diff --git a/pathways/WP5329/WP5329-datanodes.tsv b/pathways/WP5329/WP5329-datanodes.tsv index 7bae5f6be1..baba852074 100644 --- a/pathways/WP5329/WP5329-datanodes.tsv +++ b/pathways/WP5329/WP5329-datanodes.tsv @@ -59,6 +59,7 @@ MYLIP GeneProduct refseq:NM_013262 ensembl:ENSG00000007944 ncbigene:29116 hgnc. GGPS1 Protein ncbigene:9453 ensembl:ENSG00000152904 ncbigene:9453 hgnc.symbol:GGPS1 uniprot:C9J6G3;uniprot:A0A024R3R2;uniprot:C9J7M1;uniprot:O95749 SREBF2 Protein hgnc:11290 SREBF2 Protein hgnc:11290 +CP7A1 Protein uniprot:P22680 ensembl:ENSG00000167910 ncbigene:1581 hgnc.symbol:CYP7A1 uniprot:P22680 FDPS Protein refseq:NM_002004 ensembl:ENSG00000160752 ncbigene:2224 hgnc.symbol:FDPS uniprot:P14324;uniprot:A0A087WVN4;uniprot:A0A087WTP2;uniprot:A0A087X090;uniprot:A0A087X1D8 FDFT1 Protein hgnc.symbol:FDFT1 ensembl:ENSG00000079459 ncbigene:2222 hgnc.symbol:FDFT1 uniprot:E9PJG4;uniprot:P37268;uniprot:E9PQ90;uniprot:E9PNJ2;uniprot:E9PS69;uniprot:Q6IAX1;uniprot:E9PSH1;uniprot:A0A1W2PQ47;uniprot:E9PNM1 SQLE Protein hgnc:11279 diff --git a/pathways/WP5329/WP5329-info.json b/pathways/WP5329/WP5329-info.json index 46b1837972..58b31398dc 100644 --- a/pathways/WP5329/WP5329-info.json +++ b/pathways/WP5329/WP5329-info.json @@ -3,14 +3,17 @@ "organisms": ["Homo sapiens"], "description": "This pathway was constructed based on the Brown et al 2021 book chapter (Cholesterol Synthesis), combined with the Reactome Cholesterol Synthesis pathway (DOI:10.3180/R-HSA-191273.7) and the WikiPathways WP4718 (Cholesterol metabolism with Bloch and Kandutsch-Russell pathways (Homo sapiens)). Additional information was incorporated based on the literature. All protein were curated for cell-specific (hepatocyte) isoforms.", "ontology-ids": [ - "CL:0000182", - "PW:0000454" + "PW:0000454", + "CL:0000182" ], - "last-edited": "2023-02-27", + "last-edited": "2023-07-01", "title": "Cholesterol biosynthesis pathway in hepatocytes", "authors": [ "LLadeira", - "Susan" + "Susan", + "DeSl", + "Jmillanacosta", + "Egonw" ], - "revision": "r125476" + "revision": "r126886" } \ No newline at end of file diff --git a/pathways/WP5329/WP5329-refs.tsv b/pathways/WP5329/WP5329-refs.tsv index 560b0827a6..46743d8680 100644 --- a/pathways/WP5329/WP5329-refs.tsv +++ b/pathways/WP5329/WP5329-refs.tsv @@ -1 +1,7 @@ ID Database +NA Pubmed +3524618 Pubmed +1390320 Pubmed +12668600 Pubmed +11969204 Pubmed +16054061 Pubmed diff --git a/pathways/WP5372/WP5372-datanodes.tsv b/pathways/WP5372/WP5372-datanodes.tsv new file mode 100644 index 0000000000..02e5b8cfa4 --- /dev/null +++ b/pathways/WP5372/WP5372-datanodes.tsv @@ -0,0 +1,29 @@ +Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI +beta-amyloid Metabolite chebi:64645 wikidata:Q417667 chebi:64645;chebi:64645 +dopamine Metabolite