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Table 13 Incorrectly annotated protein pairs selected from the very hardest positive and negative pairs

From: A detailed error analysis of 13 kernel methods for protein-protein interaction extraction

Pair ID GT Type of error Sentence text
B.d267.s0.p14 T indirect However, a number of mammalian DNA repair proteins lack NLS clusters; these proteins include ERCC1, ERCC2 (XPD), mouse RAD51, and the HHR23B ENT 1 /p58 and HHR23B ENT 2 subunits of XPC.
B.d418.s0.p0 T functional Membranous staining and concomitant cytoplasmic localization of E-cadherin, alpha-catenin ENT 1 and gamma-catenin ENT 2 were seen in one case with abnormal beta-catenin immunoreactivity.
B.d418.s0.p1 T functional Membranous staining and concomitant cytoplasmic localization of E-cadherin ENT 2 , alpha-catenin and gamma-catenin ENT 1 were seen in one case with abnormal beta-catenin immunoreactivity.
B.d506.s0.p8 T enumeration Quantitation of the appearance of X22 banding in primary cultures of myotubes indicates that it precedes that of other myofibrillar proteins and that assembly takes place in the following order: X22 ENT 1 , titin, myosin heavy chain ENT 2 , actin, and desmin.
B.d833.s0.p15 T functional Within 1 hour of raising the concentration of calcium ions, integrins, cadherins, alpha-catenin, beta-catenin, plakoglobin, vinculin and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin ENT 1 and talin ENT 2 , did not.
B.d833.s0.p14 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins, alpha-catenin ENT 1 , beta-catenin, plakoglobin, vinculin and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
B.d594.s0.p0 T functional The clone contains an open reading frame of 139 amino acid residues which shows greater than 40% sequence identity in a 91 amino acid overlap to animal actin-depolymerizing factors ( ADF ENT 1 ), cofilin ENT 2 and destrin.
B.d296.s2.p20 T functional In normal livers, E-cad, alpha-catenin ENT 2 and beta-catenin, but not CD44s, CD44v5, CD44v6 ENT 1 , CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.
B.d296.s2.p25 T functional In normal livers, E-cad, alpha-catenin ENT 2 and beta-catenin, but not CD44s, CD44v5 ENT 1 , CD44v6, CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.
B.d541.s0.p0 T functional Since both caldesmon ENT 2 and profilin ENT 1 have been found enriched in ruffling membranes of animal cells, our in vitro findings may be relevant to the regulation of actin filaments in living cells.
B.d546.s0.p20 T functional Specific antibodies to myosin heavy chain ENT 2 isoforms (SM1, SM2, SMemb ENT 1 ), caldesmon, and alpha-smooth muscle actin and cDNAs for SMemb were used.
A.d28.s234.p1 T coreference We have identified a new TNF-related ligand, designated human GITR ENT 1 ligand ( hGITRL ENT 2 ), and its human receptor (hGITR), an ortholog of the recently discovered murine glucocorticoid-induced TNFR-related (mGITR) protein [4].
B.d765.s0.p14 T enumeration To determine the relationship between cell cycle regulation and differentiation, the spatiotemporal expression of cyclin A, cyclin B1, cyclin D1, the cyclin-dependent kinase inhibitors ENT 1 (CKIs) p27 and p57 ENT 2 , and markers of differentiating podocytes in developing human kidneys was investigated by immunohistochemistry.
B.d296.s2.p23 T functional In normal livers, E-cad ENT 1 , alpha-catenin ENT 2 and beta-catenin, but not CD44s, CD44v5, CD44v6, CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.
B.d267.s0.p18 T indirect However, a number of mammalian DNA repair proteins lack NLS clusters; these proteins include ERCC1, ERCC2 (XPD), mouse RAD51, and the HHR23B/ p58 ENT 1 and HHR23A ENT 2 subunits of XPC.
B.d833.s0.p35 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins ENT 1 , alpha-catenin, beta-catenin, plakoglobin, vinculin and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
B.d765.s0.p10 T enumeration To determine the relationship between cell cycle regulation and differentiation, the spatiotemporal expression of cyclin A, cyclin B1, cyclin D1, the cyclin-dependent kinase inhibitors ( CKIs ENT 1 ) p27 and p57 ENT 2 , and markers of differentiating podocytes in developing human kidneys was investigated by immunohistochemistry.
