These predictions are not better than a general predictor like STRING that incorporates data of higher precision but we can show replication in a tissue specific manner. Surprisingly, we don't think that the majority of the difference in associations is explainable by tissue specific expression - ThreadSky

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pedrobeltrao.bsky.social • 29 days ago

These predictions are not better than a general predictor like STRING that incorporates data of higher precision but we can show replication in a tissue specific manner. Surprisingly, we don't think that the majority of the difference in associations is explainable by tissue specific expression

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pedrobeltrao.bsky.social•29 days ago

Given the limitations in accuracy, these associations are best used in system level analyses such as comparing gene sets and/or to combine with other data such as pull-downs. As an example, we can derive trait-to-trait and trait-to-compartment distances in a tissue specific manner.

pedrobeltrao.bsky.social•29 days ago

The major application we focused on was combining the brain derived protein associations with public pull-down data and co-fractionation data generated at ETH to re-prioritize candidate disease genes in GWAS linked loci.

pedrobeltrao.bsky.social•29 days ago

This is an @opentargets.org project, in collaboration with @intact-ebi.bsky.social and several groups here at @imsb-eth.bsky.social, including @berndwollscheid.bsky.social and alumni @marcvoo.bsky.social @afossati.bsky.social. All data/code is available at https://www.ebi.ac.uk/biostudies/studies/S-BSST1423

pedrobeltrao.bsky.social•29 days ago

While I believe the associations are already very useful they need to improve in accuracy and specificity (cell-types). We are committed to doing this with ongoing experiments and computational method development. An initial portal for this is at https://www.ppiatlas.com/

tuftskerfuffle.bsky.social•29 days ago

This is amazing, and to me the future of mode of action/site of action studies. Use proteomics mass spec to identify shorter lists of associated accessions, filter that through DNA and cDNA, and then screen through the list in the lab. Make the haystack smaller to find the needle!

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