# HTP-family rows in GOA: 65876 (250 references) # distinct gene-product x term pairs: 50795 ## code x aspect x polarity (rows, distinct gene x term pairs) 46645 70.8% pairs= 37822 74.5% HDA C pos 9088 13.8% pairs= 9088 17.9% HTP C pos 7363 11.2% pairs= 2768 5.4% HDA F pos 1535 2.3% pairs= 5 0.0% HMP F pos 884 1.3% pairs= 875 1.7% HMP P pos 270 0.4% pairs= 270 0.5% HDA P pos 87 0.1% pairs= 52 0.1% HGI P pos 4 0.0% pairs= 4 0.0% HDA C NOT ## assigned_by (rows, references, years) 17449 26.5% TAIR refs= 56 2019-2024 12062 18.3% PomBase refs= 6 2004-2025 8926 13.5% UniProt refs= 45 2004-2025 7853 11.9% Others refs= 1 2025-2025 7266 11.0% SGD refs= 43 2018-2026 4316 6.6% FlyBase refs= 29 2006-2026 2988 4.5% MGI refs= 4 2005-2026 2189 3.3% BHF-UCL refs= 19 2015-2025 1170 1.8% MTBBASE refs= 4 2010-2020 779 1.2% dictyBase refs= 20 2006-2026 521 0.8% WB refs= 4 2010-2021 104 0.2% ARUK-UCL refs= 4 2019-2020 78 0.1% ParkinsonsUK-UCL refs= 3 2018-2023 62 0.1% TIGR refs= 2 2021-2021 52 0.1% GeneDB refs= 6 2009-2021 33 0.1% GO_Central refs= 7 2021-2026 23 0.0% EcoCyc refs= 2 2021-2021 5 0.0% RGD refs= 2 2021-2022 ## concentration: top 10 refs = 47.0%, top 50 = 81.3% ## top 40 references 7853 genes= 5439 PMID:36804636 Others {'HTP/C': 7853} Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. GO:0005737 cytoplasm (3355); GO:0005739 mitochondrion (957) 6257 genes= 3927 PMID:16823372 PomBase {'HDA/C': 6257} ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. GO:0005829 cytosol (2036); GO:0005634 nucleus (2000) 4090 genes= 67 PMID:40015273 PomBase {'HDA/F': 4090} A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins an GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding (4090) 3263 genes= 3221 PMID:28887381 TAIR {'HDA/C': 3263} Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. GO:0005829 cytosol (1056); GO:0009536 plastid (682) 1942 genes= 1466 PMID:14562095 SGD {'HDA/C': 1942} Global analysis of protein localization in budding yeast. GO:0005737 cytoplasm (889); GO:0005634 nucleus (545) 1796 genes= 478 PMID:14651853 MGI {'HDA/C': 1796} Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. GO:0005739 mitochondrion (1795); GO:0005759 mitochondrial matrix (1) 1535 genes= 5 PMID:26412298 PomBase {'HMP/F': 1535} A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival. GO:0140492 metal-dependent deubiquitinase activity (1535) 1498 genes= 1106 PMID:22923678 TAIR {'HDA/C': 1498} Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. GO:0005783 endoplasmic reticulum (302); GO:0005739 mitochondrion (213) 1402 genes= 1227 PMID:26928762 SGD {'HDA/C': 1402} One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. GO:0005783 endoplasmic reticulum (416); GO:0071944 cell periphery (267) 1334 genes= 1332 PMID:18431481 TAIR {'HDA/C': 1334} Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. GO:0009507 chloroplast (1333); GO:0010287 plastoglobule (1) 1263 genes= 1256 PMID:25293756 TAIR {'HDA/C': 1263} A proteomic strategy for global analysis of plant protein complexes. GO:0005829 cytosol (706); GO:0009507 chloroplast (344) 1234 genes= 1234 PMID:34800366 