Merge pull request #600 from SysBioChalmers/fix/updateNaPiTransportRx…

…nGPRs Fix/update na pi transport rxn gp rs
SysBioChalmers · May 31, 2023 · d93940b · d93940b
2 parents 8df35ec + 147a67d
commit d93940b
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Showing 4 changed files with 8 additions and 40 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -95,3 +95,5 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05295"	""	""	""	"r1110"	""	"NaKt"	""	"HMR_5295"	"RCR41002"	""	0	""	""	"HMR_5295"
 "MAR06895"	""	"GLCSGLT1le"	""	""	""	"GLCSGLT1le"	"MNXR100225"	""	""	""	0	""	""	"GLCSGLT1le"
 "MAR06894"	""	"GALSGLT1le"	""	""	""	"GALSGLT1le"	"MNXR100011"	""	""	""	0	""	""	"GALSGLT1le"
+"MAR05413"	""	"PIt2r"	""	""	""	"PIt6b"	"MNXR102872"	"HMR_5413"	"RCR41023"	""	0	"RHEA:29941"	"RHEA:29939"	"HMR_5413"
+"MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -171142,7 +171142,7 @@
           - MAM02751e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000112337 or ENSG00000124564 or ENSG00000124568 or ENSG00000131183 or ENSG00000146039 or ENSG00000157765"
+      - gene_reaction_rule: "ENSG00000112337 or ENSG00000124564 or ENSG00000124568 or ENSG00000131183 or ENSG00000146039 or ENSG00000157765 or ENSG00000144136 or ENSG00000168575"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -173129,24 +173129,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR05413"
-      - name: ""
-      - metabolites: !!omap
-          - MAM02039c: 1
-          - MAM02039e: -1
-          - MAM02751c: 1
-          - MAM02751e: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000144136 or ENSG00000168575"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR05429"
       - name: ""
@@ -230473,7 +230455,7 @@
           - MAM02751e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: ""
+      - gene_reaction_rule: "ENSG00000143324"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "4.2.1.1"
@@ -240074,24 +240056,6 @@
       - subsystem:
           - "Exchange/demand reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04411"
-      - name: "Phosphate Transport In/Out via Na+ Symporter"
-      - metabolites: !!omap
-          - MAM02519c: 1.5
-          - MAM02519e: -1.5
-          - MAM02751c: 1
-          - MAM02751e: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000144136 or ENSG00000168575"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:12759754"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04413"
       - name: "Generic Human Biomass Reaction"
@@ -312100,6 +312064,9 @@
     - !!omap
       - id: "ENSG00000143315"
       - name: "PIGM"
+    - !!omap
+      - id: "ENSG00000143324"
+      - name: "XPR1"
     - !!omap
       - id: "ENSG00000143344"
       - name: "RGL1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -1512,6 +1512,7 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000143258"	"ENST00000492950;ENST00000289865;ENST00000368002;ENST00000479344;ENST00000368001;ENST00000486299;ENST00000487163;ENST00000482385;ENST00000493054;ENST00000485277"	"ENSP00000476344;ENSP00000289865;ENSP00000356981;ENSP00000476830;ENSP00000356980;ENSP00000492693;ENSP00000491514"	"Q9UK80"	"USP21"	"27005"	"ubiquitin specific peptidase 21"	"USP16;USP23"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000143278"	"ENST00000649282;ENST00000367412;ENST00000490002"	"ENSP00000497116;ENSP00000356382"	"P05160"	"F13B"	"2165"	"coagulation factor XIII B chain"	"FXIIIB"	"Extracellular"	"DeepLoc2"