chebi:18243 wikidata:Q170304 chebi:18243;chebi:18243 inchikey:VYFYYTLLBUKUHU-UHFFFAOYSA-N +DOPAL Metabolite chebi:27978 wikidata:Q4634065 chebi:27978;chebi:27978 inchikey:IADQVXRMSNIUEL-UHFFFAOYSA-N +LGMN GeneProduct ensembl:ENSG00000100600 ensembl:ENSG00000100600 ncbigene:5641 hgnc.symbol:LGMN uniprot:Q99538;uniprot:G3V3Z4;uniprot:G3V263;uniprot:Q53XC6;uniprot:G3V2T4;uniprot:G3V4E4;uniprot:G3V2E9;uniprot:G3V5B2;uniprot:H0YJN9;uniprot:G3V4P5 +BACE1 GeneProduct uniprot:P56817 ensembl:ENSG00000186318 ncbigene:23621 hgnc.symbol:BACE1 uniprot:U3KPS1;uniprot:B7Z3Z4;uniprot:A0A7P0T924;uniprot:P56817;uniprot:Q76KP0;uniprot:B7Z3K2;uniprot:E9PJG7;uniprot:A0A024R3D5;uniprot:A0A024R3D7;uniprot:A0A024R3E8;uniprot:A0A024R3F9;uniprot:A0A7P0TAB4 +AKT 2 Protein uniprot:P31751 ensembl:ENSG00000105221 ncbigene:208 hgnc.symbol:AKT2 uniprot:M0QZK3;uniprot:J3QKW1;uniprot:A0A5F9ZHJ8;uniprot:E7EVP8;uniprot:J3KRI8;uniprot:C9JIJ1;uniprot:J3QLS6;uniprot:A8MX96;uniprot:C9JIF6;uniprot:A0A0A0MRF1;uniprot:J3QL45;uniprot:M0R0P9;uniprot:C9J258;uniprot:M0QZW8;uniprot:J3KTC6;uniprot:A0A1B0GXA2;uniprot:M0R275;uniprot:C9JC83;uniprot:J3KSY8;uniprot:J3KT31;uniprot:P31751;uniprot:C9JHS6;uniprot:J3KTP4;uniprot:M0R283 +Prolegumain Protein uniprot:Q99538 Precursor of δ-secretase
Activation by self-cleavage ensembl:ENSG00000100600 ncbigene:5641 hgnc.symbol:LGMN uniprot:Q99538;uniprot:G3V3Z4;uniprot:G3V263;uniprot:Q53XC6;uniprot:G3V2T4;uniprot:G3V4E4;uniprot:G3V2E9;uniprot:G3V5B2;uniprot:H0YJN9;uniprot:G3V4P5 +Microtubule-associated protein tau Protein uniprot:P10636 ensembl:ENSG00000186868 ncbigene:4137 hgnc.symbol:MAPT uniprot:A0A7I2PLE3;uniprot:A0A7P0T936;uniprot:I3L2Z2;uniprot:A0A024R9Y0;uniprot:A0A024R9Y1;uniprot:P10636;uniprot:A0A7I2PJZ2;uniprot:A0A024RA17;uniprot:A0A024RA19 +δ-secretase Protein uniprot:Q99538 Phosphorylated ensembl:ENSG00000100600 ncbigene:5641 hgnc.symbol:LGMN uniprot:Q99538;uniprot:G3V3Z4;uniprot:G3V263;uniprot:Q53XC6;uniprot:G3V2T4;uniprot:G3V4E4;uniprot:G3V2E9;uniprot:G3V5B2;uniprot:H0YJN9;uniprot:G3V4P5 +APP Protein uniprot:P05067 ensembl:ENSG00000142192 ncbigene:351 hgnc.symbol:APP uniprot:A0A140VJC8;uniprot:H7C2L2;uniprot:H7C0V9;uniprot:P05067;uniprot:A0A0A0MRG2;uniprot:E9PG40 +PP2A Protein uniprot:P62714 Activated ensembl:ENSG00000104695 ncbigene:5516 hgnc.symbol:PPP2CB uniprot:E5RHC1;uniprot:E5RJX4;uniprot:H0YBN9;uniprot:A0A140VJS0;uniprot:P62714;uniprot:E5RFI3;uniprot:H0YC23 +STAT1 Protein uniprot:P42224 ensembl:ENSG00000115415 ncbigene:6772 hgnc.symbol:STAT1 uniprot:E9PH66;uniprot:A0A669KBK4;uniprot:E7EPD2;uniprot:J3KPM9;uniprot:Q67C41;uniprot:A0A669KB17;uniprot:A0A669KB56;uniprot:A0A669KB68;uniprot:A0A669KB52;uniprot:A0A669KB53;uniprot:A0A669KB75;uniprot:D2KFR9;uniprot:P42224;uniprot:A0A669KBA4;uniprot:E7ENM1;uniprot:A0A669KBI6 +TrkB Protein uniprot:Q16620 ensembl:ENSG00000148053 ncbigene:4915 hgnc.symbol:NTRK2 uniprot:A0A024R230;uniprot:Q548C2;uniprot:Q16620;uniprot:Q5VWE5 +BDNF Protein uniprot:P23560 ensembl:ENSG00000176697 ncbigene:627 hgnc.symbol:BDNF uniprot:P23560;uniprot:A0A0E3SU01;uniprot:E9PMP3 +SET Protein uniprot:Q01105 ensembl:ENSG00000119335 ncbigene:6418 hgnc.symbol:SET uniprot:Q01105;uniprot:A0A0C4DFV9;uniprot:A0A024R895;uniprot:Q5VXV3 +AKT 3 Protein uniprot:Q9Y243 ensembl:ENSG00000117020 ncbigene:10000 hgnc.symbol:AKT3 uniprot:A0A7P0T8T9;uniprot:A0A7P0TBJ6;uniprot:A0A5F9ZHU3;uniprot:A0A7P0TB29;uniprot:Q9Y243;uniprot:A0A5F9ZHA9;uniprot:A0A5F9ZGY0;uniprot:A0A5F9ZGZ4;uniprot:A0A5K1VW74;uniprot:A0A7P0T872;uniprot:A0A7P0TB32 +Microtubule-associated protein tau Protein uniprot:P10636 Phosphorylated ensembl:ENSG00000186868 ncbigene:4137 hgnc.symbol:MAPT uniprot:A0A7I2PLE3;uniprot:A0A7P0T936;uniprot:I3L2Z2;uniprot:A0A024R9Y0;uniprot:A0A024R9Y1;uniprot:P10636;uniprot:A0A7I2PJZ2;uniprot:A0A024RA17;uniprot:A0A024RA19 +δ-secretase Protein uniprot:Q99538 ensembl:ENSG00000100600 ncbigene:5641 hgnc.symbol:LGMN uniprot:Q99538;uniprot:G3V3Z4;uniprot:G3V263;uniprot:Q53XC6;uniprot:G3V2T4;uniprot:G3V4E4;uniprot:G3V2E9;uniprot:G3V5B2;uniprot:H0YJN9;uniprot:G3V4P5 +C/EBP10A𝛽 Protein uniprot:P17676 Only a part of the protein (less amino acids) ensembl:ENSG00000172216 ncbigene:1051 hgnc.symbol:CEBPB uniprot:P17676 +TDP-43 Protein uniprot:Q13148 ensembl:ENSG00000120948 ncbigene:23435 hgnc.symbol:TARDBP uniprot:A0A087X260;uniprot:Q13148;uniprot:A0A087WW61;uniprot:A0A024R4E2;uniprot:K7ENM9;uniprot:A0A087WYY0;uniprot:K7EJM5;uniprot:A0A0A0MSV7;uniprot:K7EJ99;uniprot:A0A087WXV3;uniprot:K7EN94;uniprot:A0A087WVX6;uniprot:B1AKP7;uniprot:A0A087WTZ4;uniprot:A0A087WYE7;uniprot:G3V162;uniprot:A0A087WZC9;uniprot:A0A087WZM1;uniprot:A0A0A0N0M3;uniprot:A0A087WXQ5;uniprot:K7EL26;uniprot:A0A087WTG4;uniprot:A0A087WX29;uniprot:A0A087WX67;uniprot:A0A087WV68 +MAO B Protein uniprot:P27338 ensembl:ENSG00000069535 ncbigene:4129 hgnc.symbol:MAOB uniprot:P27338 +α-synuclein Protein uniprot:P37840 ensembl:ENSG00000145335 ncbigene:6622 hgnc.symbol:SNCA uniprot:P37840;uniprot:H6UYS5;uniprot:D6RA31;uniprot:E7EPV7;uniprot:H6UYS7;uniprot:A0A669KB41;uniprot:A0A669KBH5;uniprot:H6UYS0 +SRPK2 Protein uniprot:P78362 ensembl:ENSG00000135250 ncbigene:6733 hgnc.symbol:SRPK2 uniprot:A0A024R704;uniprot:F8WAV6;uniprot:C9J2M4;uniprot:H7C521;uniprot:F8WBW4;uniprot:P78362;uniprot:H7C5L6;uniprot:C9JWF7 +AKT 1 Protein uniprot:P31749 ensembl:ENSG00000142208 ncbigene:207 hgnc.symbol:AKT1 uniprot:G3V3X1;uniprot:P31749;uniprot:G3V2I6;uniprot:A0A804HJM6;uniprot:B0LPE5;uniprot:A0A087WY56 +PP2A Protein uniprot:P62714 ensembl:ENSG00000104695 ncbigene:5516 hgnc.symbol:PPP2CB