Transcript Variant Set Analysis - Frequently Asked Questions

• How do I decide which transcript to look at? This is an excellent question! Many genes will have different transcripts active in different contexts. In some cases, the question of which transcript to consider depends on the scientific question of interest. As a starting point, the TSL value can be used to help prioritise (lower numbers are better supported). Alternatively, Ensembl reports MANE select transcripts for each gene which can be used to identify the ‘default’ transcript. 

• When selecting a transcript, why are no analyses displayed? We do run pLoF VSAS analysis for transcripts that are not protein coding. Use the ‘Search by gene’ box and select a transcript specified as protein coding. 

• What are the numerical values in square brackets after phenotype names? These correspond to the data fields in the UK Biobank data showcase (e.g. https://biobank.ndph.ox.ac.uk/ukb/field.cgi?id=23406). 

• What are the VSAS ids? These are internal Genomics identifiers for VSAS studies. Each VSAS number corresponds to a single phenotype and the associated summary statistics for all protein coding transcripts. 

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