{
"bcoid": "GLY_000594",
"title": "Human Pathways (Reactome)",
"description": "The Human Pathways (Reactome) dataset contains Homo sapiens [taxid:9606] pathway information from Reactome ...",
"filename_list": "human_protein_pathways_reactome.csv",
"filename": "human_protein_pathways_reactome.csv",
"filetype": "csv",
"categories": {
"species": [
"Homo sapiens"
],
"molecule": [
"Protein"
],
"tag": [
"Reactome Pathway"
],
"file_type": [
"csv"
],
"status": [
"Reviewed"
],
"scope": [
"internal"
],
"file_category": [
"pathway/enzymes"
]
},
"minitable": {
"content": [
[
"R-HSA-970119...",
"Defective ho..."
],
[
"R-HSA-971720...",
"Sensory perc..."
]
],
"headers": [
"pathway_id...",
"pathway_name..."
],
"colwidth": [
"40%",
"20%"
]
},
"sampledata": {
"type": "table",
"data": [
[
{
"type": "string",
"label": "pathway_id"
},
{
"type": "string",
"label": "pathway_name"
},
{
"type": "string",
"label": "pathway_summary"
},
{
"type": "string",
"label": "reaction_id_list"
}
],
[
"R-HSA-9701192",
"Defective homologous recombination repair (HRR) due to BRCA1 loss of function",
"In addition to its role in DNA double-strand break (DSB) signaling, BRCA1 plays an important role in homologous recombination repair (HRR) of DSBs by directly promoting recruitment of PALB2 and indirectly BRCA2 to DSB repair sites. In addition, BRCA1 increases the speed and processivity of DNA end resection which consists of 5\u2032\u20133\u2032 nucleolytic degradation of DSBs (Cruz-Garcia et al. 2014). The direct BRCA1 interaction with PALB2 helps to fine-tune the localization of BRCA2 and RAD51 at DSBs (Zhang et al. 2009, Sy et al. 2009). PALB2 simultaneously interacts with RAD51, BRCA2 and RAD51AP1 (Modesti et al. 2007, Wiese et al. 2007, Buisson et al. 2010, Dray et al. 2010). PALB2 and RAD51AP1 synergistically stimulate RAD51 recombinase activity, thus enhancing RAD51-mediated strand exchange (branch migration) and promoting the formation of D-loop structures (synaptic complex assembly). A D-loop structure is formed when complementary duplex DNA (sister chromatid arm) is progressively invaded by the RAD51 nucleoprotein filament, with base pairing of the invading ssDNA and the complementary sister chromatid DNA strand (Sung et al. 2003).
The N-terminal region of BRCA1 contains the RING domain (residues 7-98), required for the heterodimerization of BRCA1 with BARD1. BRCA1:BARD1 heterodimer has E3 ubiquitin ligase activity which is important for DNA repair (Drost et al. 2011). Several missense mutations within the RING domain have been linked to increased risks of developing breast/ovarian cancers (Bouwman et al. 2013; Starita et al. 2018). BRCA1 mutant proteins impaired in BARD1 binding are annotated in the pathway \\Defective DNA double strand break response due to BRCA1 loss of function\\.
The C-terminal region of BRCA1 which contains two coiled coil domains (residues 1397-1424) and two BRCT domains (residues 1642-1736 for BRCT 1; residues 1756-1855 for BRCT 2) is involved in PALB2 binding, with the second coiled coil domain being essential (Sy et al. 2009). Several cancer-associated BRCA1 missense mutants that affect the C-terminal region were shown to have reduced ability to bind PALB2 (Sy et al. 2009). In addition, many nonsense and frameshift mutations in BRCA1 reported in cancer result in truncated proteins that lack the PALB2-binding domain.",
"R-HSA-9701199"
],
[
"R-HSA-9717207",
"Sensory perception of sweet, bitter, and umami (glutamate) taste",
"Taste receptors for bitter compounds, sweet compounds, and umami compounds (L-glutamate in humans, several amino acids in mice) are G protein-coupled receptors located in type II taste bud cells that signal through a common downstream pathway (reviewed in Margolskee 2002, Kinnamon 2009, Kurihara 2015, Roper and Chauhari et al. 2017, Kinnamon and Finger 2019, Servant et al. 2020). Umami (\\savoury\\, L-glutamate) taste receptors are heterodimers of the plasma membrane proteins TAS1R1 and TAS1R3. TAS1R1:TAS1R3 heterodimers also bind 5' nucleotides such as 5' IMP which synergistically augment umami taste. The glutamate receptors GRM1 (mGluR1) and GRM4 (mGluR4) act in an alternative pathway for sensing glutamate in taste cells (reviewed in Chaudhari et al. 2009). Sweet taste receptors are heterodimers of the plasma membrane proteins TAS1R2 and TAS1R3 (reviewed in Yang et al. 2021). The glucose transporters SGLT1 and GLUT4 are expressed in type II taste cells and may provide an alternative pathway for sensing glucose (reviewed in von Molitor et al. 2020). Bitter receptors are a large family of monomeric plasma membrane proteins, the TAS2R proteins.
