GORULE violations assigned by ParkinsonsUK-UCL

Contents

gorule-0000020 Violates GORULE:0000020

gorule-0000046 GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms

gorule-0000061 GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0001025 should be one of BFO:0000050

MESSAGES

gorule-0000020

Violates GORULE:0000020

• total: 33

messages

• MGI MGI:98953 Wnt1 enables GO:0048018 MGI:MGI:5770063|PMID:21752258 IC GO:1903204 F wingless-type MMTV integration site family, member 1 Int-1|Wnt-1 protein_coding_gene taxon:10090 20160914 ParkinsonsUK-UCL has_input(UniProtKB:O70421),part_of(GO:0060070)
• FB FBgn0034366 Atg7 involved_in GO:0060548 FB:FBrf0255270|GO_REF:0000024 ISS UniProtKB:Q9D906 P Autophagy-related 7 ATG-7|ATG7|Autophagy-specific gene 7|CG5489|atg-7|atg7|autophagy-related gene 7|autophagy-related protein 7|dAtg7 protein taxon:7227 20150310 ParkinsonsUK-UCL
• UniProtKB O15354 GPR37 involved_in GO:1903206 PMID:23690594 ISS UniProtKB:Q9QY42 P Prosaposin receptor GPR37 GPR37 protein taxon:9606 20140916 ParkinsonsUK-UCL
• UniProtKB O43272 PRODH involved_in GO:0010942 PMID:23743200 IDA P Proline dehydrogenase 1, mitochondrial PRODH|PIG6|POX2|PRODH2 protein taxon:9606 20160125 ParkinsonsUK-UCL
• UniProtKB O60260 PRKN involved_in GO:1903202 PMID:24252804 TAS P E3 ubiquitin-protein ligase parkin PRKN|PARK2 protein taxon:9606 20140911 ParkinsonsUK-UCL
• UniProtKB O60260 PRKN involved_in GO:1903202 PMID:24522549 NAS P E3 ubiquitin-protein ligase parkin PRKN|PARK2 protein taxon:9606 20140827 ParkinsonsUK-UCL
• UniProtKB O60883 GPR37L1 involved_in GO:1903206 PMID:23690594 ISS UniProtKB:Q99JG2 P G-protein coupled receptor 37-like 1 GPR37L1|ETBRLP2 protein taxon:9606 20140916 ParkinsonsUK-UCL
• UniProtKB O75460 ERN1 involved_in GO:0098787 PMID:21317875 IDA P Serine/threonine-protein kinase/endoribonuclease IRE1 ERN1|IRE1 protein taxon:9606 20180227 ParkinsonsUK-UCL has_input(UniProtKB:P17861),part_of(GO:0070054)
• UniProtKB P04062 GBA1 NOT|involved_in GO:0036473 PMID:25456120 IMP P Lysosomal acid glucosylceramidase GBA1|GBA|GC|GLUC protein taxon:9606 20160909 ParkinsonsUK-UCL
• UniProtKB P08254 MMP3 involved_in GO:1903209 GO_REF:0000024 ISS UniProtKB:P28862 P Stromelysin-1 MMP3|STMY1 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB P0DMV9 HSPA1B involved_in GO:0060548 PMID:12150907 IDA P Heat shock 70 kDa protein 1B HSPA1B|HSP72 protein taxon:9606 20150622 ParkinsonsUK-UCL
• UniProtKB P10599 TXN involved_in GO:1903206 PMID:22492997 IGI UniProtKB:Q99497 P Thioredoxin TXN|TRDX|TRX|TRX1 protein taxon:9606 20140915 ParkinsonsUK-UCL
• UniProtKB P18848 ATF4 involved_in GO:1903204 PMID:23392669 IGI UniProtKB:Q9ES19 P Cyclic AMP-dependent transcription factor ATF-4 ATF4|CREB2|TXREB protein taxon:9606 20140728 ParkinsonsUK-UCL
• UniProtKB P32322 PYCR1 involved_in GO:1903206 PMID:23743200 IMP P Pyrroline-5-carboxylate reductase 1, mitochondrial PYCR1 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB P35232 PHB1 involved_in GO:0010942 PMID:26310625 IGI UniProtKB:Q9Y3I1 P Prohibitin 1 PHB1|PHB protein taxon:9606 20160719 ParkinsonsUK-UCL
• UniProtKB P63244 RACK1 involved_in GO:1903208 PMID:24947010 IGI UniProtKB:Q99497 P Receptor of activated protein C kinase 1 RACK1|GNB2L1|HLC7|PIG21 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB Q04637 EIF4G1 involved_in GO:0010942 PMID:25533483 IGI UniProtKB:P32319 P Eukaryotic translation initiation factor 4 gamma 1 EIF4G1|EIF4F|EIF4G|EIF4GI protein taxon:9606 20170712 ParkinsonsUK-UCL
• UniProtKB Q04637 EIF4G1 involved_in GO:0010942 PMID:25533483 IGI UniProtKB:P34110,UniProtKB:Q96QK1 P Eukaryotic translation initiation factor 4 gamma 1 EIF4G1|EIF4F|EIF4G|EIF4GI protein taxon:9606 20170712 ParkinsonsUK-UCL has_input(UniProtKB:Q96QK1),part_of(GO:0034620)
• UniProtKB Q16236 NFE2L2 involved_in GO:1903206 PMID:22492997 IGI UniProtKB:Q99497 P Nuclear factor erythroid 2-related factor 2 NFE2L2|NRF2 protein taxon:9606 20140915 ParkinsonsUK-UCL
• UniProtKB Q5S007 LRRK2 involved_in GO:1903206 PMID:24576675 IMP P Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2|PARK8 protein taxon:9606 20140826 ParkinsonsUK-UCL
• UniProtKB Q96M98 PACRG involved_in GO:0060548 PMID:14532270 IMP P Parkin coregulated gene protein PACRG|GLUP protein taxon:9606 20140918 ParkinsonsUK-UCL
• UniProtKB Q96QK1 VPS35 involved_in GO:0060548 PMID:25533483 IGI UniProtKB:P34110,UniProtKB:Q04637 P Vacuolar protein sorting-associated protein 35 VPS35|MEM3|TCCCTA00141 protein taxon:9606 20170712 ParkinsonsUK-UCL has_input(UniProtKB:Q96QK1),part_of(GO:0034620)
• UniProtKB Q99497 PARK7 involved_in GO:0060548 PMID:14749723 IDA P Parkinson disease protein 7 PARK7 protein taxon:9606 20140624 ParkinsonsUK-UCL part_of(GO:0034599)
• UniProtKB Q99497 PARK7 involved_in GO:1903202 PMID:16632486 IDA P Parkinson disease protein 7 PARK7 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB Q99497 PARK7 involved_in GO:1903206 PMID:22492997 IMP P Parkinson disease protein 7 PARK7 protein taxon:9606 20140915 ParkinsonsUK-UCL
• UniProtKB Q99497 PARK7 involved_in GO:1903206 PMID:23743200 IMP P Parkinson disease protein 7 PARK7 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB Q99497 PARK7 involved_in GO:1903208 PMID:15983381 IDA P Parkinson disease protein 7 PARK7 protein taxon:9606 20140722 ParkinsonsUK-UCL part_of(GO:0070301)
• UniProtKB Q99497 PARK7 involved_in GO:1903208 PMID:24947010 IDA P Parkinson disease protein 7 PARK7 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB Q9BXM7 PINK1 involved_in GO:1903202 PMID:16632486 IDA P Serine/threonine-protein kinase PINK1, mitochondrial PINK1 protein taxon:9606 20140722 ParkinsonsUK-UCL
• UniProtKB Q9BXM7 PINK1 involved_in GO:1903204 PMID:24522549 TAS P Serine/threonine-protein kinase PINK1, mitochondrial PINK1 protein taxon:9606 20140827 ParkinsonsUK-UCL
• UniProtKB Q9Y3I1 FBXO7 involved_in GO:1903204 PMID:25029497 IMP P F-box only protein 7 FBXO7|FBX7 protein taxon:9606 20160913 ParkinsonsUK-UCL
• UniProtKB Q9Y3I1 FBXO7 involved_in GO:1903208 PMID:26310625 IDA P F-box only protein 7 FBXO7|FBX7 protein taxon:9606 20170207 ParkinsonsUK-UCL occurs_in(CL:0000700) UniProtKB:Q9Y3I1-1
• UniProtKB Q9Y3I1 FBXO7 involved_in GO:1903208 PMID:26310625 IDA P F-box only protein 7 FBXO7|FBX7 protein taxon:9606 20170207 ParkinsonsUK-UCL occurs_in(CL:0000700) UniProtKB:Q9Y3I1-2

