Permalink
Cannot retrieve contributors at this time
Name already in use
A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
CoNekT/docs/tutorials/003_gene_families_trees.md
Go to fileThis commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
32 lines (22 sloc)
1.86 KB
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# 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](https://www.ncbi.nlm.nih.gov/pubmed/11917018) and [OrthoFinder](https://github.com/davidemms/OrthoFinder) for | |
Homologous groups and OrthoGroups respectively. | |
## Gene Families | |
![gene family](images/gene_family.png "Gene family") | |
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 | |
Phylogenetic Trees generated by [OrthoFinder](https://github.com/davidemms/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. | |
![phylogenetic tree](images/phylo_tree_example.png "Phylogenetic tree example") | |
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. |