Table 13

Incorrectly annotated protein pairs selected from the very hardest positive and negative pairs
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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M1">View MathML</a>/p58 and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M2">View MathML</a> subunits of XPC.
B.d418.s0.p0 T functional Membranous staining and concomitant cytoplasmic localization of E-cadherin, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M3">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M4">View MathML</a> were seen in one case with abnormal beta-catenin immunoreactivity.
B.d418.s0.p1 T functional Membranous staining and concomitant cytoplasmic localization of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M5">View MathML</a>, alpha-catenin and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M6">View MathML</a> 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: <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M7">View MathML</a>, titin, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M8">View MathML</a>, 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, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M9','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M9">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M10','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M10">View MathML</a>, did not.
B.d833.s0.p14 T functional Within 1 hour of raising the concentration of calcium ions, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M11','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M11">View MathML</a>, cadherins, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M12">View MathML</a>, 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 (<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M13">View MathML</a>), <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M14','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M14">View MathML</a> and destrin.
B.d296.s2.p20 T functional In normal livers, E-cad, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M15">View MathML</a> and beta-catenin, but not CD44s, CD44v5, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M16','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M16">View MathML</a>, 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, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M17">View MathML</a> and beta-catenin, but not CD44s, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M18','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M18">View MathML</a>, CD44v6, CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.
B.d541.s0.p0 T functional Since both <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M19','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M19">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M20">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M21">View MathML</a> isoforms (SM1, SM2, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M22','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M22">View MathML</a>), 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M23','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M23">View MathML</a> ligand (<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M24','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M24">View MathML</a>), 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M25','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M25">View MathML</a> (CKIs) p27 and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M26','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M26">View MathML</a>, and markers of differentiating podocytes in developing human kidneys was investigated by immunohistochemistry.
B.d296.s2.p23 T functional In normal livers, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M27','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M27">View MathML</a>, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M28','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M28">View MathML</a> 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/<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M29','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M29">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M30','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M30">View MathML</a> subunits of XPC.
B.d833.s0.p35 T functional Within 1 hour of raising the concentration of calcium ions, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M31','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M31">View MathML</a>, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M32','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M32">View MathML</a>, 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 (<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M33','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M33">View MathML</a>) p27 and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M34','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M34">View MathML</a>, 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, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M35','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M35">View MathML</a>, cadherins, alpha-catenin, beta-catenin, plakoglobin, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M36','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M36">View MathML</a> 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, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M37">View MathML</a>, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M38','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M38">View MathML</a>, and desmin.
B.d833.s0.p7 T functional Within 1 hour of raising the concentration of calcium ions, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M39','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M39">View MathML</a>, cadherins, alpha-catenin, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M40','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M40">View MathML</a>, 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<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M41','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M41">View MathML</a>, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M42','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M42">View MathML</a>, actin, and desmin.
B.d833.s0.p29 T functional Within 1 hour of raising the concentration of calcium ions, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M43','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M43">View MathML</a>, cadherins, alpha-catenin, beta-catenin, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M44','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M44">View MathML</a>, 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, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M45','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M45">View MathML</a>, cadherins, alpha-catenin, beta-catenin, plakoglobin, vinculin and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M46','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M46">View MathML</a> appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.
A.d60.s528.p0 F T The <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M47','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M47">View MathML</a> proteins purified from cells infected with EC12 or 22W viruses activated <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M48','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M48">View MathML</a> kinase from skeletal muscle in vitro.
B.d180.s0.p0 F T

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M49','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M49">View MathML</a>

signal transduction is mediated by a complex of intracellular signaling molecules including <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M50','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M50">View MathML</a>, TRAF2, FADD, and FLICE.
A.d114.s961.p0 F T

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M51','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M51">View MathML</a>

