bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses.

Autor: Jézéquel P; Unité de Bioinfomique, Institut de Cancérologie de l'Ouest, Bd Jacques Monod, Saint Herblain Cedex 44805, France.; CRCINA Team 8, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Gouraud W; Unité de Bioinfomique, Institut de Cancérologie de l'Ouest, Bd Jacques Monod, Saint Herblain Cedex 44805, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Ben Azzouz F; Unité de Bioinfomique, Institut de Cancérologie de l'Ouest, Bd Jacques Monod, Saint Herblain Cedex 44805, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Guérin-Charbonnel C; Unité de Bioinfomique, Institut de Cancérologie de l'Ouest, Bd Jacques Monod, Saint Herblain Cedex 44805, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Juin PP; CRCINA Team 8, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Lasla H; Unité de Bioinfomique, Institut de Cancérologie de l'Ouest, Bd Jacques Monod, Saint Herblain Cedex 44805, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France., Campone M; CRCINA Team 8, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France.; SIRIC ILIAD, Institut de Recherche en Santé-Université de Nantes, 8 Quai Moncousu-BP 70721, Nantes 44007, France.; Oncologie Médicale, Institut de Cancérologie de l'Ouest-René Gauducheau, Bd Jacques Monod, Saint Herblain 44805, France.
Jazyk: angličtina
Zdroj: Database : the journal of biological databases and curation [Database (Oxford)] 2021 Feb 18; Vol. 2021.
DOI: 10.1093/database/baab007
Abstrakt: 'Breast cancer gene-expression miner' (bc-GenExMiner) is a breast cancer-associated web portal (http://bcgenex.ico.unicancer.fr). Here, we describe the development of a new statistical mining module, which permits several differential gene expression analyses, i.e. 'Expression' module. Sixty-two breast cancer cohorts and one healthy breast cohort with their corresponding clinicopathological information are included in bc-GenExMiner v4.5 version. Analyses are based on microarray or RNAseq transcriptomic data. Thirty-nine differential gene expression analyses, grouped into 13 categories, according to clinicopathological and molecular characteristics ('Targeted' and 'Exhaustive') and gene expression ('Customized'), have been developed. Output results are visualized in four forms of plots. This new statistical mining module offers, among other things, the possibility to compare gene expression in healthy (cancer-free), tumour-adjacent and tumour tissues at once and in three triple-negative breast cancer subtypes (i.e. C1: molecular apocrine tumours; C2: basal-like tumours infiltrated by immune suppressive cells and C3: basal-like tumours triggering an ineffective immune response). Several validation tests showed that bioinformatics process did not alter the pathobiological information contained in the source data. In this work, we developed and demonstrated that bc-GenExMiner 'Expression' module can be used for exploratory and validation purposes. Database URL: http://bcgenex.ico.unicancer.fr.
(© The Author(s) 2021. Published by Oxford University Press.)
Databáze: MEDLINE
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