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fix: GPR curation for transport reactions (6) #956

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Jan 13, 2025
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62 changes: 23 additions & 39 deletions model/Human-GEM.yml
Original file line number Diff line number Diff line change
Expand Up @@ -149956,7 +149956,7 @@
- MAM02900e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700"
- gene_reaction_rule: "ENSG00000084453 or ENSG00000111700"
- rxnFrom: "HMRdatabase"
- references: "PMID:14579113"
- subsystem:
Expand Down Expand Up @@ -150126,7 +150126,7 @@
- MAM02901e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700"
- gene_reaction_rule: "ENSG00000084453 or ENSG00000111700"
- rxnFrom: "HMRdatabase"
- references: "PMID:14579113"
- subsystem:
Expand Down Expand Up @@ -150458,7 +150458,6 @@
- MAM02170e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000169710"
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.85"
- references: "PMID:1550832;PMID:8438778"
Expand Down Expand Up @@ -151472,7 +151471,7 @@
- MAM01986e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000164363 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000164363"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151485,7 +151484,7 @@
- MAM01307e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000155465"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151498,7 +151497,7 @@
- MAM01975e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151511,7 +151510,7 @@
- MAM02896e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151524,7 +151523,7 @@
- MAM03089e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151537,7 +151536,7 @@
- MAM02724e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000112394 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151550,7 +151549,7 @@
- MAM01628e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151563,7 +151562,7 @@
- MAM02360e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151576,7 +151575,7 @@
- MAM02770e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003989 or ENSG00000092068 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "ENSG00000092068 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151589,7 +151588,7 @@
- MAM01369e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151602,7 +151601,7 @@
- MAM03135e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand All @@ -151615,7 +151614,7 @@
- MAM02993e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand Down Expand Up @@ -155072,7 +155071,7 @@
- MAM02724e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -155276,7 +155275,7 @@
- MAM02896e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000105281"
- gene_reaction_rule: "ENSG00000105281"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -155871,7 +155870,7 @@
- MAM03089e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -156007,7 +156006,6 @@
- MAM02724e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -157603,7 +157601,6 @@
- MAM03135e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -158164,7 +158161,6 @@
- MAM02770e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -161260,7 +161256,7 @@
- MAM02403e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- gene_reaction_rule: "ENSG00000100156 or ENSG00000118596 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- rxnFrom: "HMRdatabase"
- references: "PMID:12739169"
- subsystem:
Expand Down Expand Up @@ -161500,7 +161496,7 @@
- MAM02833e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- gene_reaction_rule: "ENSG00000100156 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- rxnFrom: "HMRdatabase"
- references: "PMID:12739169"
- subsystem:
Expand Down Expand Up @@ -166516,7 +166512,6 @@
- MAM01517g: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000174669"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -170108,7 +170103,7 @@
- MAM02519e: -2
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000196517 or ENSG00000268104"
- gene_reaction_rule: "ENSG00000268104"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -173575,7 +173570,6 @@
- MAM01642m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172"
- subsystem:
Expand Down Expand Up @@ -173665,7 +173659,6 @@
- MAM02914m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000160190"
- rxnFrom: "HMRdatabase"
- references: "PMID:12811562"
- subsystem:
Expand Down Expand Up @@ -173976,7 +173969,6 @@
- MAM01680m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -174214,7 +174206,6 @@
- MAM01756m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -174452,7 +174443,6 @@
- MAM01747m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -177314,7 +177304,6 @@
- MAM02471l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000123643"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand Down Expand Up @@ -177429,7 +177418,6 @@