gorule-0000046

GORULE:0000046: The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms

• total: 7

messages

• MGI MGI:1921256 Dnm1l enables GO:0042803 MGI:MGI:4459561|PMID:20585624 IPI UniProtKB:Q8K1M6 F dynamin 1-like 6330417M19Rik|Dnmlp1|Drp1|python protein_coding_gene taxon:10090 20230309 ParkinsonsUK-UCL
• MGI MGI:1352504 Hip1r enables GO:0042803 MGI:MGI:5805365|PMID:18790740 IPI UniProtKB:Q9JKY5 F huntingtin interacting protein 1 related protein_coding_gene taxon:10090 20230309 ParkinsonsUK-UCL
• MGI MGI:1352504 Hip1r enables GO:0042803 MGI:MGI:5763378|PMID:15533940 IPI UniProtKB:Q9JKY5 F huntingtin interacting protein 1 related protein_coding_gene taxon:10090 20230309 ParkinsonsUK-UCL
• MGI MGI:1352504 Hip1r enables GO:0042803 MGI:MGI:5805370|PMID:11564758 IPI UniProtKB:Q9JKY5 F huntingtin interacting protein 1 related protein_coding_gene taxon:10090 20230309 ParkinsonsUK-UCL
• RGD 2326 Cebpa enables GO:0042803 PMID:8657121|RGD:1599740 IPI UniProtKB:P05554 F CCAAT/enhancer binding protein alpha gene taxon:10116 20141016 ParkinsonsUK-UCL
• RGD 619781 Erp29 enables GO:0042803 PMID:9714535|RGD:10047223 IPI UniProtKB:P52555 F endoplasmic reticulum protein 29 gene taxon:10116 20230309 ParkinsonsUK-UCL
• RGD 68397 Syt4 enables GO:0042803 PMID:10397765|RGD:11535116 IPI UniProtKB:P50232 F synaptotagmin 4 gene taxon:10116 20230309 ParkinsonsUK-UCL

