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CoNekT/docs/tutorials/004_compare_specificity.md

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Tutorial: Compare Specificity Conserved Expression Sub- or Neofunctionalization
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Tutorial: Compare Specificity

Tissue specificity can be combined with gene families to pick up genes with conserved expression between species but 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 be greatly reduced by looking for genes that are specific in a certain tissue in one species and have an ortholog (or homolog) specifically for the corresponding tissue is another species.

In this example Arabidopsis thaliana silique specific genes are matched with their orthologs expressed specifically in Tomato (Solanum lycopersicum) fruis. This feature is available from the tools menu below the button Compare specificity. The SPM (Specificity Metric) slider for tomato is adjusted to yield a similar number of hits as in Arabidopsis thaliana.

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 result

Here, the first reported hit is AGL1 aka. SHATTERPROOF 1, a known fruit development gene, 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).

Compare specificity result2

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.