B.d833.s0.p34 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins, alpha-catenin, beta-catenin, plakoglobin, vinculin ENT 1 and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
B.d506.s0.p4 T enumeration Quantitation of the appearance of X22 banding in primary cultures of myotubes indicates that it precedes that of other myofibrillar proteins and that assembly takes place in the following order: X22, titin, myosin heavy chain ENT 2 , actin ENT 1 , and desmin.
B.d833.s0.p7 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins, alpha-catenin, beta-catenin ENT 1 , plakoglobin, vinculin and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
B.d506.s0.p11 T enumeration Quantitation of the appearance of X22 banding in primary cultures of myotubes indicates that it precedes that of other myofibrillar proteins and that assembly takes place in the following order: X22, titin EN T 1 , myosin heavy chain ENT 2 , actin, and desmin.
B.d833.s0.p29 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins, alpha-catenin, beta-catenin, plakoglobin ENT 1 , vinculin and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
B.d833.s0.p32 T functional Within 1 hour of raising the concentration of calcium ions, integrins ENT 2 , cadherins, alpha-catenin, beta-catenin, plakoglobin, vinculin and alpha-actinin ENT 1 appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
A.d60.s528.p0 F T The v-Raf ENT 1 proteins purified from cells infected with EC12 or 22W viruses activated MAP kinase ENT 2 kinase from skeletal muscle in vitro.
B.d180.s0.p0 F T DR3 ENT 2 signal transduction is mediated by a complex of intracellular signaling molecules including TRADD ENT 1 , TRAF2, FADD, and FLICE.
A.d114.s961.p0 F T Syntrophin ENT 1 binds to an alternatively spliced exon of dystrophin ENT 2 .
B.d93.s0.p9 F T Because histone ENT 1 H3 shares many structural features with histone H4 and is intimately associated with H4 ENT 2 in the assembled nucleosome, we asked whether H3 has similar functions.
B.d749.s0.p2 F T Three actin-associated proteins, actin-binding protein, gelsolin ENT 1 , and profilin, influence gelation, solation, and polymerization, respectively, of actin ENT 2 in vitro.
B.d639.s0.p0 F T The main inhibitory action of p27, a cyclin-dependent kinase inhibitor ( CDKI ENT 1 ), arises from its binding with the cyclin E/ cyclin-dependent kinase 2 ENT 2 (Cdk2) complex that results in G(1)-S arrest.
B.d334.s0.p0 F T In extracts from mouse brain, profilin I ENT 2 and profilin II can form complexes with regulators of endocytosis, synaptic vesicle recycling and actin ENT 1 assembly.
A.d141.s1189.p0 F T The cyclin-dependent kinase Cdk2 ENT 1 associates with cyclins A ENT 2 , D, and E and has been implicated in the control of the G1 to S phase transition in mammals.
B.d485.s0.p2 F T PF4-dependent downregulation of cyclin E-cdk2 activity was associated with increased binding of the cyclin-dependent kinase inhibitor ENT 1 , p21(Cip1/WAF1), to the cyclin E ENT 2 -cdk2 complex.
A.d157.s1329.p4 F T Deletion analysis and binding studies demonstrate that a third enzyme, protein kinase C ( PKC ENT 1 ), binds AKAP79 ENT 2 at a site distinct from those bound by PKA or CaN.
A.d60.s529.p0 F T Furthermore, a bacterially expressed v-Raf ENT 1 fusion protein (glutathione S-transferase-p3722W) also activated MAP kinase ENT 2 kinase in vitro.
A.d199.s1701.p0 F T Sos ENT 1 in complex with a previously identified 90-kDa protein and designated protein 80K-H ENT 2 .
A.d161.s1355.p0 F T SHPTP2 ENT 1 associates with the platelet-derived growth factor ENT 2 (PDGF) receptor after ligand stimulation, and binding of SHPTP2 to this receptor promotes tyrosine phosphorylation of SHPTP2.
