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PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling
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Update on gene expression databases including pre-clinical and animal species #2071

Closed HenrikCordes closed 9 months ago

HenrikCordes commented 2 years ago

Dear open-systems-pharmacology community,

we are currently working on an update of the gene expression databases of PK-Sim. To this end we're preparing a publication that will outline the database generation, the R-Code that creates them and the first release the of the databases. Ideally we could include them in one of the next releases and make the scripts part of the git repository, let's see.

It will still take a while, but nevertheless we wanted to keep you updated and a first glimpse of what you can expect within 2022.

As requested in previous posts #1505 #1452 #931, the next line of gene expression databases will cover various animal species relevant in pre-clincial research, animal healthy and toxicology, as well as an update on the human data. Currently we cover the following species: Human, Monkey (Macaca mulatta & Macaca fascicularis), Minipig, Dog, Rat, Mouse, Rabbit, Zebrafish, Cattle #1957, Horse, Cat #293, Guinea Pig, Chicken, Turkey, Goat and Sheep

Please note, the expression value normalization does not include alternatives as discussed in #1637 All gene annotations are made with the biomaRt - Bioconductor package and are based on ensemble and NCBI gene identifiers. For animal species, the databases include a link to the human homolog #1036 #1034 #946, such that you can query for example for a human CYP3A4 and the database suggests the animal homologs.

The source data is based generated from RNAseq experiments derived from healthy primary tissue samples gathered from public sources. No cell line or disease data is included #2068. Note that the databases also do not include protein abundance information as suggested #2034 #1332.

Feel free to check out the beta versions of Rat and Chicken. Let me know if you find bugs or have any suggestions, I'm happy to include them in the final release.

GENEDB_rat_TPM_ONLY_BgeeRelease_14_0_2022-01-26.zip GENEDB_rabbit_TPM_ONLY_BgeeRelease_14_1_2022-01-26.zip

Kind regards, Henrik

finattig commented 2 years ago

Hi, thank you for the update. Just to confirm:

GENEDB_rat_TPM_ONLY_BgeeRelease_14_0_2022-01-26.zip for Rats

GENEDB_rabbit_TPM_ONLY_BgeeRelease_14_1_2022-01-26.zip for Rabbits?

HenrikCordes commented 2 years ago

Hi @finattig,

yes, the rat_TPM database is supposed to be for the Rats in PK-Sim, same for Rabbits.

Please be aware that these are not officially released or supported databases.

The manuscript and code for the database generation are currently under review and once accepted, we will update / publish the latest peer-reviewed versions.

Best Henrik