TAS1R-containing sweet and umami receptors and TAS2R bitter receptors are each physically associated with a particular heterotrimeric G protein complex, the gustducin complex, containing GNAT3 (gustducin), GNB1 or GNB3, and GNG13. Upon binding an agonist ligand, the receptor activates the alpha subunit, GNAT3, to exchange GDP for GTP, which results in a conformational change in GNAT3 that causes the receptor-gustducin complex to dissociate, yielding GNAT3:GTP, GNB1,3:GNG13, and the receptor:ligand. The GNB1,3:GNG13 complex binds and activates Phospholipase C beta-2 (PLCB2), which then hydrolyzes phosphoinositol 4,5-bisphosphate (PI(4,5)P2) to yield diacylglycerol and inositol 1,4,5-trisphosphate (I(1,4,5)P3). I(1,4,5)P3 binds and activates the calcium channel IP3-gated Ca-channel type 3 (ITPR3) and ITPR3 then releases calcium ions from the endoplasmic reticulum into the cytosol. The increased cytosolic calcium activates the TRPM5 cation channels, which then transport sodium ions along the concentration gradient from the extracellular region to the cytosol (reviewed in Aroke et al. 2020). The depolarization activates SCN2A, SCN3A, and SCN9A channels, which transport further sodium ions from the extracellular region to the cytosol. The depolarization of the plasma membrane opens CALHM1:CALHM3 channels, which transport ATP, a neurotransmitter in the olfactory system, from the cytosol to the extracellular region.
Taste receptors were initially discovered in taste buds of the tongue and have now been found in several other tissues including nasal epithelium (Barnham et al. 2015, inferred from rodent homologs in Tizzano et al. 2011), the respiratory system, pancreatic islet cells, sperm (Governini et al. 2020), leukocytes (Malki et al. 2015), and enteroendocrine cells of the gut (inferred from rat and mouse homologs in Wu et al. 2002).",
"R-HSA-9717374,R-HSA-9717382,R-HSA-9717396,R-HSA-9717214,R-HSA-9717215,R-HSA-9717182,R-HSA-9717193,R-HSA-9717202,R-HSA-9717205,R-HSA-9717206,R-HSA-9728697,R-HSA-9728723,R-HSA-9728729,R-HSA-9737035,R-HSA-9737046,R-HSA-9717395,R-HSA-9717383,R-HSA-9728747,R-HSA-9728748,R-HSA-9728752,R-HSA-9717392"
]
]
},
"readme": "Name\n - Human Pathways (Reactome)\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2021-10-15T06:14:22.181602\n\nModified on\n - 2024-05-21T15:39:19.176Z\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Human Pathways (Reactome) dataset contains Homo sapiens [taxid:9606] pathway information from Reactome database and mapped to the UniProtKB canonical accessions. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Reactome and GlyGen.\n - REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. \n\nDescription Domain\n Keywords\n - pathways\n - reactions\n - REACTOME\n\n Pipeline Steps\n - Step-1: The script loads the Reactome Pathways for UniProtKB canonical accessions from the triplestore containing triples from nt file and extracts the data as a csv dataset. \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-homo-sapiens.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-homo-sapiens.nt\n Output Subdomain\n Name: human_protein_pathways_reactome.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_pathways_reactome.csv\n Name: human_protein_pathways_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_pathways_reactome.stat.csv\n\nFields\n Name: \"pathway_id\"\"\n Description: \"\"\n Unique Values: \"2296\"",
"downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_protein_pathways_reactome.csv"
}