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

B.d267.s0.p14

However, a number of mammalian DNA repair proteins lack NLS clusters; these proteins include ERCC1, ERCC2 (XPD), mouse RAD51, and the ${\mathbf{\text{HHR23B}}}_{{\text{ENT}}_1}$/p58 and ${\mathbf{\text{HHR23B}}}_{{\text{ENT}}_2}$ subunits of XPC.

B.d418.s0.p0

Membranous staining and concomitant cytoplasmic localization of E-cadherin, ${\mathbf{\text{alpha-catenin}}}_{{\text{ENT}}_1}$ and ${\mathbf{\text{gamma-catenin}}}_{{\text{ENT}}_2}$ were seen in one case with abnormal beta-catenin immunoreactivity.

B.d418.s0.p1

Membranous staining and concomitant cytoplasmic localization of ${\mathbf{\text{E-cadherin}}}_{{\text{ENT}}_2}$, alpha-catenin and ${\mathbf{\text{gamma-catenin}}}_{{\text{ENT}}_1}$ were seen in one case with abnormal beta-catenin immunoreactivity.

B.d506.s0.p8

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: ${\mathbf{\text{X22}}}_{{\text{ENT}}_1}$, titin, ${\mathbf{\text{myosin heavy chain}}}_{{\text{ENT}}_2}$, actin, and desmin.

B.d833.s0.p15

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, ${\mathbf{\text{paxillin}}}_{{\text{ENT}}_1}$ and ${\mathbf{\text{talin}}}_{{\text{ENT}}_2}$, did not.

B.d833.s0.p14

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, cadherins, ${\mathbf{\text{alpha-catenin}}}_{{\text{ENT}}_1}$, 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

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 (${\mathbf{\text{ADF}}}_{{\text{ENT}}_1}$), ${\mathbf{\text{cofilin}}}_{{\text{ENT}}_2}$ and destrin.

B.d296.s2.p20

In normal livers, E-cad, ${\mathbf{\text{alpha-catenin}}}_{{\text{ENT}}_2}$ and beta-catenin, but not CD44s, CD44v5, ${\mathbf{\text{CD44v6}}}_{{\text{ENT}}_1}$, CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.

B.d296.s2.p25

In normal livers, E-cad, ${\mathbf{\text{alpha-catenin}}}_{{\text{ENT}}_2}$ and beta-catenin, but not CD44s, ${\mathbf{\text{CD44v5}}}_{{\text{ENT}}_1}$, CD44v6, CD44v7-8, and CD44v10, were expressed at the cell membrane of normal intrahepatic bile ducts.

B.d541.s0.p0

Since both ${\mathbf{\text{caldesmon}}}_{{\text{ENT}}_2}$ and ${\mathbf{\text{profilin}}}_{{\text{ENT}}_1}$ 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

Specific antibodies to ${\mathbf{\text{myosin heavy chain}}}_{{\text{ENT}}_2}$ isoforms (SM1, SM2, ${\mathbf{\text{SMemb}}}_{{\text{ENT}}_1}$), caldesmon, and alpha-smooth muscle actin and cDNAs for SMemb were used.

A.d28.s234.p1

We have identified a new TNF-related ligand, designated human ${\mathbf{\text{GITR}}}_{{\text{ENT}}_1}$ ligand (${\mathbf{\text{hGITRL}}}_{{\text{ENT}}_2}$), and its human receptor (hGITR), an ortholog of the recently discovered murine glucocorticoid-induced TNFR-related (mGITR) protein [4].

B.d765.s0.p14

To determine the relationship between cell cycle regulation and differentiation, the spatiotemporal expression of cyclin A, cyclin B1, cyclin D1, the ${\mathbf{\text{cyclin-dependent kinase inhibitors}}}_{{\text{ENT}}_1}$ (CKIs) p27 and ${\mathbf{\text{p57}}}_{{\text{ENT}}_2}$, and markers of differentiating podocytes in developing human kidneys was investigated by immunohistochemistry.