FlyBase {'HTP/C': 1234} Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. GO:0005739 mitochondrion (1234) 1142 genes= 1142 PMID:19946888 UniProt {'HDA/C': 1142} Defining the membrane proteome of NK cells. GO:0016020 membrane (1142) 1046 genes= 1046 PMID:23533145 UniProt {'HDA/C': 1046} In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. GO:0070062 extracellular exosome (1046) 1025 genes= 1025 PMID:18614015 MGI {'HDA/C': 1025} A mitochondrial protein compendium elucidates complex I disease biology. GO:0005739 mitochondrion (1025) 1016 genes= 1016 PMID:19056867 UniProt {'HDA/C': 1016} Large-scale proteomics and phosphoproteomics of urinary exosomes. GO:0070062 extracellular exosome (1016) 966 genes= 785 PMID:20061580 TAIR {'HDA/C': 966} AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated informati GO:0009570 chloroplast stroma (456); GO:0009941 chloroplast envelope (302) 857 genes= 851 PMID:16823961 SGD {'HDA/C': 857} Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial pro GO:0005739 mitochondrion (857) 854 genes= 854 PMID:22658674 UniProt {'HDA/F': 854} Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. GO:0003723 RNA binding (854) 831 genes= 826 PMID:21533090 TAIR {'HDA/C': 831} Arabidopsis plasmodesmal proteome. GO:0009506 plasmodesma (831) 792 genes= 791 PMID:22681889 UniProt {'HDA/F': 792} The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. GO:0003723 RNA binding (791); GO:0030674 protein-macromolecule adaptor activity (1) 728 genes= 728 PMID:14532352 MTBBASE {'HDA/C': 728} Comprehensive proteomic profiling of the membrane constituents of a Mycobacterium tuberculosis strain. GO:0005886 plasma membrane (728) 706 genes= 588 PMID:25294944 FlyBase {'HDA/C': 706} Subcellular localisations of the CPTI collection of YFP-tagged proteins in Drosophila embryos. GO:0005829 cytosol (254); GO:0005654 nucleoplasm (168) 647 genes= 527 PMID:20458337 UniProt {'HDA/C': 636, 'HDA/F': 11} MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenes GO:0070062 extracellular exosome (636); GO:0023026 MHC class II protein complex binding (11) 546 genes= 544 PMID:24769239 SGD {'HDA/C': 546} Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory GO:0005739 mitochondrion (546) 533 genes= 322 PMID:22842922 SGD {'HDA/C': 533} Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA rep GO:0005737 cytoplasm (211); GO:0005634 nucleus (185) 511 genes= 508 PMID:14576278 SGD {'HDA/C': 511} The proteome of Saccharomyces cerevisiae mitochondria. GO:0005739 mitochondrion (511) 466 genes= 465 PMID:19317464 FlyBase {'HDA/C': 466} Mapping organelle proteins and protein complexes in Drosophila melanogaster. GO:0012505 endomembrane system (224); GO:0005886 plasma membrane (164) 443 genes= 443 PMID:17644812 TAIR {'HDA/C': 443} A high content in lipid-modified peripheral proteins and integral receptor kinases features in the arabidopsis GO:0005886 plasma membrane (443) 429 genes= 322 PMID:21611156 WB {'HDA/C': 429} Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle. GO:0055120 striated muscle dense body (82); GO:0005737 cytoplasm (66) 415 genes= 415 PMID:22430844 