diff --git a/docs/tutorials/002_expression_profiles.md b/docs/tutorials/002_expression_profiles.md index 91a3cc3..7c1beba 100644 --- a/docs/tutorials/002_expression_profiles.md +++ b/docs/tutorials/002_expression_profiles.md @@ -45,7 +45,25 @@ buttons in the top right. ## Expression Specificity +To pick up genes expressed *specifically* in a certain tissue/condition the **Find specific profile** function, under the +tools button in the menu, is available. Select the **species**, the **method** (complete profile or a summary if any are +available), the desired **tissue/condition** and **SPM-cutoff** (specificity metric). +![specificity entry](images/specificity_entry.png "Find specific genes form") + +Note that if settings change, the number in the button **Show genes** is updated. This shows the number of genes in the +results. Once you have decided on the settings click that button to show the result. + +![specificity example](images/specificity_entry.png "Find specific genes result") + +An overview of genes specific for a certain tissue (here Root Apices, 7 days after germination). Note that by clicking +the table header the results can be sorted. Genes with an expression level below 10 TPM are flagged as low abundant, +such low expressed genes should be treated carefully as they might comprise false positives ! ## Export *all* expressed genes +To enable local analysis, all expressed genes in a certain condition/tissue can be exported using the +**Export expression levels** feature under the tools button in the menu. Select the **species**, the **method** (full profile or +summary if any are available) and the **condition** you wish to export. Click **Export genes** to get the data. + +Note that exporting large sets of data can take up to a minute. \ No newline at end of file diff --git a/docs/tutorials/images/specificity_example.png b/docs/tutorials/images/specificity_example.png new file mode 100644 index 0000000..f7410c3 Binary files /dev/null and b/docs/tutorials/images/specificity_example.png differ diff --git a/docs/tutorials/images/specificty_entry.png b/docs/tutorials/images/specificty_entry.png new file mode 100644 index 0000000..1d0d13b Binary files /dev/null and b/docs/tutorials/images/specificty_entry.png differ