B.d296.s2.p23

In normal livers, ${\mathbf{\text{E-cad}}}_{{\text{ENT}}_1}$, ${\mathbf{\text{alpha-catenin}}}_{{\text{ENT}}_2}$ 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

However, a number of mammalian DNA repair proteins lack NLS clusters; these proteins include ERCC1, ERCC2 (XPD), mouse RAD51, and the HHR23B/${\mathbf{\text{p58}}}_{{\text{ENT}}_1}$ and ${\mathbf{\text{HHR23A}}}_{{\text{ENT}}_2}$ subunits of XPC.

B.d833.s0.p35

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, ${\mathbf{\text{cadherins}}}_{{\text{ENT}}_1}$, 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

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 (${\mathbf{\text{CKIs}}}_{{\text{ENT}}_1}$) p27 and ${\mathbf{\text{p57}}}_{{\text{ENT}}_2}$, and markers of differentiating podocytes in developing human kidneys was investigated by immunohistochemistry.

B.d833.s0.p34

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, cadherins, alpha-catenin, beta-catenin, plakoglobin, ${\mathbf{\text{vinculin}}}_{{\text{ENT}}_1}$ and alpha-actinin appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.

B.d506.s0.p4

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, ${\mathbf{\text{myosin heavy chain}}}_{{\text{ENT}}_2}$, ${\mathbf{\text{actin}}}_{{\text{ENT}}_1}$, and desmin.

B.d833.s0.p7

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, cadherins, alpha-catenin, ${\mathbf{\text{beta-catenin}}}_{{\text{ENT}}_1}$, 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

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${\mathit{\text{EN}}T}_1$, ${\mathbf{\text{myosin heavy chain}}}_{{\text{ENT}}_2}$, actin, and desmin.

B.d833.s0.p29

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, cadherins, alpha-catenin, beta-catenin, ${\mathbf{\text{plakoglobin}}}_{{\text{ENT}}_1}$, 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

Within 1 hour of raising the concentration of calcium ions, ${\mathbf{\text{integrins}}}_{{\text{ENT}}_2}$, cadherins, alpha-catenin, beta-catenin, plakoglobin, vinculin and ${\mathbf{\text{alpha-actinin}}}_{{\text{ENT}}_1}$ appeared to accumulate at cell-cell borders, whereas the focal contact proteins, paxillin and talin, did not.

A.d60.s528.p0

The ${\mathbf{\text{v-Raf}}}_{{\text{ENT}}_1}$ proteins purified from cells infected with EC12 or 22W viruses activated ${\mathbf{\text{MAP kinase}}}_{{\text{ENT}}_2}$ kinase from skeletal muscle in vitro.

B.d180.s0.p0

${\mathbf{\text{DR3}}}_{{\text{ENT}}_2}$ signal transduction is mediated by a complex of intracellular signaling molecules including ${\mathbf{\text{TRADD}}}_{{\text{ENT}}_1}$, TRAF2, FADD, and FLICE.

A.d114.s961.p0

${\mathbf{\text{Syntrophin}}}_{{\text{ENT}}_1}$ binds to an alternatively spliced exon of ${\mathbf{\text{dystrophin}}}_{{\text{ENT}}_2}$.

B.d93.s0.p9

Because ${\mathbf{\text{histone}}}_{{\text{ENT}}_1}$ H3 shares many structural features with histone H4 and is intimately associated with ${\mathbf{\text{H4}}}_{{\text{ENT}}_2}$ in the assembled nucleosome, we asked whether H3 has similar functions.

B.d749.s0.p2

Three actin-associated proteins, actin-binding protein, ${\mathbf{\text{gelsolin}}}_{{\text{ENT}}_1}$, and profilin, influence gelation, solation, and polymerization, respectively, of ${\mathbf{\text{actin}}}_{{\text{ENT}}_2}$ in vitro.