TAIR {'HDA/C': 415} Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components invo GO:0005794 Golgi apparatus (415) 412 genes= 412 PMID:14671022 TAIR {'HDA/C': 412} Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components GO:0005739 mitochondrion (412) 411 genes= 410 PMID:17151019 TAIR {'HDA/C': 411} A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture. GO:0000325 plant-type vacuole (411) 404 genes= 380 PMID:16618929 TAIR {'HDA/C': 404} Mapping the Arabidopsis organelle proteome. GO:0005783 endoplasmic reticulum (178); GO:0005886 plasma membrane (90) 400 genes= 400 PMID:21630459 UniProt {'HDA/C': 400} Proteomic characterization of the human sperm nucleus. GO:0005634 nucleus (400) 396 genes= 396 PMID:19199708 UniProt {'HDA/C': 396} Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudP GO:0070062 extracellular exosome (396) 395 genes= 395 PMID:15539469 TAIR {'HDA/C': 395} The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. GO:0000325 plant-type vacuole (395) 349 genes= 211 PMID:18981222 FlyBase {'HDA/C': 349} Conservation of the protein composition and electron microscopy structure of Drosophila melanogaster and human GO:0071011 precatalytic spliceosome (199); GO:0071013 catalytic step 2 spliceosome (150) 343 genes= 334 PMID:18633119 TAIR {'HDA/C': 343} Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabi GO:0009570 chloroplast stroma (271); GO:0009579 thylakoid (72) 340 genes= 296 PMID:11914276 SGD {'HDA/C': 340} Subcellular localization of the yeast proteome. GO:0005737 cytoplasm (221); GO:0005634 nucleus (60) ## molecular function rows: top terms (code, rows, references) 4090 genes= 67 HDA GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding refs=1 1645 genes= 1093 HDA GO:0003723 RNA binding refs=2 1535 genes= 5 HMP GO:0140492 metal-dependent deubiquitinase activity refs=1 421 genes= 418 HDA GO:0003729 mRNA binding refs=3 255 genes= 255 HDA GO:0045296 cadherin binding refs=1 140 genes= 140 HDA GO:0017171 serine hydrolase activity refs=2 118 genes= 115 HDA GO:0005507 copper ion binding refs=2 105 genes= 105 HDA GO:0003735 structural constituent of ribosome refs=3 101 genes= 87 HDA GO:0043565 sequence-specific DNA binding refs=2 82 genes= 82 HDA GO:0004672 protein kinase activity refs=1 74 genes= 74 HDA GO:0008270 zinc ion binding refs=1 65 genes= 65 HDA GO:0004674 protein serine/threonine kinase activity refs=1 53 genes= 53 HDA GO:0005524 ATP binding refs=1 45 genes= 45 HDA GO:0050897 cobalt ion binding refs=1 26 genes= 26 HDA GO:1901149 salicylic acid binding refs=1 -- references behind molecular function rows (>=40 rows) 4090 PMID:40015273 A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with p 1535 PMID:26412298 A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival. 854 PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. 792 PMID:22681889 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. 298 PMID:27729395 In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. 271 PMID:25468996 E-cadherin interactome complexity and robustness resolved by quantitative proteomics. 