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Jan 13, 2022 14 tweets 12 min read Read on X
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…

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More from @ensembl

Feb 8
1/ Do you have a list of @ensembl IDs that you want to convert to IDs from other databases?

Here's how you can retrieve the @NCBI gene IDs from a list of #Ensembl IDs. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 A table showing Ensembl stable gene IDs in one column and the corresponding NCBI gene IDs in the next column, with a red arrow between them
2/ The #BioMart tool is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/biomart/martvi…
Screenshot of the Ensembl genome browser homepage with a labelled red arrow pointing towards the link for the BioMart tool
3/ First, you’ll need to select your database type and species of interest using the drop-down menus. In this case, we want to select ‘Ensembl Genes 111’ and the ‘Human genes’ dataset.
Read 14 tweets
Nov 23, 2023
1/ From ~20,000 coding genes in humans, biological complexity is also the result of gene/transcript expression levels in different tissues 📈

Want to see the expression of a #gene using @ensembl? A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 Screenshot from the Ensembl genome browser showing the location tab with tracks displaying gene models and RNASeq alignments from adipose and blood tissue
2/ Gene-level tissue-specific expression patterns from @ExpressionAtlas are displayed in the Gene tab. Just search for your gene of interest, click through to the gene tab and then click on ‘Gene Expression’ in the left-hand menu. Let’s use SERPINA3 as an example:
@ExpressionAtlas 3/ On this page, you can view baseline expression results as a heatmap with all tissues studied (columns) in different experiments (rows) in which the gene is expressed above the default minimum expression level. Screenshot from the Ensembl genome browser showing tissue specific expression patterns of the SERPINA3 gene
Read 11 tweets
Jul 6, 2023
1/ Do you want to know if a variant will affect the structure and function of a protein?

We’ve got lots of tools and #data in @ensembl to help you investigate and we’re here to show you how! A thread...🧵

#genomics #bioinformatics # #tweetorial #Ensembltraining🧬
2/ If you are working with human 🧑‍🤝‍🧑 variation data, genome-wide variant deleteriousness rankings from the CADD algorithm are available as well as pathogenicity predictions from SIFT, Polyphen-2, REVEL, MutationAssessor and MetaLR for missense variants.
3/ You can see all this data in the ‘Variant Table’ page in the gene tab
👉 https://t.co/vZAsntjEXYensembl.org/Homo_sapiens/G…
Read 10 tweets
Feb 23, 2023
1/ My favourite gene has 15 transcripts, which one should I use for further analysis? To report the position of variants? To design primers for? 🤯

This #tweetorial will show you how to filter and prioritise transcripts… 🧵

#genomics #bioinformatics #Ensembltraining 🧬 Screenshot of the transcript table of the LAMA3 gene in the
2/ To start, look for the #canonical tag in the flags column of the transcript table. The canonical transcript is based on conservation, expression, concordance with @appris_cnio and @uniprot, length, clinically important variants and completeness. Screenshot of the transcript table of the LAMA3 gene in the
3/ Many Ensembl #canonical transcripts will also be the #MANESelect, which is our collaboration with @NCBI. These transcripts match perfectly with RefSeq transcripts, so are the best to report variant location. Screenshot of the transcript table of the LAMA3 gene in the
Read 8 tweets
Dec 22, 2022
1/ Are you ready for 🎄🎅Chirstmas #Tweetorial? Whether you need the sequence for a single exon or whole #genome we got you covered! In the spirit of #Christmas, we will use Vitis vinifera 🍇 🍷in our example
#genomics #bioinformatics #Ensembltraining
2/ If you need the sequence of a single #gene, you can search for the gene symbol or ID from Ensembl homepage and click on ‘Sequence’ in the menu on the left
3/ From this page, you can download the sequence of the gene by clicking on the blue ‘Download Sequence’ button just above the sequence display.
Read 10 tweets
Aug 11, 2022
1/
It’s another Thursday, and that means it’s time for another #tweetorial! Today, we want to show you how you can view RefSeq #annotations on Ensembl 🥳

#bioinf #genomics #assembly #EnsemblTraining
2/
While Ensembl gene models are annotated directly on the reference genome, #RefSeq are annotated on mRNA sequences. In other words: genome browsers will have different annotation methods, so you might be interested in comparing these annotations side-by-side 📖🤔
3/
👂🏽You say you want to make direct comparisons of annotations between @NCBI’s RefSeq and Ensembl? Now is your time to try it out on Ensembl! 🏃🏽
Read 9 tweets

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