- MAM02993l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000123643"
- rxnFrom: "HMRdatabase"
- references: "PMID:911815"
- subsystem:
Expand Down Expand Up @@ -179499,7 +179487,7 @@
- MAM02200g: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000065923 or ENSG00000197818"
- gene_reaction_rule: "ENSG00000065923"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -210617,7 +210605,6 @@
- MAM02770e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115902"
- rxnFrom: "Recon3D"
- references: "PMID:14502423;PMID:11824937"
- subsystem:
Expand Down Expand Up @@ -212865,7 +212852,7 @@
- MAM02946e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000137204 or ENSG00000149452 or ENSG00000168065"
- gene_reaction_rule: "ENSG00000137204 or ENSG00000149452"
- rxnFrom: "Recon3D"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -215335,7 +215322,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000073734 or ENSG00000108846 or ENSG00000121270"
- gene_reaction_rule: "ENSG00000073734 or ENSG00000108846"
- rxnFrom: "Recon3D"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -265896,9 +265883,6 @@
- !!omap
- id: "ENSG00000160179"
- name: "ABCG1"
- !!omap
- id: "ENSG00000160190"
- name: "SLC37A1"
- !!omap
- id: "ENSG00000160191"
- name: "PDE9A"
Expand Down
1 change: 0 additions & 1 deletion model/genes.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -1815,7 +1815,6 @@
"ENSG00000160014" "ENST00000391918;ENST00000597743;ENST00000477244;ENST00000598871;ENST00000291295;ENST00000595072;ENST00000602169;ENST00000594523;ENST00000597868;ENST00000599839;ENST00000596362;ENST00000482455;ENST00000486500" "ENSP00000375785;ENSP00000470308;ENSP00000470502;ENSP00000291295;ENSP00000499372;ENSP00000468877;ENSP00000471225;ENSP00000472141" "P0DP25" "CALM3" "808" "calmodulin 3" "PHKD" "Cytosol" "SwissProt"
"ENSG00000160087" "ENST00000450390;ENST00000349431;ENST00000400929;ENST00000464036;ENST00000360466;ENST00000400930;ENST00000467339;ENST00000473215;ENST00000435198;ENST00000509720;ENST00000491779;ENST00000466752;ENST00000503294;ENST00000477894;ENST00000471154;ENST00000422076;ENST00000502382;ENST00000461142;ENST00000488418;ENST00000347370" "ENSP00000407565;ENSP00000305826;ENSP00000383718;ENSP00000423880;ENSP00000353653;ENSP00000383719;ENSP00000427024;ENSP00000393301;ENSP00000425419;ENSP00000422103;ENSP00000425543;ENSP00000423480;ENSP00000401898;ENSP00000424342;ENSP00000427244;ENSP00000344857" "Q8N2K1" "UBE2J2" "118424" "ubiquitin conjugating enzyme E2 J2" "NCUBE2;Ubc6p" "Endoplasmic reticulum" "SwissProt"
"ENSG00000160179" "ENST00000398457;ENST00000462050;ENST00000347800;ENST00000450121;ENST00000361802;ENST00000398449;ENST00000343687;ENST00000398437;ENST00000472587;ENST00000467818;ENST00000496783" "ENSP00000381475;ENSP00000291524;ENSP00000414541;ENSP00000354995;ENSP00000381467;ENSP00000339744;ENSP00000381464" "P45844" "ABCG1" "9619" "ATP binding cassette subfamily G member 1" "ABC8" "Endoplasmic reticulum;Golgi apparatus" "SwissProt;CellAtlas"
"ENSG00000160190" "ENST00000454800;ENST00000419522;ENST00000398341;ENST00000484887;ENST00000352133;ENST00000471277;ENST00000398343;ENST00000487951;ENST00000496416" "ENSP00000410129;ENSP00000381383;ENSP00000344648;ENSP00000381385" "P57057" "SLC37A1" "54020" "solute carrier family 37 member 1" "" "Cell membrane;Endoplasmic reticulum" "DeepLoc2"
"ENSG00000160191" "ENST00000291539;ENST00000460905;ENST00000472401;ENST00000335512;ENST00000470987;ENST00000490803;ENST00000486902;ENST00000328862;ENST00000335440;ENST00000380328;ENST00000398225;ENST00000398227;ENST00000398229;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000460989;ENST00000462571;ENST00000467403;ENST00000468805;ENST00000495521;ENST00000497805;ENST00000349112;ENST00000398224;ENST00000467162;ENST00000495343;ENST00000489319;ENST00000466472" "ENSP00000291539;ENSP00000335242;ENSP00000328699;ENSP00000335365;ENSP00000369685;ENSP00000381281;ENSP00000381283;ENSP00000381285;ENSP00000381287;ENSP00000381289;ENSP00000381291;ENSP00000344730;ENSP00000381280" "O76083" "PDE9A" "5152" "phosphodiesterase 9A" "" "Endoplasmic reticulum;Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000160194" "ENST00000460259;ENST00000340344;ENST00000354250;ENST00000460740" "ENSP00000342895;ENSP00000346196" "P56181" "NDUFV3" "4731" "NADH:ubiquinone oxidoreductase subunit V3" "CI-10k" "Inner mitochondria" "SwissProt;CellAtlas"
"ENSG00000160200" "ENST00000461686;ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000451248;ENST00000462349;ENST00000491776;ENST00000458223;ENST00000430013;ENST00000496485;ENST00000486098;ENST00000441030;ENST00000470912;ENST00000465732;ENST00000488526;ENST00000478709" "ENSP00000381225;ENSP00000381231;ENSP00000352643;ENSP00000344460;ENSP00000402823;ENSP00000408014;ENSP00000405929;ENSP00000388235" "P35520" "CBS" "875" "cystathionine beta-synthase" "HIP4" "Nucleus;Cytosol" "SwissProt;CellAtlas"
Expand Down
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