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Ensembl Profile picture
@ensembl
Feb 23, 2023 • 8 tweets • 5 min read • Read on X
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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
4/ Some genes have mutually exclusive exons which are clinically important. These genes may also have a #MANEPlusClinical, a second transcript with the other exon, and you should report variant positions in both. Screenshot of the transcript table of the LAMA3 gene in the Screenshot of a graphical representation of LAMA3 transcript
5/ ⚠️WARNING ⚠️ The MANE project has only focussed on human protein coding genes on the human GRCh38 assembly, so MANE Select or MANE Plus Clinical transcripts are only annotated for this assembly.
6/ ⚠️WARNING ⚠️: Don’t use the transcript numbers (eg LAMA3-201) or transcripts IDs (eg ENST00000269217) as rankings or a guide for choosing. Both are completely arbitrary and only the ENSTs are stable between releases. Screenshot of the transcript table of the LAMA3 gene in the
7/ Whatever you use to report, note down the transcript stable ID with the version number, eg ENST00000313654.14. Transcripts change and can differ between databases. Only way to be 100% clear about which sequence is with a versioned stable identifier.
8/ You can find more information in the Ensembl documentation pages:
👉 ensembl.org/info/genome/ge…

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More from @ensembl

Ensembl Profile picture
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
Ensembl Profile picture
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
Ensembl Profile picture
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
Ensembl Profile picture
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
Ensembl Profile picture
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
Ensembl Profile picture
Aug 4, 2022
1/ You’ve sequenced your samples and identified variants. Great! 🙌

Now, here's how you can use @ensembl to find out the effect of your variants on #protein structures and interactions. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 A screenshot from Ensembl's Alphafold protein viewer with va
2/ The Variant Effect Predictor (VEP) is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/info/docs/tool…

#VEP Screenshot of Ensembl's homepage with annotated arrow pointi
3/ Click the ‘Launch VEP’ button to open the VEP web tool and enter your input data using instructions in the documentation:
👉ensembl.org/info/docs/tool… Screenshot of Ensembl's VEP web interface documentation and
Read 10 tweets

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