202 PMID:20018591 Divalent metal ions in plant mitochondria and their role in interactions with proteins and oxidative 136 PMID:33827210 A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster. 120 PMID:23222640 Global analysis of yeast mRNPs. 82 PMID:16319894 Global analysis of protein phosphorylation in yeast. 65 PMID:21477822 Autophosphorylation profiling of Arabidopsis protein kinases using the cell-free system. 57 PMID:19111667 A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting n 53 PMID:17137349 Analysis of the soluble ATP-binding proteome of plant mitochondria identifies new proteins and nucle 52 PMID:16889426 Characterization of the Drosophila melanogaster ribosomal proteome. 44 PMID:19158363 High-resolution DNA-binding specificity analysis of yeast transcription factors. ## biological process rows: top terms (code, rows, references) 70 genes= 70 HMP GO:0030587 sorocarp development refs=1 67 genes= 67 HMP GO:0050829 defense response to Gram-negative bacterium refs=1 65 genes= 65 HDA GO:0046777 protein autophosphorylation refs=1 64 genes= 64 HMP GO:0000381 regulation of alternative mRNA splicing, via spliceosome refs=1 57 genes= 57 HMP GO:0007419 ventral cord development refs=1 48 genes= 48 HMP GO:0045089 positive regulation of innate immune response refs=1 48 genes= 48 HMP GO:0043123 positive regulation of canonical NF-kappaB signal transduction refs=1 47 genes= 47 HMP GO:0042060 wound healing refs=1 46 genes= 46 HMP GO:0000278 mitotic cell cycle refs=1 42 genes= 42 HDA GO:0001649 osteoblast differentiation refs=1 32 genes= 32 HMP GO:0034976 response to endoplasmic reticulum stress refs=1 30 genes= 8 HGI GO:0034975 protein folding in endoplasmic reticulum refs=1 27 genes= 27 HMP GO:0048477 oogenesis refs=1 27 genes= 27 HDA GO:0042742 defense response to bacterium refs=1 26 genes= 26 HMP GO:1903749 obsolete positive regulation of protein localization to mitochondrion refs=2 -- references behind biological process rows (>=40 rows) 133 PMID:19520911 Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. 81 PMID:17659086 High-throughput analysis of spatio-temporal dynamics in Dictyostelium. 65 PMID:21477822 Autophosphorylation profiling of Arabidopsis protein kinases using the cell-free system. 64 PMID:15492211 Identification of alternative splicing regulators by RNA interference in Drosophila. 57 PMID:26092715 Novel Genes Involved in Controlling Specification of Drosophila FMRFamide Neuropeptide Cells. 57 PMID:1783295 Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking 48 PMID:12761501 Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK sign 48 PMID:18320040 The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulatio 47 PMID:19884309 Genetic screen in Drosophila melanogaster uncovers a novel set of genes required for embryonic epith 46 PMID:18463163 Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase Pontin. 