gorule-0000061

GORULE:0000061: Found violation of: `Only certain gene product to term relations are allowed for a given GO term` but was repaired: RO:0001025 should be one of BFO:0000050

• total: 16

messages

• MGI MGI:1934811 Nucks1 located_in GO:0000785 MGI:MGI:5695791|PMID:26205492 IDA C nuclear casein kinase and cyclin-dependent kinase substrate 1 2700010L10Rik|8430423A01Rik|Nucks protein_coding_gene taxon:10090 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167)
• RGD 3738 Sp1 located_in GO:0000785 PMID:26908121|RGD:11059577 IDA C Sp1 transcription factor gene taxon:10116 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167),part_of(CL:0000746)
• RGD 727889 Rela located_in GO:0000785 PMID:26908121|RGD:11059577 IDA C RELA proto-oncogene, NF-kB subunit gene taxon:10116 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167),part_of(CL:0000746) UniProtKB:Q7TQN4
• UniProtKB O15047 SETD1A located_in GO:0000785 PMID:27141965 IDA C Histone-lysine N-methyltransferase SETD1A SETD1A|KIAA0339|KMT2F|SET1|SET1A protein taxon:9606 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167)
• UniProtKB O43464 HTRA2 located_in GO:0000785 PMID:24798695 IDA C Serine protease HTRA2, mitochondrial HTRA2|OMI|PRSS25 protein taxon:9606 20140701 ParkinsonsUK-UCL
• UniProtKB P21675 TAF1 located_in GO:0000785 PMID:20181722 IDA C Transcription initiation factor TFIID subunit 1 TAF1|BA2R|CCG1|CCGS|TAF2A protein taxon:9606 20210107 ParkinsonsUK-UCL existence_overlaps(GO:0071383),coincident_with(SO:0001668)|existence_overlaps(GO:0071383),coincident_with(SO:0000165)
• UniProtKB P22415 USF1 located_in GO:0000785 PMID:27141965 IDA C Upstream stimulatory factor 1 USF1|BHLHB11|USF protein taxon:9606 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167)
• UniProtKB P23246 SFPQ located_in GO:0000785 PMID:16731528 IDA C Splicing factor, proline- and glutamine-rich SFPQ|PSF protein taxon:9606 20140716 ParkinsonsUK-UCL
• UniProtKB Q06609 RAD51 located_in GO:0000785 PMID:26323318 IDA C DNA repair protein RAD51 homolog 1 RAD51|RAD51A|RECA protein taxon:9606 20160602 ParkinsonsUK-UCL existence_overlaps(GO:0006974)
• UniProtKB Q12830 BPTF located_in GO:0000785 PMID:27141965 IDA C Nucleosome-remodeling factor subunit BPTF BPTF|FAC1|FALZ protein taxon:9606 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167)
• UniProtKB Q13547 HDAC1 located_in GO:0000785 PMID:16731528 IDA C Histone deacetylase 1 HDAC1|RPD3L1 protein taxon:9606 20140716 ParkinsonsUK-UCL
• UniProtKB Q96B01 RAD51AP1 located_in GO:0000785 PMID:26323318 IDA C RAD51-associated protein 1 RAD51AP1|PIR51 protein taxon:9606 20160602 ParkinsonsUK-UCL existence_overlaps(GO:0006974)
• UniProtKB Q99497 PARK7 located_in GO:0000785 PMID:16731528 IDA C Parkinson disease protein 7 PARK7 protein taxon:9606 20140716 ParkinsonsUK-UCL
• UniProtKB Q9BXM7 PINK1 located_in GO:0000785 PMID:24798695 IDA C Serine/threonine-protein kinase PINK1, mitochondrial PINK1 protein taxon:9606 20140701 ParkinsonsUK-UCL
• UniProtKB Q9H1E3 NUCKS1 located_in GO:0000785 GO_REF:0000024 ISS UniProtKB:Q80XU3 C Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 NUCKS1|NUCKS|JC7 protein taxon:9606 20210107 ParkinsonsUK-UCL coincident_with(SO:0000167)
• UniProtKB Q9H1E3 NUCKS1 located_in GO:0000785 PMID:26323318 IDA C Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 NUCKS1|NUCKS|JC7 protein taxon:9606 20160602 ParkinsonsUK-UCL