feat: remove pseudogenes, read through genes, and ones with only predicted functions

[haowang-bioinfo]

Description of the issue:

It is proposed to remove following genes, because they are either pseudogenes, or genes from read through transcripts (from two adjacent genes in the same strand with same orientation), or the ones with only predicted functions.

gene id	check results
ENSG00000011052	read through
ENSG00000099984	pseudogene
ENSG00000100101	novel transcript
ENSG00000114786	read through
ENSG00000125954	read through
ENSG00000133475	pseudogene
ENSG00000137700	with only predicted function
ENSG00000168970	read through
ENSG00000172782	with only predicted function
ENSG00000189366	pseudogene, only predicted function
ENSG00000250741	read through, no annotation
ENSG00000255730	with only predicted function
ENSG00000259030	read through
ENSG00000259075	read through, only predicted function
ENSG00000259916	only predicted function
ENSG00000272916	novel transcript, only predicted function
ENSG00000275183	only predicted function
ENSG00000276380	pseudogene
ENSG00000282301	read through
ENSG00000284844	only predicted function
ENSG00000285043	novel protein, without function annotation
ENSG00000285269	read through, only predicted function

[feiranl]

Looks good! May I know how these genes were identified here? I double checked some read through, which is clear. As for the novel protein or predicted function, I am not sure how to double check them

[haowang-bioinfo]

May I know how these genes were identified here?

very good question!

Now the number of genes is 2292 in genes.tsv. When loading all these Ensembl ids to uniprot.org/id-mapping for mapping to UniProtKB, then these genes pop out as unmapped.

As for the novel protein or predicted function, I am not sure how to double check them

Obviously they don't have annotated function by Uniprot. But they can be checked on Ensembl (eg, ENSG00000011052) and NCBI (654364)

[haowang-bioinfo]

as the only gene for MAR01621 and MAR06386, the deletion of ENSG00000137700 is suspended.

[haowang-bioinfo]

as the only gene for MAR01621 and MAR06386, the deletion of ENSG00000137700 is suspended.

as a follow-up, replace ENSG00000137700 with ENSG00000281500, because both refer to the same gene SLC37A4 while the later was reviewed with proper annotation and substrates.

[haowang-bioinfo]

now there are still 5 genes that are left unmapped to Uniprot, here are manually checked and associated as below:

Ensembl id	Uniprot id	check results
ENSG00000139304	A0A087WZU1	protein-tyrosine-phosphatase
ENSG00000161133	Q3LFD5	ubiquitin specific peptidase 41
ENSG00000175164	A0A087X009	predicted function
ENSG00000181222	A0A6Q8PGB0	DNA-dependent RNA polymerase
ENSG00000249948	Q9H227	beta-glucosidase, with both normal and pseudogene isoforms

[haowang-bioinfo]

fixed in #537