Enriched GO Process terms associated with at least 4 genes in the bcr-abl cluster. Color: red = terms found in GOA and PubGene, green = terms only found in GOA, blue = terms only found in PubGene. Shape: rectangle = significantly enriched annotated terms (p < = 0.05) ; ellipse = non-significantly enriched annotated terms (p > 0.05).