RCA rows downloaded: 8610 ## Rows by analysis_class 4159 48.3% pathway_or_metabolic_model 2029 23.6% proteome_scale_prediction 1465 17.0% proteomics 387 4.5% single_gene_study 237 2.8% family_or_genome_survey 151 1.8% unclassified 90 1.0% unresolved 72 0.8% interactomics 17 0.2% other_omics 3 0.0% genetic_screen ## References by analysis_class 111 single_gene_study 101 unclassified 36 family_or_genome_survey 18 proteomics 7 proteome_scale_prediction 3 pathway_or_metabolic_model 2 interactomics 2 other_omics 2 genetic_screen 1 unresolved ## Rows by how the class was assigned 8273 96.1% curated 186 2.2% title-rule 151 1.8% unclassified OMICS rows (classes ['genetic_screen', 'interactomics', 'other_omics', 'proteomics', 'transcriptomics']): 1557 (18.1%) ## analysis_class x aspect (P/F/C) and NOT rows pathway_or_metabolic_model P= 1271 F= 1553 C= 1335 NOT=0 proteome_scale_prediction P= 2 F= 587 C= 1440 NOT=0 proteomics P= 0 F= 724 C= 741 NOT=627 single_gene_study P= 69 F= 147 C= 171 NOT=0 family_or_genome_survey P= 100 F= 61 C= 76 NOT=0 unclassified P= 21 F= 35 C= 95 NOT=0 unresolved P= 84 F= 5 C= 1 NOT=0 interactomics P= 0 F= 6 C= 66 NOT=0 other_omics P= 1 F= 0 C= 16 NOT=0 genetic_screen P= 0 F= 1 C= 2 NOT=0 ## analysis_class x assigned_by pathway_or_metabolic_model SGD=4133, GeneDB=26 proteome_scale_prediction GeneDB=1314, SGD=580, EcoCyc=120, WB=15 proteomics BHF-UCL=688, TAIR=627, GeneDB=79, FlyBase=70, EcoCyc=1 single_gene_study EcoCyc=167, AgBase=158, TAIR=30, GeneDB=28, GR=3, UniProt=1 family_or_genome_survey MGI=98, GeneDB=59, EcoCyc=52, AspGD=13, AgBase=11, ARUK-UCL=2, PAMGO_MGG=1, GR=1 unclassified EcoCyc=88, AgBase=35, ARUK-UCL=13, GeneDB=8, UniProt=2, TAIR=2, AspGD=1, GR=1, MGI=1 unresolved PAMGO_MGG=90 interactomics GeneDB=72 other_omics EcoCyc=17 genetic_screen EcoCyc=3 ## Omics rows by assigned_by x aspect x polarity (annotation years) 688 BHF-UCL F positive 2018-2025 627 TAIR C NOT 2011-2012 145 GeneDB C positive 2009-2022 35 FlyBase F positive 2019-2019 35 FlyBase C positive 2019-2019 18 EcoCyc C positive 2013-2021 6 GeneDB F positive 2009-2009 2 EcoCyc F positive 2013-2019 1 EcoCyc P positive 2017-2017 ## Omics references (>=3 rows): rows, aspects, top terms 436 PMID:21166475 [proteomics/curated] TAIR aspects={'C': 436} NOT=436 annotated=2011 Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism GO:0005829 cytosol (436) 191 PMID:22430844 [proteomics/curated] TAIR aspects={'C': 191} NOT=191 annotated=2012 Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components invo GO:0005794 Golgi apparatus (191) 150 PMID:25037231 [proteomics/curated] BHF-UCL aspects={'F': 150} NOT=0 annotated=2018 Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. GO:0005201 extracellular matrix structural constituent (71); GO:0030020 extracellular matrix structural constituent conferring tensile strength (52); GO:0030021 extracellular matrix structural constituent conferring compression resistance (19) 105 PMID:22159717 [proteomics/curated] BHF-UCL aspects={'F': 105} NOT=0 annotated=2018 The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellul GO:0005201 extracellular matrix structural constituent (60); GO:0030020 extracellular matrix structural constituent conferring tensile strength (30); GO:0030021 extracellular matrix structural constituent conferring compression resistance (9) 96 PMID:28071719 [proteomics/curated] BHF-UCL aspects={'F': 96} NOT=0 annotated=2018,2019 Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch GO:0005201 extracellular matrix structural constituent (51); GO:0030020 extracellular matrix structural constituent conferring tensile strength (32); GO:0030021 extracellular matrix structural constituent conferring compression resistance (9) 84 PMID:28675934 [proteomics/curated] BHF-UCL aspects={'F': 84} NOT=0 annotated=2018 Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics. GO:0005201 extracellular matrix structural constituent (41); GO:0030020 extracellular matrix structural constituent conferring tensile strength (31); GO:0030021 extracellular matrix structural constituent conferring compression resistance (8) 70 PMID:21761556 [proteomics/curated] FlyBase aspects={'F': 35, 'C': 35} NOT=0 annotated=2019 Proteomic analysis of larval integument, trachea and adult scale from the silkworm, Bombyx mori. GO:0005214 structural constituent of chitin-based cuticle (35); GO:0062129 chitin-based extracellular matrix (35) 64 PMID:26991453 [interactomics/curated] GeneDB aspects={'C': 64} NOT=0 annotated=2016 A Protein Complex Map of Trypanosoma brucei. GO:0031019 mitochondrial mRNA editing complex (64) 61 PMID:19834910 [proteomics/curated] GeneDB aspects={'C': 61} NOT=0 annotated=2009 Protein composition of