B.d357.s0.p1 F T Integrin ENT 1 (beta) chains, for example, interact with actin-binding proteins (e.g. talin ENT 2 and filamin), which form mechanical links to the cytoskeleton.
A.d195.s1663.p2 F T Intriguingly, NR1- calmodulin ENT 1 binding is directly antagonized by Ca2+/ alpha-actinin ENT 2 .
A.d151.s1288.p1 F T Immunoprecipitation assays also show a weak substoichiometric association of the TATA-binding protein ENT 1 (TBP) with PTF ENT 2 , consistent with the previous report of a PTF-related complex (SNAPc) containing substoichiometric levels of TBP and a component (SNAPc43) identical in sequence to the PTF gamma reported here.
B.d485.s0.p4 F T PF4-dependent downregulation of cyclin E-cdk2 activity was associated with increased binding of the cyclin-dependent kinase inhibitor ENT 1 , p21(Cip1/WAF1), to the cyclin E- cdk2 ENT 2 complex.
B.d814.s0.p26 F T We have shown that the FH proteins ENT 2 Bni1p and Bnr1p are potential targets of the Rho family small GTP-binding proteins and bind to an actin-binding protein, profilin ENT 1 , at their proline-rich FH1 domains to regulate reorganization of the actin cytoskeleton in the yeast Saccharomyces cerevisiae.
B.d14.s0.p4 F T Actin-binding proteins such as profilin ENT 2 and gelsolin bind to phosphatidylinositol (PI) 4,5-bisphosphate (PI 4,5-P2) and regulate the concentration of monomeric actin ENT 1 .
A.d39.s340.p0 F indirect Chloramphenicol acetyltransferase assays in F9 cells showed that PS1 ENT 1 suppresses transactivation by c-Jun ENT 2 /c-Jun but not by c-Jun/c-Fos heterodimers, consistent with the reported function of QM/Jif-1.
B.d307.s0.p4 F indirect In Acanthamoeba actin ENT 2 polymerization is regulated, at least in part, by profilin, which binds to actin ENT 1 monomers, and by capping protein, which both nucleates polymerization and blocks monomer addition at the ’barbed’ end of the filament.
B.d35.s4.p9 F indirect We conclude that Aip1p is a cofilin ENT 2 -associated protein that enhances the filament disassembly activity of cofilin and restricts cofilin ENT 1 localization to cortical actin patches.
L.d35.s1.p1 F indirect Our data demonstrate that the CtsR ENT 1 protein acts as a global repressor of the clpC operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the sigmaB- or sigmaA ENT 2 -dependent promoter and might be inactivated or dissociate under inducing stress conditions.
B.d14.s1.p2 F indirect These studies suggest that profilin and gelsolin ENT 2 may control the generation of 3-OH phosphorylated phosphoinositides, which in turn may regulate the actin ENT 1 polymerization.
I.d11.s28.p1 F coreference The phospholipase C ENT 1 inhibitor U 71322 prevented the activation of phospholipase C by A beta P ENT 2
L.d13.s0.p1 F indirect Production of sigmaK ENT 1 about 1 h earlier than normal does affect Spo0A, which when phosphorylated is an activator of sigE ENT 2 transcription.
A.d78.s669.p2 F indirect Our data suggest that TR6 ENT 1 inhibits the interactions of LIGHT with HVEM / / TR2 ENT 2 and LTbetaR, thereby suppressing LIGHT-mediated HT29 cell death.
B.d223.s0.p9 F functional Furthermore, the deletion of SJL1 ENT 2 suppresses the temperature-sensitive growth defect of sac6, a mutant in yeast fimbrin ENT 1 , supporting a role for synaptojanin family members in actin function.
  1. Pair id abbreviations: A - AIMed; B - BioInfer; I - IEPA, L - LLL; ground truth (GT): T (true), F (false); type of errors: indirect - no direct interaction between the entities are described; functional - only functional similarity between entities are described; enumeration - entities are just listed together in an enumeration; coreference - the same protein with different referencing. Entities (in the pair) are highlighted with bold typeface.