B.d639.s0.p0

The main inhibitory action of p27, a cyclin-dependent kinase inhibitor (${\mathbf{\text{CDKI}}}_{{\text{ENT}}_1}$), arises from its binding with the cyclin E/${\mathbf{\text{cyclin-dependent kinase 2}}}_{{\text{ENT}}_2}$ (Cdk2) complex that results in G(1)-S arrest.

B.d334.s0.p0

In extracts from mouse brain, ${\mathbf{\text{profilin I}}}_{{\text{ENT}}_2}$ and profilin II can form complexes with regulators of endocytosis, synaptic vesicle recycling and ${\mathbf{\text{actin}}}_{{\text{ENT}}_1}$ assembly.

A.d141.s1189.p0

The cyclin-dependent kinase ${\mathbf{\text{Cdk2}}}_{{\text{ENT}}_1}$ associates with ${\mathbf{\text{cyclins A}}}_{{\text{ENT}}_2}$, D, and E and has been implicated in the control of the G1 to S phase transition in mammals.

B.d485.s0.p2

PF4-dependent downregulation of cyclin E-cdk2 activity was associated with increased binding of the ${\mathbf{\text{cyclin-dependent kinase inhibitor}}}_{{\text{ENT}}_1}$, p21(Cip1/WAF1), to the ${\mathbf{\text{cyclin E}}}_{{\text{ENT}}_2}$-cdk2 complex.

A.d157.s1329.p4

Deletion analysis and binding studies demonstrate that a third enzyme, protein kinase C (${\mathbf{\text{PKC}}}_{{\text{ENT}}_1}$), binds ${\mathbf{\text{AKAP79}}}_{{\text{ENT}}_2}$ at a site distinct from those bound by PKA or CaN.

A.d60.s529.p0

Furthermore, a bacterially expressed ${\mathbf{\text{v-Raf}}}_{{\text{ENT}}_1}$ fusion protein (glutathione S-transferase-p3722W) also activated ${\mathbf{\text{MAP kinase}}}_{{\text{ENT}}_2}$ kinase in vitro.

A.d199.s1701.p0

${\mathbf{\text{Sos}}}_{{\text{ENT}}_1}$ in complex with a previously identified 90-kDa protein and designated protein ${\mathbf{\text{80K-H}}}_{{\text{ENT}}_2}$.

A.d161.s1355.p0

${\mathbf{\text{SHPTP2}}}_{{\text{ENT}}_1}$ associates with the ${\mathbf{\text{platelet-derived growth factor}}}_{{\text{ENT}}_2}$ (PDGF) receptor after ligand stimulation, and binding of SHPTP2 to this receptor promotes tyrosine phosphorylation of SHPTP2.

B.d357.s0.p1

${\mathbf{\text{Integrin}}}_{{\text{ENT}}_1}$ (beta) chains, for example, interact with actin-binding proteins (e.g. ${\mathbf{\text{talin}}}_{{\text{ENT}}_2}$ and filamin), which form mechanical links to the cytoskeleton.

A.d195.s1663.p2

Intriguingly, NR1-${\mathbf{\text{calmodulin}}}_{{\text{ENT}}_1}$ binding is directly antagonized by Ca2+/${\mathbf{\text{alpha-actinin}}}_{{\text{ENT}}_2}$.

A.d151.s1288.p1

Immunoprecipitation assays also show a weak substoichiometric association of the ${\mathbf{\text{TATA-binding protein}}}_{{\text{ENT}}_1}$ (TBP) with ${\mathbf{\text{PTF}}}_{{\text{ENT}}_2}$, 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

PF4-dependent downregulation of cyclin E-cdk2 activity was associated with increased binding of the ${\mathbf{\text{cyclin-dependent kinase inhibitor}}}_{{\text{ENT}}_1}$, p21(Cip1/WAF1), to the cyclin E-${\mathbf{\text{cdk2}}}_{{\text{ENT}}_2}$ complex.

