| Breast Cancer Gene-Expression Miner v5.2
(bc-GenExMiner v5.2) | |  |
Tutorial - Gene correlation exhaustive analysis
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Gene correlation exhaustive analysis permits to identify genes best correlated (positively and negatively) to a chosen gene, with associated Gene Ontology terms enrichments.
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| Step one |
Criterion 1:
gene expression data
First choose the data source (All DNA microarrays or All RNA-seq), then fill the textbox with one actualised* gene symbol.
*: see actualised web databases (e.g.:
Ensembl,
GeneCards,
HGNC,
NCBI Gene...)
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Criterion 2:
criterion for studied population
Choose one of the population characteristics (all patients, oestrogen receptor,
progesterone receptor, oestrogen and progesterone receptor combinations, nodal status,
intrinsic molecular subtypes [from PAM50], intrinsic molecular subtypes [from RIMSPC],
TNBC subtypes or basal-like/TNBC (IHC status), TNBC subtypes classification (more details here :
Jézéquel et al. Breast Cancer. 2024 May 22.) of the cohorts to be explored.
These datasets are retrieved from
annotated
transcriptomic data.
Once the 2 criteria have been chosen, click on "Submit".
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Step two |
After submission, a validation page shows detailed information about:
- tested gene,
- number of patients from original studies tested,
1 complete data before filtering;
2 if the gene is found or not; and
3 patients finally analysed (if no missing genomic data).
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After visualising the validation screen and reading the summary, at the bottom of the page, you can then choose to validate or cancel your submission according
to these intermediate descriptive data summarized at the bottom of the page.
- "Start analysis" will launch
statistical analyses
with the chosen gene and direct you to exhaustive correlation analysis result page.
- "Cancel" will redirect you back to previous screen, and offer you to choose a new gene.
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Tables corresponding to analysis with patients from the five molecular subtypes,
as determined by the PAM50,
can be displayed by clicking on the corresponding button in the upper menu.
The buttons with the color gradient display the colors of the correlation score codes (r), indicating the best correlation of your gene with a maximum of 50 genes.
After choosing one of the molecular subtype buttons (here luminal B was chosen), the results corresponding to analysis with all patients are presented in two separated tables displaying
gene symbol, correlation coefficient, p-value and corresponding number of patients for the 50 (or less) genes most correlated to the chosen gene:
The left table displays the positive correlations and the right table, the negative ones.
Help to interpret correlation coefficient value is available by clicking on the "?" symbol below the colour scale.
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Only correlations with coefficient greater than 0.40 in absolute value and p-value less than 0.05 are displayed.
Full table (i.e. table with all correlations fulfilling above criteria) can be downloaded and saved in csv format.
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Additionally, a "Gene Ontology" button permits to know the
gene ontology analysis
enrichment results, i.e. the Gene Ontology
terms significantly associated with the genes most correlated to the chosen gene.
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Three lists of genes are tested: genes most positively correlated to the chosen gene, including the chosen gene,
genes most negatively correlated to the chosen gene, and the union of the two lists.
All Gene Ontology trees are explored (biological process, molecular function, cellular component).
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In order to lighten the presentation of the Gene Ontology results, only the seven best first results are displayed.
The full result list can be saved by clicking on the corresponding button below the tables.
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