diff --git a/docs/tutorials/004_compare_specificity.md b/docs/tutorials/004_compare_specificity.md index 6e46de7..178b71f 100644 --- a/docs/tutorials/004_compare_specificity.md +++ b/docs/tutorials/004_compare_specificity.md @@ -4,7 +4,6 @@ Tissue specificity can be combined with gene families to pick up genes with cons also to detect genes within one species that sub- or neo-functionalized after duplication. Look at the examples below to see how. - ## Conserved Expression Some low-abudant genes can cause false positives when looking for tissue/condition specificity. These adverse results can @@ -16,14 +15,22 @@ Tomato (*Solanum lycopersicum*) fruis. This feature is available from the tools **Compare specificity**. The SPM (Specificity Metric) slider for tomato is adjusted to yield a similar number of hits as in *Arabidopsis thaliana*. -![Compare specificity](images/compare_specificity_entry.png "Compare specificity entry") +![Compare specificity entry](images/compare_specificity_entry.png "Compare specificity entry") In the resulting page orthogroups with a member expressed in one, the other or both selected conditions are shown in a venn diagram, with a detailed list below. By hovering over a gene, the description can be observed. -![Compare specificity](images/compare_specificity_result.png "Compare specificity result") +![Compare specificity result](images/compare_specificity_result.png "Compare specificity result") + +Here, the first reported hit is AGL1 *aka.* SHATTERPROOF 1, a known +[fruit development gene](https://www.ncbi.nlm.nih.gov/pubmed/10903201), clearly illustrating the power of this approach. + +## Sub- or Neofunctionalization + +Similarly you can compare *Arabidopsis thaliana* root specific genes (default SPM of 0.85) with pollen in the same +species (using the same SPM cutoff). -Here, the first reported hit is AGL1 aka. SHATTERPROOF 1, a known fruit development gene, clearly illustrating the power of this -approach. +![Compare specificity result2](images/compare_specificity_result2.png "Compare specificity result2") -## Sub- or Neofunctionalization \ No newline at end of file +Here **74** orthogroups are reported to show signs of sub- or neo-functionalization. This includes +**Cellulose Synthase (like)** genes included in the example from the [previous section](004_compare_specificity.md). \ No newline at end of file diff --git a/docs/tutorials/images/compare_specificity_result2.png b/docs/tutorials/images/compare_specificity_result2.png new file mode 100644 index 0000000..5bbb63f Binary files /dev/null and b/docs/tutorials/images/compare_specificity_result2.png differ