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

Abstract

‘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

MicroRNA‐192‐5p inhibits migration of triple negative breast cancer cells and directly regulates Rho GTPase activating protein 19

“… 10 Although the percentage of breast cancer patients with altered miR‐192/miR‐194‐2 copy numbers is low, breast cancer patients with altered miR‐192 copy number show a significantly poorer survival compared to patients with unaltered miR‐192 copy number (Figure S2). To analyze the expression of miR‐192 and miR‐194‐2 in different breast cancer subtypes and normal breast‐like tissue, we performed meta‐analyses on microRNA expression using bc‐GenExMiner 4.5, 11 a statistical mining tool of published annotated breast cancer transcriptomic data from DNA microarrays and RNA‐sequencing. For the expression analysis of miR‐192 the following datasets GSE55348, 12 GSE36295, 13 GSE37751, 14 and GSE86166 15 were used.…”

“…Due to the fact that ARHGAP19, a Rho GTPase activating protein, is known to play a role in developmental processes and is expressed more in fetal than in adult tissue, we performed metaanalyses on expression data of different breast cancer samples. Expression data of ARHGAP19 were available in 54 different data sets 11 . The expression of ARHGAP19 was significantly lower in breast cancer subtypes compared to normal breast‐like tissue (Figure S10A).…”

Expression Characteristics and Significant Prognostic Values of PGK1 in Breast Cancer

“…The online dataset is a statistical mining tool of published annotated breast cancer transcriptomic data including DNA microarrays, RNA-seq with large amount of published annotated genomic data and can perform statistical analysis of gene expression, correlation and prognosis. The data on this website were last updated in June 2020 ( Jézéquel et al, 2021 ). The relationship between PGK1 and the clinic pathologic parameters of breast cancer were evaluated by using bc-GenExMiner v4.5.…”

Distinct Clinical Impact and Biological Function of Angiopoietin and Angiopoietin-like Proteins in Human Breast Cancer

“…The fold change (FC) and the significance were calculated for each gene using GEO2R (|log 2 (FC)| > 1.5 and adjusted p-values < 0.05). Further comparisons of gene expression data between normal, cancer-adjacent, and cancer tissues in the Cancer Genome Atlas (TCGA) were performed using Breast Cancer Gene-Expression Miner v4.6 (bc-GenExMiner v4.6, http://bcgenex.ico.unicancer.fr/BC-GEM/ GEM-Accueil.php?js=1) from 1 October 2020 [26][27][28].…”