uniprot:E5RHC1;uniprot:E5RJX4;uniprot:H0YBN9;uniprot:A0A140VJS0;uniprot:P62714;uniprot:E5RFI3;uniprot:H0YC23 +AKT 1 Protein uniprot:P31749 Phosphorylated ensembl:ENSG00000142208 ncbigene:207 hgnc.symbol:AKT1 uniprot:G3V3X1;uniprot:P31749;uniprot:G3V2I6;uniprot:A0A804HJM6;uniprot:B0LPE5;uniprot:A0A087WY56 +AKT 2 Protein uniprot:P31751 Phosphorylated ensembl:ENSG00000105221 ncbigene:208 hgnc.symbol:AKT2 uniprot:M0QZK3;uniprot:J3QKW1;uniprot:A0A5F9ZHJ8;uniprot:E7EVP8;uniprot:J3KRI8;uniprot:C9JIJ1;uniprot:J3QLS6;uniprot:A8MX96;uniprot:C9JIF6;uniprot:A0A0A0MRF1;uniprot:J3QL45;uniprot:M0R0P9;uniprot:C9J258;uniprot:M0QZW8;uniprot:J3KTC6;uniprot:A0A1B0GXA2;uniprot:M0R275;uniprot:C9JC83;uniprot:J3KSY8;uniprot:J3KT31;uniprot:P31751;uniprot:C9JHS6;uniprot:J3KTP4;uniprot:M0R283 +AKT 3 Protein uniprot:Q9Y243 Phosphorylated ensembl:ENSG00000117020 ncbigene:10000 hgnc.symbol:AKT3 uniprot:A0A7P0T8T9;uniprot:A0A7P0TBJ6;uniprot:A0A5F9ZHU3;uniprot:A0A7P0TB29;uniprot:Q9Y243;uniprot:A0A5F9ZHA9;uniprot:A0A5F9ZGY0;uniprot:A0A5F9ZGZ4;uniprot:A0A5K1VW74;uniprot:A0A7P0T872;uniprot:A0A7P0TB32 diff --git a/pathways/WP5372/WP5372-info.json b/pathways/WP5372/WP5372-info.json new file mode 100644 index 0000000000..78602c707f --- /dev/null +++ b/pathways/WP5372/WP5372-info.json @@ -0,0 +1,23 @@ +{ + "wpid": "WP5372", + "organisms": ["Homo sapiens"], + "description": "Mammalian asparagine endopeptidase, also known as δ-secretase , is a key player in a number of neurodegenerative illnesses, including Alzheimer's, Parkinson's or ALS. The enzyme can get activated in the aging brain and starts to cleave amyloid precursor protein (APP) and promotes the production of amyloid-β (Aβ). δ-secretase also breaks down tau, alpha-synuclein, SET, and TAR DNA-binding protein 43, generating neurotoxic fragments and impairing their physiological processes. Each fragment has either been identified in patient samples with the relevant disease or has undergone testing to determine whether it can cause the disease pathology. This pathway is based on Figure 1 from the paper:\"δ-secretase in neurodegenerative diseases: mechanisms, regulators and therapeutic opportunities. published by Zhang Z, Tian Y, Ye K.", + "ontology-ids": [ + "DOID:332", + "PW:0000018", + "PW:0000015", + "DOID:14330", + "DOID:10652", + "DOID:1289", + "DOID:9255" + ], + "last-edited": "2023-07-01", + "title": "Involvement of δ-secretase in neurodegenerative diseases", + "authors": [ + "Pat hofer", + "Tamara Fitzinger", + "Marlenef97", + "DeSl" + ], + "revision": "r126830" +} \ No newline at end of file diff --git a/pathways/WP5372/WP5372-refs.tsv b/pathways/WP5372/WP5372-refs.tsv new file mode 100644 index 0000000000..6495f2d34a --- /dev/null +++ b/pathways/WP5372/WP5372-refs.tsv @@ -0,0 +1,3 @@ +ID Database +31911834 Pubmed +23948891 Pubmed