42 PMID:16210410 Differential expression profiling of membrane proteins by quantitative proteomics in a human mesench 42 PMID:19325107 Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. ## NOT-qualified rows ubp8 NOT|is_active_in GO:0005730 nucleolus PMID:20838651 PomBase ubp14 NOT|is_active_in GO:0005730 nucleolus PMID:20838651 PomBase ubp6 NOT|is_active_in GO:0005730 nucleolus PMID:20838651 PomBase Homo sapiens (human) hsa-miR-221-3p NOT|located_in GO:0005576 extracellular region PMID:18766170 BHF-UCL ## papers cited by both HTP-family and RCA rows: 12 PMID:22430844 {'HDA/C': 415} {'RCA/C-NOT': 191} Isolation and proteomic characterization of the Arabidopsis Golgi defines functi PMID:25037231 {'HDA/C': 230} {'RCA/F': 150} Extracellular matrix signatures of human primary metastatic colon cancers and th PMID:22159717 {'HDA/C': 180} {'RCA/F': 105} The matrisome: in silico definition and in vivo characterization by proteomics o PMID:28071719 {'HDA/C': 164} {'RCA/F': 96} Quantitative proteomic profiling of the extracellular matrix of pancreatic islet PMID:28675934 {'HDA/C': 135} {'RCA/F': 84} Characterization of the Extracellular Matrix of Normal and Diseased Tissues Usin PMID:20551380 {'HDA/C': 136} {'RCA/F': 59} Proteomics characterization of extracellular space components in the human aorta PMID:27068509 {'HDA/C': 149, 'HDA/F': 3} {'RCA/F': 33} Extracellular matrix remodelling in response to venous hypertension: proteomics PMID:27559042 {'HDA/C': 94} {'RCA/F': 55} Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human A PMID:28327460 {'HDA/C': 86} {'RCA/F': 54} Comprehensive proteomic characterization of stem cell-derived extracellular matr PMID:22261194 {'HDA/C': 48} {'RCA/F': 30} Proteomics analysis of cardiac extracellular matrix remodeling in a porcine mode PMID:19834910 {'HDA/C': 13} {'RCA/C': 61} Protein composition of Trypanosoma brucei mitochondrial membranes. PMID:23979707 {'HDA/C': 33} {'RCA/F': 22} SILAC-based proteomics of human primary endothelial cell morphogenesis unveils t # Reviewed HTP-family rows: 2799 in 1435 gene folders ## code x aspect x action 2113 HDA C ACCEPT= 34.0% KEEP_AS_NON_CORE=791, ACCEPT=719, MARK_AS_OVER_ANNOTATED=401, UNDECIDED=124, REMOVE=57, MODIFY=18, NEW=3 371 HTP C ACCEPT= 63.1% ACCEPT=234, KEEP_AS_NON_CORE=95, MARK_AS_OVER_ANNOTATED=31, MODIFY=5, UNDECIDED=3, REMOVE=3 253 HDA F ACCEPT= 34.8% ACCEPT=88, MARK_AS_OVER_ANNOTATED=74, KEEP_AS_NON_CORE=61, UNDECIDED=13, REMOVE=9, MODIFY=8 41 HMP P ACCEPT= 12.2% KEEP_AS_NON_CORE=22, UNDECIDED=7, MARK_AS_OVER_ANNOTATED=6, ACCEPT=5, MODIFY=1 15 HDA P ACCEPT= 20.0% MARK_AS_OVER_ANNOTATED=7, KEEP_AS_NON_CORE=4, ACCEPT=3, UNDECIDED=1 6 HGI P ACCEPT= 83.3% ACCEPT=5, UNDECIDED=1 ## reviewed location (C) rows, HDA+HTP: vesicle-type / generic membrane / other 712 vesicle-type (exosome, EV, microparticle, vesicle) ACCEPT= 5.9% KEEP_NON_CORE= 58.7% over/remove/modify= 26.1% 289 generic membrane ACCEPT= 22.5% KEEP_NON_CORE= 24.6% over/remove/modify= 48.1% 1483 all other locations ACCEPT= 57.0% KEEP_NON_CORE= 26.8% over/remove/modify= 12.8% ## organism folders 2112 human 206 yeast 176 SCHPO 161 ARATH 53 DROME 29 DICDI 27 mouse 17 ECOLI 14 worm 3 MYCTU 1 rat ## reviewed references (>=12 rows): action split 371 PMID:34800366 ACCEPT= 63.1% KEEP_AS_NON_CORE=95, MARK_AS_OVER_ANNOTATED=31, MODIFY=5, UNDECIDED=3, REMOVE=3 Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. 