Thread by @ensembl

Want to learn about a gene function, but there’s no functional data in your species of interest? Or maybe looking for a homologue of your fav gene in a model organism to carry out functional work? Look no further! This #tweetorial will show you how to find orthologues in @ensembl

2/14
Let’s start on the Ensembl homepage and search for our #gene of interest SCP2 by typing its name into the search box. Then go to the gene tab by clicking on the gene name in the search results.

#Ensembltraining #genomics #bioinformatics #EnsemblCompara

3/14
You can learn more about the #gene function by exploring gene ontology terms and associated phenotypes. Let’s click on Phenotypes in the side menu. This view shows phenotypes associated with our gene of interest and variants in this gene.

4/14
You can learn more about your #gene by examining phenotypes, diseases and traits associated with #orthologues of this gene in other species listed in the table below, as they might be functionally equivalent. There are numerous phenotypes found in mouse models 🐁

5/14
If you’d like to look through a list of all #orthologues found across various vertebrates and some non-vertebrate model organisms, click on Orthologues in the side menu.

6/14
You’ll find here a summary of orthology types across different taxa, followed by a table of orthologues of our #gene of interested in various species. Let’s search for the zebrafish #orthologue 🐟

7/14
You can explore #sequence alignment of the human and zebrafish orthologues by clicking on the ‘View Sequence Alignments’ link, which gives you an option to view protein or cDNA alignment. Let’s have a look at the protein alignment.

8/14
You can also view #homologues of our #gene of interest and their relationship illustrated as a gene tree. Click on the Gene tree in the side menu.

9/14
We calculate #ComparativeGenomics analyses by taxa. #EnsemblCompara is dedicated to vertebrates (with a couple of non-vertebrate model organisms 🪰 🪱). You can find similar analysis done for plants 🌱, invertebrate metazoans 🦟, protists 🦠 and fungi 🍄 in @ensemblgenomes

10/14
We also calculate genomic comparison across all divisions for a subset of representative species called pan-taxonomic Compara, which can be found in @ensemblgenomes

11/14
If you’d like to look at your vertebrate #gene of interest in the pan-taxonomic context, you can get there through a non-vertebrate #orthologue of your gene. Let’s go back to the Orthologue table and search for the Drosophila melanogaster orthologue 🪰

12/14
Knowing the Drosophila #orthologue (ScpX), we can search for it in Ensembl Metazoa. You can find the Pan-taxonomic Compara section in the side menu on the #gene tab.
ensemblgenomes.org

13/14
There are #orthologues of the human SCP2 gene in invertebrates, plants and bacteria shown in the pan-taxonomic #GeneTree and in the table of orthologues.

14/14
You can also mine #homologues at a larger scale using:
🔹BioMart: ensembl.org/biomart/martvi…
🔹Ensembl REST API: rest.ensembl.org
🔹EMF files on our FTP site: ftp.ensembl.org/pub/release-10…
🔹XML files on our FTP site: ftp.ensembl.org/pub/release-10…