binds to an alternatively spliced exon of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M52','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M52">View MathML</a>.
B.d93.s0.p9 F T Because <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M53','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M53">View MathML</a> H3 shares many structural features with histone H4 and is intimately associated with <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M54','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M54">View MathML</a> in the assembled nucleosome, we asked whether H3 has similar functions.
B.d749.s0.p2 F T Three actin-associated proteins, actin-binding protein, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M55','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M55">View MathML</a>, and profilin, influence gelation, solation, and polymerization, respectively, of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M56','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M56">View MathML</a> in vitro.
B.d639.s0.p0 F T The main inhibitory action of p27, a cyclin-dependent kinase inhibitor (<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M57','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M57">View MathML</a>), arises from its binding with the cyclin E/<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M58','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M58">View MathML</a> (Cdk2) complex that results in G(1)-S arrest.
B.d334.s0.p0 F T In extracts from mouse brain, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M59','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M59">View MathML</a> and profilin II can form complexes with regulators of endocytosis, synaptic vesicle recycling and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M60','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M60">View MathML</a> assembly.
A.d141.s1189.p0 F T The cyclin-dependent kinase <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M61','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M61">View MathML</a> associates with <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M62','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M62">View MathML</a>, 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M63','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M63">View MathML</a>, p21(Cip1/WAF1), to the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M64','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M64">View MathML</a>-cdk2 complex.
A.d157.s1329.p4 F T Deletion analysis and binding studies demonstrate that a third enzyme, protein kinase C (<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M65','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M65">View MathML</a>), binds <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M66','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M66">View MathML</a> at a site distinct from those bound by PKA or CaN.
A.d60.s529.p0 F T Furthermore, a bacterially expressed <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M67','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M67">View MathML</a> fusion protein (glutathione S-transferase-p3722W) also activated <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M68','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M68">View MathML</a> kinase in vitro.
A.d199.s1701.p0 F T

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M69','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M69">View MathML</a>

in complex with a previously identified 90-kDa protein and designated protein <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M70','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M70">View MathML</a>.
A.d161.s1355.p0 F T

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M71','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M71">View MathML</a>

associates with the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M72','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M72">View MathML</a> (PDGF) receptor after ligand stimulation, and binding of SHPTP2 to this receptor promotes tyrosine phosphorylation of SHPTP2.
B.d357.s0.p1 F T

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M73','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M73">View MathML</a>

(beta) chains, for example, interact with actin-binding proteins (e.g. <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M74','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M74">View MathML</a> and filamin), which form mechanical links to the cytoskeleton.
A.d195.s1663.p2 F T Intriguingly, NR1-<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M75','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M75">View MathML</a> binding is directly antagonized by Ca2+/<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M76','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M76">View MathML</a>.
A.d151.s1288.p1 F T Immunoprecipitation assays also show a weak substoichiometric association of the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M77','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M77">View MathML</a> (TBP) with <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M78','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M78">View MathML</a>, 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M79','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M79">View MathML</a>, p21(Cip1/WAF1), to the cyclin E-<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M80','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M80">View MathML</a> complex.
B.d814.s0.p26 F T We have shown that the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M81','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M81">View MathML</a> Bni1p and Bnr1p are potential targets of the Rho family small GTP-binding proteins and bind to an actin-binding protein, <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M82','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M82">View MathML</a>, 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M83','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M83">View MathML</a> and gelsolin bind to phosphatidylinositol (PI) 4,5-bisphosphate (PI 4,5-P2) and regulate the concentration of monomeric <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M84','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M84">View MathML</a>.
A.d39.s340.p0 F indirect Chloramphenicol acetyltransferase assays in F9 cells showed that <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M85','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M85">View MathML</a> suppresses transactivation by <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M86','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M86">View MathML</a>/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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M87','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M87">View MathML</a> polymerization is regulated, at least in part, by profilin, which binds to <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M88','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M88">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M89','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M89">View MathML</a>-associated protein that enhances the filament disassembly activity of cofilin and restricts <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M90','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M90">View MathML</a> localization to cortical actin patches.
L.d35.s1.p1 F indirect Our data demonstrate that the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M91','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M91">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M92','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M92">View MathML</a>-dependent promoter and might be inactivated or dissociate under inducing stress conditions.
B.d14.s1.p2 F indirect These studies suggest that profilin and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M93','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M93">View MathML</a> may control the generation of 3-OH phosphorylated phosphoinositides, which in turn may regulate the <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M94','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M94">View MathML</a> polymerization.
I.d11.s28.p1 F coreference The <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M95','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M95">View MathML</a> inhibitor U 71322 prevented the activation of phospholipase C by

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M96','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M96">View MathML</a>

L.d13.s0.p1 F indirect Production of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M97','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M97">View MathML</a> about 1 h earlier than normal does affect Spo0A, which when phosphorylated is an activator of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M98','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M98">View MathML</a> transcription.
A.d78.s669.p2 F indirect Our data suggest that <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M99','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M99">View MathML</a> inhibits the interactions of LIGHT with HVEM / / <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M100','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M100">View MathML</a> and LTbetaR, thereby suppressing LIGHT-mediated HT29 cell death.
B.d223.s0.p9 F functional Furthermore, the deletion of <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M101','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M101">View MathML</a> suppresses the temperature-sensitive growth defect of sac6, a mutant in yeast <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/12/mathml/M102','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/12/mathml/M102">View MathML</a>, supporting a role for synaptojanin family members in actin function.

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.

Tikk et al.

Tikk et al. BMC Bioinformatics 2013 14:12   doi:10.1186/1471-2105-14-12

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