273 PMID:19946888 ACCEPT= 21.6% MARK_AS_OVER_ANNOTATED=113, KEEP_AS_NON_CORE=65, UNDECIDED=13, REMOVE=13, MODIFY=10 Defining the membrane proteome of NK cells. 233 PMID:19056867 ACCEPT= 3.9% KEEP_AS_NON_CORE=142, MARK_AS_OVER_ANNOTATED=65, UNDECIDED=14, REMOVE=3 Large-scale proteomics and phosphoproteomics of urinary exosomes. 202 PMID:23533145 ACCEPT= 5.0% KEEP_AS_NON_CORE=118, MARK_AS_OVER_ANNOTATED=52, UNDECIDED=20, REMOVE=2 In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. 164 PMID:16823372 ACCEPT= 62.8% KEEP_AS_NON_CORE=51, MODIFY=3, UNDECIDED=3, REMOVE=2, MARK_AS_OVER_ANNOTATED=2 ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces 116 PMID:20458337 ACCEPT= 3.4% KEEP_AS_NON_CORE=68, MARK_AS_OVER_ANNOTATED=29, UNDECIDED=11, REMOVE=4 MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosom 92 PMID:22658674 ACCEPT= 34.8% MARK_AS_OVER_ANNOTATED=26, KEEP_AS_NON_CORE=24, UNDECIDED=6, REMOVE=2, MODIFY=2 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. 85 PMID:21630459 ACCEPT= 27.1% KEEP_AS_NON_CORE=28, MARK_AS_OVER_ANNOTATED=25, UNDECIDED=5, REMOVE=4 Proteomic characterization of the human sperm nucleus. 72 PMID:19199708 ACCEPT= 11.1% KEEP_AS_NON_CORE=42, MARK_AS_OVER_ANNOTATED=17, UNDECIDED=5 Proteomic analysis of human parotid gland exosomes by multidimensional protein identification techno 72 PMID:22681889 ACCEPT= 45.8% KEEP_AS_NON_CORE=19, MARK_AS_OVER_ANNOTATED=18, REMOVE=1, MODIFY=1 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. 55 PMID:25468996 ACCEPT= 3.6% MARK_AS_OVER_ANNOTATED=29, KEEP_AS_NON_CORE=16, REMOVE=4, UNDECIDED=4 E-cadherin interactome complexity and robustness resolved by quantitative proteomics. 44 PMID:14562095 ACCEPT= 81.8% KEEP_AS_NON_CORE=6, MARK_AS_OVER_ANNOTATED=2 Global analysis of protein localization in budding yeast. 40 PMID:21423176 ACCEPT= 20.0% KEEP_AS_NON_CORE=20, MARK_AS_OVER_ANNOTATED=8, UNDECIDED=3, REMOVE=1 Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative re 39 PMID:17897319 ACCEPT= 64.1% KEEP_AS_NON_CORE=11, MARK_AS_OVER_ANNOTATED=2, UNDECIDED=1 Integral and associated lysosomal membrane proteins. 38 PMID:20833797 ACCEPT= 52.6% KEEP_AS_NON_CORE=14, MARK_AS_OVER_ANNOTATED=2, UNDECIDED=1, MODIFY=1 Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals exten 30 PMID:27068509 ACCEPT= 86.7% KEEP_AS_NON_CORE=2, MODIFY=1, MARK_AS_OVER_ANNOTATED=1 Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose ve 30 PMID:16502470 ACCEPT= 66.7% KEEP_AS_NON_CORE=9, UNDECIDED=1 Human colostrum: identification of minor proteins in the aqueous phase by proteomics. 29 PMID:26928762 ACCEPT= 72.4% KEEP_AS_NON_CORE=6, MODIFY=1, UNDECIDED=1 One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. 27 PMID:20551380 ACCEPT= 88.9% KEEP_AS_NON_CORE=2, MODIFY=1 Proteomics characterization of extracellular space components in the human aorta. 26 PMID:22516433 ACCEPT= 15.4% KEEP_AS_NON_CORE=14, UNDECIDED=6, MARK_AS_OVER_ANNOTATED=2 Proteomic analysis of microvesicles from plasma of healthy donors reveals high individual variabilit 25 PMID:28887381 ACCEPT= 16.0% MARK_AS_OVER_ANNOTATED=15, KEEP_AS_NON_CORE=3, UNDECIDED=2, REMOVE=1 Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. 