Trypanosoma brucei mitochondrial membranes. GO:0005743 mitochondrial inner membrane (47); GO:0031966 mitochondrial membrane (14) 59 PMID:20551380 [proteomics/curated] BHF-UCL aspects={'F': 59} NOT=0 annotated=2018 Proteomics characterization of extracellular space components in the human aorta. GO:0005201 extracellular matrix structural constituent (32); GO:0030020 extracellular matrix structural constituent conferring tensile strength (14); GO:0030021 extracellular matrix structural constituent conferring compression resistance (11) 55 PMID:27559042 [proteomics/curated] BHF-UCL aspects={'F': 55} NOT=0 annotated=2018 Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. GO:0005201 extracellular matrix structural constituent (26); GO:0030020 extracellular matrix structural constituent conferring tensile strength (17); GO:0030021 extracellular matrix structural constituent conferring compression resistance (10) 54 PMID:28327460 [proteomics/curated] BHF-UCL aspects={'F': 54} NOT=0 annotated=2018 Comprehensive proteomic characterization of stem cell-derived extracellular matrices. GO:0005201 extracellular matrix structural constituent (29); GO:0030020 extracellular matrix structural constituent conferring tensile strength (16); GO:0030021 extracellular matrix structural constituent conferring compression resistance (5) 33 PMID:27068509 [proteomics/curated] BHF-UCL aspects={'F': 33} NOT=0 annotated=2018 Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veins. GO:0005201 extracellular matrix structural constituent (22); GO:0030020 extracellular matrix structural constituent conferring tensile strength (6); GO:0030021 extracellular matrix structural constituent conferring compression resistance (4) 30 PMID:22261194 [proteomics/curated] BHF-UCL aspects={'F': 30} NOT=0 annotated=2018,2019,2025 Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion inju GO:0005201 extracellular matrix structural constituent (14); GO:0030020 extracellular matrix structural constituent conferring tensile strength (8); GO:0030021 extracellular matrix structural constituent conferring compression resistance (6) 22 PMID:23979707 [proteomics/curated] BHF-UCL aspects={'F': 22} NOT=0 annotated=2018 SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers. GO:0005201 extracellular matrix structural constituent (14); GO:0030020 extracellular matrix structural constituent conferring tensile strength (5); GO:0030021 extracellular matrix structural constituent conferring compression resistance (2) 16 PMID:15919996 [other_omics/curated] EcoCyc aspects={'C': 16} NOT=0 annotated=2014,2017,2018,2019,2021 Global topology analysis of the Escherichia coli inner membrane proteome. GO:0005886 plasma membrane (16) 11 PMID:21136929 [proteomics/curated] GeneDB aspects={'C': 11} NOT=0 annotated=2013 Food vacuole proteome of the malarial parasite Plasmodium falciparum. GO:0020020 food vacuole (11) 8 PMID:12649499 [interactomics/curated] GeneDB aspects={'F': 6, 'C': 2} NOT=0 annotated=2009,2022 Identification of novel components of Trypanosoma brucei editosomes. GO:0045293 mRNA editing complex (2); GO:0004525 ribonuclease III activity (2); GO:0004518 nuclease activity (2) 6 PMID:16603573 [proteomics/curated] GeneDB aspects={'C': 6} NOT=0 annotated=2014 Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malar GO:0005886 plasma membrane (6) ## Unclassified references (>=3 rows) -- curate in rca_reference_classes.yaml 4 PMID:26631410 ARUK-UCL Cation dependencies and turnover rates of the human K⁺-dependent Na⁺-Ca²⁺ exchangers NCKX1, NCKX2, NCKX3 and N 4 PMID:10417723 AgBase Oxygen deprivation stimulates Ca2+-mediated phosphorylation of mRNA cap-binding protein eIF4E in maize roots. 4 PMID:11421275 EcoCyc Bacterial transporters for sulfate and organosulfur compounds. 4 DOI:10.1016/j.pmpp.2005.09.006 AgBase 3 PMID:18541913 GeneDB Specific DNA-binding by apicomplexan AP2 transcription factors. 3 PMID:21488939 EcoCyc Overproduction of YjbB reduces the level of polyphosphate in Escherichia coli: a hypothetical role of YjbB in 3 PMID:19688190 AgBase Relationship between expression of voltage-dependent anion channel (VDAC) isoforms and type of hexokinase bind 3 PMID:15090514 EcoCyc The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm 3 PMID:28842488 ARUK-UCL Conserved functional consequences of disease-associated mutations in the slide helix of Kir6.1 and Kir6.2 subu 3 PMID:15557092 AgBase A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibe 3 PMID:12746521 AgBase The cotton kinesin-like calmodulin-binding protein associates with cortical microtubules in cotton fibers. 3 PMID:12137958 AgBase Metal resistance in yeast mediated by the expression of a maize 20S proteasome alpha subunit.