Fix-remove unused genes

SysBioChalmers · Oct 23, 2024 · fdcd122 · fdcd122
1 parent e94dcf0
commit fdcd122
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diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -308924,9 +308924,6 @@
     - !!omap
       - id: "ENSG00000139914"
       - name: "FITM1"
-    - !!omap
-      - id: "ENSG00000139977"
-      - name: "NAA30"
     - !!omap
       - id: "ENSG00000139988"
       - name: "RDH12"
@@ -309920,9 +309917,6 @@
     - !!omap
       - id: "ENSG00000156256"
       - name: "USP16"
-    - !!omap
-      - id: "ENSG00000156269"
-      - name: "NAA11"
     - !!omap
       - id: "ENSG00000156411"
       - name: "ATP5MJ"
@@ -312074,9 +312068,6 @@
     - !!omap
       - id: "ENSG00000183654"
       - name: "MARCHF11"
-    - !!omap
-      - id: "ENSG00000183665"
-      - name: "TRMT12"
     - !!omap
       - id: "ENSG00000183696"
       - name: "UPP1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -1409,7 +1409,6 @@ ENSG00000139631	"ENST00000267085;ENST00000475890;ENST00000379850;ENST00000379846
 ENSG00000139684	"ENST00000378720;ENST00000378697;ENST00000412582;ENST00000471867;ENST00000495654"	"ENSP00000367992;ENSP00000367969;ENSP00000391350;ENSP00000476193"	P10768	ESD	2098	esterase D		"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000139718	"ENST00000604567;ENST00000542440;ENST00000619791;ENST00000267197"	"ENSP00000474253;ENSP00000442924;ENSP00000481531;ENSP00000267197"	Q9UPS6	SETD1B	23067	SET domain containing 1B, histone lysine methyltransferase	"KIAA1076;KMT2G;Set1B"	Nucleus	"SwissProt;CellAtlas"
 ENSG00000139914	"ENST00000267426;ENST00000559294"	"ENSP00000267426;ENSP00000453741"	A5D6W6	FITM1	161247	fat storage inducing transmembrane protein 1	FIT1	Endoplasmic reticulum	DeepLoc2
-ENSG00000139977	"ENST00000555166;ENST00000556492;ENST00000554703;ENST00000298406"	"ENSP00000450939;ENSP00000452521;ENSP00000451255;ENSP00000298406"	Q147X3	NAA30	122830	N-alpha-acetyltransferase 30, NatC catalytic subunit	"C14orf35;FLJ35355;MAK3;Mak3p;NAT12"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000139988	"ENST00000551171;ENST00000547463;ENST00000267502;ENST00000552873"	"ENSP00000449079;ENSP00000267502"	Q96NR8	RDH12	145226	retinol dehydrogenase 12	"FLJ30273;LCA13;RP53;SDR7C2"	Endoplasmic reticulum	SwissProt
 ENSG00000140057	"ENST00000267584;ENST00000555570;ENST00000556643;ENST00000554313;ENST00000554706"	"ENSP00000267584;ENSP00000451068;ENSP00000450453"	Q96M32	AK7	122481	adenylate kinase 7	"CFAP75;FAP75;FLJ32864"	Cytosol	SwissProt
 ENSG00000140090	"ENST00000393265;ENST00000532405;ENST00000676001;ENST00000531433;ENST00000554461;ENST00000525557;ENST00000554925;ENST00000556739;ENST00000526482"	"ENSP00000376948;ENSP00000431840;ENSP00000502715;ENSP00000433302;ENSP00000452099;ENSP00000432464"	Q8NFF2	SLC24A4	123041	solute carrier family 24 member 4	NCKX4	Cytosol	SwissProt
@@ -1739,7 +1738,6 @@ ENSG00000156136	"ENST00000509617;ENST00000286648;ENST00000503359;ENST00000504730
 ENSG00000156219	"ENST00000513353;ENST00000510669;ENST00000341029;ENST00000513122;ENST00000504914;ENST00000355810;ENST00000349321;ENST00000513494;ENST00000510423;ENST00000395688;ENST00000504112;ENST00000506667;ENST00000506313;ENST00000511188;ENST00000510863"	"ENSP00000421345;ENSP00000343843;ENSP00000422287;ENSP00000421431;ENSP00000348064;ENSP00000304313;ENSP00000425327;ENSP00000422249"	Q13508	ART3	419	ADP-ribosyltransferase 3 (inactive)	ARTC3	Cell membrane	DeepLoc2
 ENSG00000156222	"ENST00000338602;ENST00000538177;ENST00000394573;ENST00000286749"	"ENSP00000341629;ENSP00000443752;ENSP00000378074;ENSP00000286749"	O00337	SLC28A1	9154	solute carrier family 28 member 1	CNT1	"Cytosol;Nucleus"	CellAtlas
