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fix: remove non-transporter genes #448
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Note that removal of CLTRN (ENSG00000147003) and SLC6A18 (ENSG00000164363) in this PR led to 14 amino acid transport reactions with empty GPR rules. These 14 reactions are retained as such. Further changes will be conducted when actual transporters are identified. |
@@ -172044,7 +172044,7 @@ | |||
- MAM02751c: 1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 | |||
- gene_reaction_rule: "(ENSG00000101892 and ENSG00000137731 and ENSG00000163399) or (ENSG00000018625 and ENSG00000129244 and ENSG00000137731) or (ENSG00000018625 and ENSG00000069849 and ENSG00000137731) or (ENSG00000101892 and ENSG00000105409 and ENSG00000137731) or (ENSG00000105409 and ENSG00000137731 and ENSG00000143153) or (ENSG00000105409 and ENSG00000129244 and ENSG00000137731) or (ENSG00000069849 and ENSG00000105409 and ENSG00000137731) or (ENSG00000101892 and ENSG00000132681 and ENSG00000137731) or (ENSG00000132681 and ENSG00000137731 and ENSG00000143153) or (ENSG00000129244 and ENSG00000132681 and ENSG00000137731) or (ENSG00000069849 and ENSG00000132681 and ENSG00000137731) or (ENSG00000137731 and ENSG00000143153 and ENSG00000163399) or (ENSG00000129244 and ENSG00000137731 and ENSG00000163399) or (ENSG00000069849 and ENSG00000137731 and ENSG00000163399) or (ENSG00000018625 and ENSG00000101892 and ENSG00000137731) or (ENSG00000018625 and ENSG00000137731 and ENSG00000143153)" |
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The first and you have removed here contains ENSG00000137731, which is not in the remove list in issue 444. I'm not sure if the other two are signaling enzymes that activates this enzyme, or how this works, but please check that this is correct.
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The same goes for ENSG00000163399. Looking this over is probably good.
@@ -172506,7 +172506,7 @@ | |||
- MAM02751c: 1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 | |||
- gene_reaction_rule: "(ENSG00000101892 and ENSG00000137731 and ENSG00000163399) or (ENSG00000018625 and ENSG00000129244 and ENSG00000137731) or (ENSG00000018625 and ENSG00000069849 and ENSG00000137731) or (ENSG00000101892 and ENSG00000105409 and ENSG00000137731) or (ENSG00000105409 and ENSG00000137731 and ENSG00000143153) or (ENSG00000105409 and ENSG00000129244 and ENSG00000137731) or (ENSG00000069849 and ENSG00000105409 and ENSG00000137731) or (ENSG00000101892 and ENSG00000132681 and ENSG00000137731) or (ENSG00000132681 and ENSG00000137731 and ENSG00000143153) or (ENSG00000129244 and ENSG00000132681 and ENSG00000137731) or (ENSG00000069849 and ENSG00000132681 and ENSG00000137731) or (ENSG00000137731 and ENSG00000143153 and ENSG00000163399) or (ENSG00000129244 and ENSG00000137731 and ENSG00000163399) or (ENSG00000069849 and ENSG00000137731 and ENSG00000163399) or (ENSG00000018625 and ENSG00000101892 and ENSG00000137731) or (ENSG00000018625 and ENSG00000137731 and ENSG00000143153)" |
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Same thing here
@@ -249224,8 +249224,8 @@ | |||
- MAM02519c: 1 | |||
- MAM02519e: -1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 | |||
- gene_reaction_rule: "ENSG00000147003 and ENSG00000164363" |
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ENSG00000147003 is not listed in issue 444.
@@ -249264,8 +249264,8 @@ | |||
- MAM02519c: 1 | |||
- MAM02519e: -1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 | |||
- gene_reaction_rule: "ENSG00000147003 and ENSG00000164363" |
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Same here
@@ -249284,8 +249284,8 @@ | |||
- MAM02519c: 1 | |||
- MAM02519e: -1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 | |||
- gene_reaction_rule: "ENSG00000147003 and ENSG00000164363" |
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and here
@@ -249362,8 +249362,8 @@ | |||
- MAM02519c: 1 | |||
- MAM02519e: -1 | |||
- lower_bound: 0 | |||
- upper_bound: 1000 |
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and here
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And a whole bunch of places further down
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Can you take a look at the comments I added - I some of the removed genes are not in the removal list in issue 444.
good job @johan-gson, you correctly pinpointed the mistakes I made, now close this to fix the problme. |
The removal of ENSG00000137731 and ENSG00000163399 is due to ENSG00000101892, while ENSG00000147003 was removed because of ENSG00000164363. They are subunits of two complexes that are striped away as a whole when any subunit is deleted. To avoid this unexpected outcome, ENSG00000101892 and ENSG00000164363 are taken away from the list in #444, while the updated change is implemented afresh in #450. |
Main improvements in this PR:
Transporter reactions
, as proposed in remove non-transporter genes from transport reactions #444I hereby confirm that I have:
develop
as a target branch