25 PMID:16823961 ACCEPT= 56.0% KEEP_AS_NON_CORE=5, REMOVE=4, MARK_AS_OVER_ANNOTATED=2 Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitocho 24 PMID:28675934 ACCEPT= 58.3% KEEP_AS_NON_CORE=7, UNDECIDED=2, MARK_AS_OVER_ANNOTATED=1 Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics. 21 PMID:25037231 ACCEPT= 52.4% KEEP_AS_NON_CORE=4, MARK_AS_OVER_ANNOTATED=2, UNDECIDED=2, REMOVE=2 Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to li 21 PMID:24769239 ACCEPT= 57.1% KEEP_AS_NON_CORE=8, MARK_AS_OVER_ANNOTATED=1 Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and re 20 PMID:22842922 ACCEPT= 75.0% KEEP_AS_NON_CORE=5 Dissecting DNA damage response pathways by analysing protein localization and abundance changes duri 19 PMID:22664934 ACCEPT= 10.5% KEEP_AS_NON_CORE=7, MARK_AS_OVER_ANNOTATED=6, UNDECIDED=2, REMOVE=2 Comparison of tear protein levels in breast cancer patients and healthy controls using a de novo pro 18 PMID:16210410 ACCEPT= 16.7% MARK_AS_OVER_ANNOTATED=9, KEEP_AS_NON_CORE=4, UNDECIDED=2 Differential expression profiling of membrane proteins by quantitative proteomics in a human mesench 18 PMID:11914276 ACCEPT= 88.9% MARK_AS_OVER_ANNOTATED=1, KEEP_AS_NON_CORE=1 Subcellular localization of the yeast proteome. 17 PMID:16858726 ACCEPT= 70.6% KEEP_AS_NON_CORE=4, UNDECIDED=1 A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel ele 17 PMID:27559042 ACCEPT= 88.2% KEEP_AS_NON_CORE=2 Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. 16 PMID:28327460 ACCEPT= 75.0% KEEP_AS_NON_CORE=4 Comprehensive proteomic characterization of stem cell-derived extracellular matrices. 16 PMID:21362503 ACCEPT= 18.8% KEEP_AS_NON_CORE=8, UNDECIDED=3, MARK_AS_OVER_ANNOTATED=2 Protein profile of exosomes from trabecular meshwork cells. 16 PMID:21525035 ACCEPT= 75.0% MARK_AS_OVER_ANNOTATED=2, KEEP_AS_NON_CORE=1, UNDECIDED=1 PEX14 is required for microtubule-based peroxisome motility in human cells. 15 PMID:25293756 ACCEPT= 60.0% KEEP_AS_NON_CORE=4, MARK_AS_OVER_ANNOTATED=2 A proteomic strategy for global analysis of plant protein complexes. 15 PMID:26477565 ACCEPT= 53.3% KEEP_AS_NON_CORE=3, REMOVE=2, MARK_AS_OVER_ANNOTATED=2 Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mito 14 PMID:18431481 ACCEPT= 64.3% MARK_AS_OVER_ANNOTATED=3, REMOVE=1, KEEP_AS_NON_CORE=1 Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. 14 PMID:23580065 ACCEPT= 21.4% KEEP_AS_NON_CORE=5, UNDECIDED=3, MARK_AS_OVER_ANNOTATED=2, REMOVE=1 Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary ope 13 PMID:19317464 ACCEPT= 38.5% KEEP_AS_NON_CORE=8 Mapping organelle proteins and protein complexes in Drosophila melanogaster. 13 PMID:28344315 ACCEPT= 38.5% REMOVE=5, UNDECIDED=2, MODIFY=1 Proteomic characterization of human multiple myeloma bone marrow extracellular matrix. 