 ENSG00000156256	"ENST00000399975;ENST00000399976;ENST00000334352;ENST00000474835;ENST00000399973;ENST00000485067"	"ENSP00000382857;ENSP00000382858;ENSP00000334808;ENSP00000382855"	Q9Y5T5	USP16	10600	ubiquitin specific peptidase 16	Ubp-M	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-ENSG00000156269	"ENST00000511542;ENST00000513733;ENST00000286794"	"ENSP00000422022;ENSP00000286794"	Q9BSU3	NAA11	84779	N-alpha-acetyltransferase 11, NatA catalytic subunit	"ARD1B;ARD2;hARD2"	"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000156411	"ENST00000286953;ENST00000554880;ENST00000555030;ENST00000414262;ENST00000553430;ENST00000554287;ENST00000557040;ENST00000553449;ENST00000554089;ENST00000554713;ENST00000557260;ENST00000554528"	"ENSP00000286953;ENSP00000452133;ENSP00000452186;ENSP00000401770;ENSP00000452462;ENSP00000450894;ENSP00000451500"	P56378	ATP5MJ	9556	ATP synthase membrane subunit j	"6.8PL;ATP5MPL;C14orf2;MLQ;MP68"	"Mitochondria;Nucleus"	CellAtlas
 ENSG00000156413	"ENST00000318336;ENST00000524754;ENST00000527106;ENST00000286955;ENST00000592563;ENST00000531085;ENST00000531199;ENST00000532464;ENST00000528505;ENST00000526499;ENST00000591079"	"ENSP00000313398;ENSP00000431708;ENSP00000432954;ENSP00000286955;ENSP00000466016;ENSP00000432161;ENSP00000436413;ENSP00000431880;ENSP00000433811"	P51993	FUT6	2528	fucosyltransferase 6	"FCT3A;FLJ40754;FT1A;FucT-VI"	Golgi apparatus	"SwissProt;CellAtlas"
 ENSG00000156463	"ENST00000359120;ENST00000506591;ENST00000511217;ENST00000509286;ENST00000503848;ENST00000511705;ENST00000504522"	"ENSP00000352028;ENSP00000424497"	Q8TEC5	SH3RF2	153769	SH3 domain containing ring finger 2	"FLJ23654;Hepp1;POSHER;PPP1R39;RNF158"	Nucleus	"SwissProt;CellAtlas"
@@ -2449,7 +2447,6 @@ ENSG00000183479	"ENST00000370231;ENST00000393862;ENST00000330912;ENST00000334497
 ENSG00000183549	"ENST00000575584;ENST00000331849;ENST00000575070;ENST00000570305;ENST00000574748;ENST00000573920;ENST00000577024"	"ENSP00000460112;ENSP00000327916;ENSP00000478073;ENSP00000461752"	Q6NUN0	ACSM5	54988	acyl-CoA synthetase medium chain family member 5	FLJ20581	Mitochondria	SwissProt
 ENSG00000183648	"ENST00000553514;ENST00000605997;ENST00000329559;ENST00000553666;ENST00000555441;ENST00000617122;ENST00000556555"	"ENSP00000451090;ENSP00000475170;ENSP00000330787;ENSP00000450776;ENSP00000483888"	O75438	NDUFB1	4707	NADH:ubiquinone oxidoreductase subunit B1	"CI-MNLL;MNLL"	"Nucleus;Inner mitochondria"	"SwissProt;CellAtlas"
 ENSG00000183654	"ENST00000332432;ENST00000507111;ENST00000505509"	"ENSP00000333181;ENSP00000424425"	A6NNE9	MARCHF11	441061	membrane associated ring-CH-type finger 11	"MARCH-XI;MARCH11;RNF226"	"Cell membrane;Endoplasmic reticulum;Lysosome;Golgi apparatus"	DeepLoc2
-ENSG00000183665	"ENST00000328599;ENST00000521443;ENST00000522518"	"ENSP00000329858;ENSP00000429771"	Q53H54	TRMT12	55039	tRNA methyltransferase 12 homolog	"FLJ20772;Trm12;TYW2"	"Mitochondria;Nucleus"	CellAtlas
 ENSG00000183696	"ENST00000416681;ENST00000331803;ENST00000432131;ENST00000457596;ENST00000421046;ENST00000395564;ENST00000436673;ENST00000395560;ENST00000444999;ENST00000482015;ENST00000417464;ENST00000495446"	"ENSP00000405209;ENSP00000330032;ENSP00000387607;ENSP00000408899;ENSP00000414963;ENSP00000378931;ENSP00000390118;ENSP00000378927;ENSP00000396820;ENSP00000413611"	Q16831	UPP1	7378	uridine phosphorylase 1	"UDRPASE;UP;UPASE;UPP"	Nucleus	CellAtlas
 ENSG00000183747	"ENST00000574251;ENST00000570698;ENST00000573854;ENST00000576361;ENST00000417235;ENST00000575558;ENST00000219054;ENST00000575690;ENST00000571204;ENST00000574692;ENST00000571894;ENST00000396104;ENST00000572921;ENST00000572843;ENST00000576101;ENST00000576119"	"ENSP00000460153;ENSP00000459451;ENSP00000460948;ENSP00000392169;ENSP00000219054;ENSP00000460349;ENSP00000460884;ENSP00000460031;ENSP00000379411"	Q08AH3	ACSM2A	123876	acyl-CoA synthetase medium chain family member 2A	"A-923A4.1;ACSM2;MGC150530"	Mitochondria	SwissProt
 ENSG00000183760	"ENST00000601575;ENST00000331256;ENST00000594229;ENST00000601531"	"ENSP00000469048;ENSP00000327557;ENSP00000470989;ENSP00000470089"	Q6ZNF0	ACP7	390928	acid phosphatase 7, tartrate resistant (putative)	"FLJ16165;PAPL;PAPL1"	"Extracellular;Lysosome"	DeepLoc2