Customised expression analysis permits to screen the expression level of a gene according to
another gene by dichotomizing the latter (based on median value) and taking the resulting binary value as criterion.
gene expression data
First choose the data source (All DNA microarrays, METABRIC, TCGA...), then fill the first textbox with actualised* gene symbol (at least 2 characters must be entered)
Affymetrix® probeset ID.
A dropdown list will appear, you can then select the gene you want to test (called gene A), this is the gene whose distribution will be studied.
The list of available genes depends on the previously chosen data source,
if any option, except "Affymetrix®", is checked only gene symbols available with selected data are shown in list.
If "Affymetrix® platform" is checked only gene symbols represented by a probeset are listed. In particular for this analysis module, only probes from the U133 Plus 2.0 array are available.
Each probeset can be selected, if there is more than one probeset, three additional options are available:
Median probe: median value of all probesets corresponding to the selected gene is taken,
Highest probe: the probeset having the highest expression level is retained for the analysis (highest median value in a majority of U133P2 and U133A datasets;
in case of ties, decision was based on the total number of patients in the cohorts.),
JetSet probe: probeset with the highest score given by
Then fill the second textbox with another actualised* gene symbol (called gene B), this gene will be your criterion to split your gene A in two groups.
The same type of gene A expression data will be used for gene B automatically, you do not have to select data type.
Choose the kind of discretisation used for correlation analyses as a splitting criterion:
optimal: gene or probeset is split according to all percentiles from the 20th to the 80th, with a step of 5,
and the cutoff giving the best p-value (Welch's test) is kept,
customised percentile: choose any percentile from the 20th to the 80th, with a step of 1, to dichotomise the gene.
Once the 2 criteria have been chosen, click on "Submit".
Validation of analysis plan.
After submission, a validation page shows detailed information about tested genes and:
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 the two genomic data is present for a same patient).
A summary is given at the bottom of the page, you can then choose to validate (by hitting "Start analysis" button) or cancel your submission.
"Cancel" will redirect you back to previous screen, and offer you to choose new criteria on the form.
Results are presented with four distinct plots showing distribution of gene A expression according to median-dichotomised expression of gene B.
Click on one of the "plot" button to display or hide the chosen figure. (here raincloud plot was selected)
Each expression plots 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.