Implement expression data from GTEx and Descartes for Gene curation

[constantinwolff]

Use data from GTEx https://gtexportal.org/home/ and Descartes https://descartes.brotmanbaty.org/bbi/human-gene-expression-during-development/dataset/kidney :

-consider using GTEx function of Multi-Gene Query to compare the different Genes regarding a CutOff value --> as CutOff value the TPMs could be valid for division into 4-5 different categories -TPM (take median TPM) evidence is explained here: https://gtexportal.org/home/methods ; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356847/ ; https://www.ebi.ac.uk/gxa/FAQ.html -also consider other quality controls as negative CutOffs

-EBI categorization (expression atlas): _1. White box: there is no data available (0.0 FPKM 0.0 TPM)

2. Yellow box: expression level is below cutoff (0.5 FPKM or 0.5 TPM)
3. Light blue box: expression level is low (between 0.5 to 10 FPKM or 0.5 to 10 TPM)
4. Medium blue box: expression level is medium (between 11 to 1000 FPKM or 11 to 1000 TPM)
5. Dark blue box: expression level is high (more than 1000 FPKM or more than 1000 TPM)_

-GTEx categorization: _1. yellow: 0.0 TPM

2. light green: >3.6 TPM
3. dark green: >20.0 TPM
4. light blue: >98.0 TPM
5. medium blue: >460.0 TPM
6. dark blue: >2100.0 TPM_

TODO:

• [x] use GTEx data for adult expression with categorization into the above mentioned 6 groups
• [x] use Descartes data for developmental expression with categorization into the above mentioned 6 groups
• [x] mark the cutoffs in the respective columns of the output table

--> while using Descartes pay attention of selecting the right tissue --> kidney (then you have only kidney expression) --> TPM values for Descartes and GTEx aren't normalized... in fact they should be comparable

[berntpopp]

see the link to the current GTEx API: https://gtexportal.org/api/v2/redoc#tag/GTEx-Portal-API-Info

[berntpopp]

Add the gene_version to HGNC table using gnomAD EP at: https://gnomad.broadinstitute.org/api/