| Breast Cancer Gene-Expression Miner v4.6
(bc-GenExMiner v4.6) | |  |
Tutorial - Gene correlation targeted analysis
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Gene correlation targeted analysis permits to know the linear dependence between each pair of the 2 to 20 submitted genes.
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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 at least two and up to twenty actualised* gene symbols.
Gene symbols must be entered separately and validated one at a time (e.g.: SERPINE1 [enter]
UBE2C [enter] TACC3...).
A second way of requesting can be used by uploading your own gene list within a file.
Store your genes in a text file, with the text separator of your choice : tabulation, carriage return, comma or space. Note that only gene symbols will be taken into account.
Then upload your file with the second text box by clicking on "Browse" (here "Parcourir") button.
The screen capture have been made with a english browser, your own browser will use your personnal langage settings.
*: see actualised web databases (e.g.:
GeneCards,
Ensembl,
HGNC,
NCBI Gene...)
You can delete each gene symbol independently by clicking on the cross at the right side of the name, or delete whole list by clicking on trash bin (right side of the box).
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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,
intrinsic molecular subtypes [from PAM50], intrinsic molecular subtypes [from RIMSPC],
basal-like/TNBC status or TNBC subtypes) 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(s),
- patients from original studies tested,
1 complete data before filtering;
2 number of genes found;
3 patients finally analysed (if no missing genomic data).
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At this step, you can validate or cancel your submission according
to these intermediate descriptive data summarized at the bottom of the page.
"Start analysis" will launch
correlation analysis
with the chosen genes and direct you to corresponding result page.
"Cancel" will redirect you back to previous screen and offer you to choose new genes.
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Results page displays first
correlation map corresponding
to analysis with all patients.
Help to interpret correlation coefficient value is available by clicking on the "?" symbol below the colour scale.
Correlation maps corresponding to analysis among patients with respectively:
- all patients,
- positive or negative oestrogen receptor (ER) status,
- positive or negative progesterone receptor (PR) status,
- combination of ER/PR statuses,
- patients of the five molecular subtypes as determined by the PAM50,
- patients of the four molecular subtypes as determined by the RIMSPC,
- patients determined by basal-like PAM50 subtyped and/or triple-negative breast cancer typed by immunohistochemistry,
- and finally triple-negative breast cancer subtypes patients (C1, C2 and C3 subtypes)
can be displayed by clicking on the corresponding button below.
Depending on population criterion chosen before, respectively like the first request page, the "above buttons bar" will be presented like following capture :
For each pair of genes,
correlation plot
can be displayed, along with correlation coefficient value,
corresponding p-value and number of patients involved, by clicking on the corresponding cell in the correlation map.
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Correlation maps can be saved in png ([portable network graphics] universal and easy to use format),
and emf ([enhanced metafile] lossless scalable vector format that allows adjusting figure for your research article) format.
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Tables with all detailed values (correlation coefficient, p-value, number of patients) can be saved in csv [comma separated values] format.
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