Tutorial: Gene families and Phylogenetic Trees
Homologous genes (genes derived from a common ancestor) are usually group into gene families. Orthologs, genes derived from a common ancestor through speciation, are similarly grouped into OrthoGroups. CoNekT supports tribeMCL and OrthoFinder for Homologous groups and OrthoGroups respectively.
Sequence pages link to the gene family a sequence belongs to, on the gene family page you can find a distribution (shown above) depicting how many members for each species there are. Furthermore you can find associated domains and functional annotation, a suggested function (based on the function of members)...
Phylogenetic Trees generated by OrthoFinder can be imported into CoNekT. These can be accessed from gene pages for sequences included in the tree or the corresponding gene family page.
A unique feature of CoNekT is that conditions can be manually curated per species and expression levels of genes in comparable tissues/organs can be added to the phylogenetic tree. This allows for changes in expression patterns between duplicated genes or after speciation events to be visualized.
In the example above various genes related with cellulose synthase (an important component of plant cell walls) is shown. Here it is immediately clear that some groups of cellulose syntases are specific for leaves while others play a role in reproductive structure.
Furthermore, links to view this information in the heatmap viewer are present top-right of the phylogenetic tree. From the heatmap expression levels can also be exported.