B.d814.s0.p26

We have shown that the ${\mathbf{\text{FH proteins}}}_{{\text{ENT}}_2}$ Bni1p and Bnr1p are potential targets of the Rho family small GTP-binding proteins and bind to an actin-binding protein, ${\mathbf{\text{profilin}}}_{{\text{ENT}}_1}$, at their proline-rich FH1 domains to regulate reorganization of the actin cytoskeleton in the yeast Saccharomyces cerevisiae.

B.d14.s0.p4

Actin-binding proteins such as ${\mathbf{\text{profilin}}}_{{\text{ENT}}_2}$ and gelsolin bind to phosphatidylinositol (PI) 4,5-bisphosphate (PI 4,5-P2) and regulate the concentration of monomeric ${\mathbf{\text{actin}}}_{{\text{ENT}}_1}$.

A.d39.s340.p0

Chloramphenicol acetyltransferase assays in F9 cells showed that ${\mathbf{\text{PS1}}}_{{\text{ENT}}_1}$ suppresses transactivation by ${\mathbf{\text{c-Jun}}}_{{\text{ENT}}_2}$/c-Jun but not by c-Jun/c-Fos heterodimers, consistent with the reported function of QM/Jif-1.

B.d307.s0.p4

In Acanthamoeba ${\mathbf{\text{actin}}}_{{\text{ENT}}_2}$ polymerization is regulated, at least in part, by profilin, which binds to ${\mathbf{\text{actin}}}_{{\text{ENT}}_1}$ monomers, and by capping protein, which both nucleates polymerization and blocks monomer addition at the ’barbed’ end of the filament.

B.d35.s4.p9

We conclude that Aip1p is a ${\mathbf{\text{cofilin}}}_{{\text{ENT}}_2}$-associated protein that enhances the filament disassembly activity of cofilin and restricts ${\mathbf{\text{cofilin}}}_{{\text{ENT}}_1}$ localization to cortical actin patches.

L.d35.s1.p1

Our data demonstrate that the ${\mathbf{\text{CtsR}}}_{{\text{ENT}}_1}$ 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 ${\mathbf{\text{sigmaA}}}_{{\text{ENT}}_2}$-dependent promoter and might be inactivated or dissociate under inducing stress conditions.

B.d14.s1.p2

These studies suggest that profilin and ${\mathbf{\text{gelsolin}}}_{{\text{ENT}}_2}$ may control the generation of 3-OH phosphorylated phosphoinositides, which in turn may regulate the ${\mathbf{\text{actin}}}_{{\text{ENT}}_1}$ polymerization.

I.d11.s28.p1

The ${\mathbf{\text{phospholipase C}}}_{{\text{ENT}}_1}$ inhibitor U 71322 prevented the activation of phospholipase C by ${\mathbf{\text{A beta P}}}_{{\text{ENT}}_2}$

L.d13.s0.p1

Production of ${\mathbf{\text{sigmaK}}}_{{\text{ENT}}_1}$ about 1 h earlier than normal does affect Spo0A, which when phosphorylated is an activator of ${\mathbf{\text{sigE}}}_{{\text{ENT}}_2}$ transcription.

A.d78.s669.p2

Our data suggest that ${\mathbf{\text{TR6}}}_{{\text{ENT}}_1}$ inhibits the interactions of LIGHT with HVEM / / ${\mathbf{\text{TR2}}}_{{\text{ENT}}_2}$ and LTbetaR, thereby suppressing LIGHT-mediated HT29 cell death.

B.d223.s0.p9

Furthermore, the deletion of ${\mathbf{\text{SJL1}}}_{{\text{ENT}}_2}$ suppresses the temperature-sensitive growth defect of sac6, a mutant in yeast ${\mathbf{\text{fimbrin}}}_{{\text{ENT}}_1}$, supporting a role for synaptojanin family members in actin function.