 "ENSG00000143315"	"ENST00000368090"	"ENSP00000357069"	"Q9H3S5"	"PIGM"	"93183"	"phosphatidylinositol glycan anchor biosynthesis class M"	"GPI-MT-I"	"Endoplasmic reticulum"	"DeepLoc2"
+"ENSG00000143324"	"ENST00000367590;ENST00000367589"	"ENSP00000356562;ENSP00000356561"	"Q9UBH6"	"XPR1"	"9213"	"xenotropic and polytropic retrovirus receptor 1"	"SYG1;X3;SLC53A1"	""	""
 "ENSG00000143344"	"ENST00000304685;ENST00000360851"	"ENSP00000303192;ENSP00000354097"	"Q9NZL6"	"RGL1"	"23179"	"ral guanine nucleotide dissociation stimulator like 1"	"RGL"	"Golgi apparatus;Nucleus"	"CellAtlas"
 "ENSG00000143363"	"ENST00000467771;ENST00000271620;ENST00000462440;ENST00000650332;ENST00000475722;ENST00000450884;ENST00000368937;ENST00000431193;ENST00000368936;ENST00000368935;ENST00000368934"	"ENSP00000271620;ENSP00000497847;ENSP00000387696;ENSP00000357933;ENSP00000392632;ENSP00000357932;ENSP00000357931;ENSP00000357930"	"Q86TP1"	"PRUNE1"	"58497"	"prune exopolyphosphatase 1"	"DRES-17;H-PRUNE;HTCD37;PRUNE"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000143379"	"ENST00000525956;ENST00000487584;ENST00000463774;ENST00000271640;ENST00000448029;ENST00000368962;ENST00000534805;ENST00000368969;ENST00000368963;ENST00000459773;ENST00000498193;ENST00000368964;ENST00000423081;ENST00000481219;ENST00000497314;ENST00000528749;ENST00000533529"	"ENSP00000435922;ENSP00000271640;ENSP00000409379;ENSP00000357958;ENSP00000436148;ENSP00000357965;ENSP00000357959;ENSP00000432348;ENSP00000357960;ENSP00000407831"	"Q15047"	"SETDB1"	"9869"	"SET domain bifurcated histone lysine methyltransferase 1"	"ESET;KG1T;KIAA0067;KMT1E;TDRD21"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -5435,7 +5435,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05332"	""	"GLUVESSEC"	""	""	""	"GLUVESSEC"	"MNXR100297"	"HMR_5332"	"RCR40227"	""	0	""	""	"HMR_5332"
 "MAR05333"	""	"HISt4"	""	"r1145"	""	"HISt4"	"MNXR100646"	"HMR_5333"	"RCR41021"	"2.A.18.6.5"	0	""	""	"HMR_5333"
 "MAR05335"	""	"HIStN1"	""	""	""	"HIStN1"	"MNXR100648"	"HMR_5335"	"RCR41022"	""	0	""	""	"HMR_5335"
-"MAR05413"	""	"PIt2r"	""	""	""	"PIt6b"	"MNXR102872"	"HMR_5413"	"RCR41023"	""	0	"RHEA:29941"	"RHEA:29939"	"HMR_5413"
 "MAR05429"	""	"NaKt"	""	"r1489"	""	""	"MNXR102073"	"HMR_5429"	"RCR41024"	"3.A.3.1.1"	0	""	""	"HMR_5429"
 "MAR05430"	""	"NAt3_1"	""	"r1490"	""	"NAt3_1"	"MNXR101803"	"HMR_5430"	"RCR41025"	"2.A.36.1.1"	0	""	""	"HMR_5430"
 "MAR05432"	""	"HCO3_NAt"	""	"r1491"	""	"HCO3_NAt"	"MNXR100485"	"HMR_5432"	"RCR41026"	"2.A.31.2.1"	0	""	""	"HMR_5432"
@@ -9244,7 +9243,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04405"	""	"EX_CE5853_e"	""	""	""	"EX_CE5853[e]"	"MNXR98128"	""	""	""	0	""	""	"EX_CE5853[e]"
 "MAR04407"	""	"EX_CE1925_e"	""	""	""	"EX_CE1925[e]"	"MNXR98104"	""	""	""	0	""	""	"EX_CE1925[e]"
 "MAR04409"	""	"EX_C04849_e"	""	""	""	"EX_C04849[e]"	"MNXR98102"	""	""	""	0	""	""	"EX_C04849[e]"
-"MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
 "MAR04413"	""	""	""	""	""	""	""	""	""	""	0	""	""	"biomass_Recon3D"
 "MAR04438"	""	"2MB2COAc"	""	""	""	"2MB2COAc"	"MNXR94807"	""	""	""	0	""	""	"2MB2COAc"
 "MAR04439"	""	"3HBCOARc"	""	""	""	"3HBCOARc"	"MNXR94892"	""	""	""	0	""	""	"3HBCOARc"