13 PMID:24769233 ACCEPT= 0.0% KEEP_AS_NON_CORE=9, UNDECIDED=3, MARK_AS_OVER_ANNOTATED=1 Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset. 12 PMID:22923678 ACCEPT= 58.3% UNDECIDED=3, KEEP_AS_NON_CORE=2 Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteom 12 PMID:18570454 ACCEPT= 0.0% MARK_AS_OVER_ANNOTATED=5, KEEP_AS_NON_CORE=3, UNDECIDED=3, REMOVE=1 Proteomic analysis of exosomes from human neural stem cells by flow field-flow fractionation and nan 12 PMID:19190083 ACCEPT= 16.7% KEEP_AS_NON_CORE=8, REMOVE=1, MARK_AS_OVER_ANNOTATED=1 Characterization of exosome-like vesicles released from human tracheobronchial ciliated epithelium: ## papers cited by both codes (12): reviewed actions HTP-family rows n= 148 ACCEPT= 73.6% ACCEPT=109, KEEP_AS_NON_CORE=22, MARK_AS_OVER_ANNOTATED=8, UNDECIDED=5, MODIFY=2, REMOVE=2 RCA rows n= 62 ACCEPT= 56.5% ACCEPT=35, MARK_AS_OVER_ANNOTATED=13, MODIFY=10, REMOVE=4 ## reviewed terms with the most non-ACCEPT rows (top 20) 625/661 HDA GO:0070062 extracellular exosome KEEP_AS_NON_CORE=387, MARK_AS_OVER_ANNOTATED=171, UNDECIDED=57, ACCEPT=36, REMOVE=10 224/289 HDA GO:0016020 membrane MARK_AS_OVER_ANNOTATED=116, KEEP_AS_NON_CORE=71, ACCEPT=65, UNDECIDED=14, REMOVE=13, MODIFY=10 137/371 HTP GO:0005739 mitochondrion ACCEPT=234, KEEP_AS_NON_CORE=95, MARK_AS_OVER_ANNOTATED=31, MODIFY=5, UNDECIDED=3, REMOVE=3 99/164 HDA GO:0003723 RNA binding ACCEPT=65, MARK_AS_OVER_ANNOTATED=44, KEEP_AS_NON_CORE=43, UNDECIDED=6, REMOVE=3, MODIFY=3 85/189 HDA GO:0005634 nucleus ACCEPT=104, KEEP_AS_NON_CORE=41, MARK_AS_OVER_ANNOTATED=30, UNDECIDED=9, REMOVE=4, MODIFY=1 65/131 HDA GO:0005739 mitochondrion ACCEPT=66, KEEP_AS_NON_CORE=42, MARK_AS_OVER_ANNOTATED=11, REMOVE=9, UNDECIDED=2, MODIFY=1 48/50 HDA GO:0045296 cadherin binding MARK_AS_OVER_ANNOTATED=28, KEEP_AS_NON_CORE=12, REMOVE=4, UNDECIDED=4, ACCEPT=2 35/78 HDA GO:0005576 extracellular region ACCEPT=43, KEEP_AS_NON_CORE=19, MARK_AS_OVER_ANNOTATED=9, UNDECIDED=3, REMOVE=3, MODIFY=1 34/124 HDA GO:0031012 extracellular matrix ACCEPT=90, KEEP_AS_NON_CORE=17, MARK_AS_OVER_ANNOTATED=6, UNDECIDED=6, REMOVE=5 33/83 HDA GO:0005829 cytosol ACCEPT=50, KEEP_AS_NON_CORE=26, UNDECIDED=4, MARK_AS_OVER_ANNOTATED=3 32/40 HDA GO:0005925 focal adhesion KEEP_AS_NON_CORE=20, ACCEPT=8, MARK_AS_OVER_ANNOTATED=8, UNDECIDED=3, REMOVE=1 22/77 HDA GO:0005737 cytoplasm ACCEPT=55, KEEP_AS_NON_CORE=18, UNDECIDED=2, NEW=1, MARK_AS_OVER_ANNOTATED=1 22/26 HDA GO:0072562 blood microparticle KEEP_AS_NON_CORE=14, UNDECIDED=6, ACCEPT=4, MARK_AS_OVER_ANNOTATED=2 14/39 HDA GO:0005765 lysosomal membrane ACCEPT=25, KEEP_AS_NON_CORE=11, MARK_AS_OVER_ANNOTATED=2, UNDECIDED=1 13/40 HDA GO:0005783 endoplasmic reticulum ACCEPT=27, KEEP_AS_NON_CORE=8, MODIFY=3, UNDECIDED=1, NEW=1 13/13 HDA GO:1903561 extracellular vesicle KEEP_AS_NON_CORE=9, UNDECIDED=3, MARK_AS_OVER_ANNOTATED=1 12/31 HDA GO:0005886 plasma membrane ACCEPT=19, KEEP_AS_NON_CORE=8, MARK_AS_OVER_ANNOTATED=4 12/27 HDA GO:0005615 extracellular space ACCEPT=15, KEEP_AS_NON_CORE=8, UNDECIDED=3, MODIFY=1 10/12 HDA GO:0031982 vesicle KEEP_AS_NON_CORE=8, ACCEPT=2, REMOVE=1, MARK_AS_OVER_ANNOTATED=1 9/9 HDA GO:0001649 osteoblast differentiation MARK_AS_OVER_ANNOTATED=6, KEEP_AS_NON_CORE=2, UNDECIDED=1