| Breast Cancer Gene-Expression Miner v4.5
(bc-GenExMiner v4.5) | |  |
Tutorial - Targeted expression analysis
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Targeted expression analysis permits to visually compare gene expression between two or more groups of patients, according to the selected criterion.
A Welch's test is also performed (along with Dunnett-Tukey-Kramer's tests for pairwise comparison when appropriate).
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| Step one |
There are two criteria to choose.
Criterion 1:
gene expression data
First choose the data source (All DNA microarrays, METABRIC, TCGA...), then fill the textbox with actualised* gene symbol (at least 2 characters must be entered)
or
Affymetrix® probeset ID.
A dropdown list will appear, you can then select the gene you want to test.
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.
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
JetSet algorithm.
*: see actualised web databases
(e.g.: GeneCards,
Ensembl,
HGNC,
NCBI Gene...)
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Criterion 2: studied population
Choose one of the characteristics (nature of the tissue, receptors, nodal status, histological types, SBR grade, NPI stage, Age...)
of the cohorts to be explored.
For age criterion, 51 years-old cutoff [≤51 / >51] was retained as age at menopause in western industrialised countries.
These datasets are retrieved from
annotated
genomic data.
Once the 2 criteria have been chosen, click on "Submit".
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Step two |
Validation of analysis plan.
After submission, a validation page shows detailed information about:
- tested gene,
- patients from original studies tested,
1 complete data before filtering;
2 results of filtering process;
3 if the gene is present or not;
4 patients finally analysed
(if no missing genomic data).
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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.
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Results are presented with four kinds of plot showing distribution of gene expression according to groups :
- box and whisker,
- beeswarm,
- violin,
- and raincloud.
Click on one of the "plot" button of your choice to display the figure.
In this tutorial, SBR analysis was chosen.
For age criterion, the case 2 [≤51 / >51 years old] was determined by the age at menopause in western industrialised countries.
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Global significant difference between groups is assessed by Welch's test, the corresponding p-value is indicated on the bottom right of the figure.
If a global significant difference exists (p < 0.05) and there are more than 2 groups, a Dunnett-Tukey-Kramer's test is computed for each pairwise comparison.
The results table is shown below the figure.
The colour of the p-value depends on the result: the p-value is written in green if a significant difference exists (p < 0.05),
in orange if there is a trend (p = 0.05-0.10)
and in red if there is no difference (p > 0.10).
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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. |
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