Table 7.

Examples of relations in the test set. For each example we give the article identifier (PMID), the relation as extracted by curators specified as two Entrez Gene IDs, the number of systems that extracted that particular relation and a text excerpt from the corresponding abstract that describes the relation. The gene mentions are highlighted in the text excerpt, and the Entrez Gene IDs are given in parenthesis. The relations that have not been detected by systems are typically described in several sentences, describe the absence of an interaction with another protein or contain a self-interaction

PMID	Relation	Number of systems	Text
15700267	1398, 1793	13	Contrary to the effects of the true dominant negative SH2 domain mutants (R38K CrkII) and SH3-N domain mutants (W170K CrkII) that prevent macromolecular assembly of signaling proteins, W276K CrkII increases association between DOCK180 (1793) and CrkII (1398) as well as constitutive tethering of the Crk/DOCK180/ELMO protein complex that interacted with RhoG.
16969499	672, 7157	13	Co-immunoprecipitation assays of Escherichia coli-expressed wild-type and mutated BRCTs challenged with a HeLa cell extract revealed, for the S1841 N variant a significant reduction in the binding activity to p53, while the W1837R mutant showed an inverse effect. Furthermore, a clonogenic soft agar growth assay performed on HeLa cells stably transfected with either wild-type or mutant BRCA1 showed a marked decrease of the growth in wild-type BRCA1-overexpressing cells and in BRCA1S1841N-transfected cells, while no significant changes were detected in the BRCA1W1837R-transfected cells. These results demonstrate that distinct single nucleotide changes in the BRCT domain of BRCA1 (672) affect binding of this protein to the tumor suppressor p53 (7157).
11463845	1026, 207	5	Here we demonstrate that Akt (207) phosphorylates the cell cycle inhibitory protein p21(Cip1) (1026) at Thr 145 in vitro and in intact cells as shown by in vitro kinase assays, site-directed mutagenesis and phospho-peptide analysis.
9234717	12402, 18595	4	In vitro, Cbl-N (12402) directly bound to PDGFR alpha (18595) derived from PDGF-AA-stimulated cells but not to that from unstimulated cells, and this binding was abrogated by a point mutation (G306E) corresponding to a loss-of-function mutation in SLI-1.
16144832	300772, 60590	0	Pias1(300772) binding to mGluR8-C60590 required a region N-terminal to a consensus sumoylation motif and was not affected by arginine substitution of the conserved lysine 882 within this motif.
8623535	1489075, 1489080	0	The E2 binding activity of E1 deletion and point mutant proteins were assayed using glutathione S-transferase E1 fusion proteins and in vitro translated proteins. At 4, the C-terminal portion of E1 (1489075) including amino acids 312–644 was sufficient for E2 (1489080) binding. Introduction of C-terminal deletions or a point mutation at position 586 (Pro → Glu) resulted in the loss of the E2 binding activity.
14985338	6804, 9751	0	cAMP-dependent protein kinase (PKA) can modulate synaptic transmission by acting directly on the neurotransmitter secretory machinery. Here we identify one possible target, syntaphilin, which was identified as a molecular clamp that controls free syntaxin-1 and dynamin-1 availability and thereby regulates synaptic vesicle exocytosis and endocytosis. Deletion mutation and site-directed mutagenesis experiments pinpoint dominant PKA phosphorylation sites to serines 43 and 56. PKA phosphorylation of syntaphilin significantly decreases its binding to syntaxin-1A (6804) in vitro. A syntaphilin (9751) mutation of serine 43 to aspartic acid (S43D) shows similar effects on binding.
15769741	285, 285	0	In addition, improper creation of a new cysteine in Ang2 (285) (Ang2S263C) dramatically induced Ang2 aggregation without activating Tie2.
9099695	495516, 495516	0	These mutants confirmed that Ser-190 is a major autophosphorylation site of Pim-1 (495516).
9786907	1030, 1030	0	Analytical centrifugation allowed to determine that p15 (1030) assembles as a rod-shaped tetramer. Oxidative cross-linking of N-terminal cysteines of the peptide generated specific covalent oligomers, indicating that the N terminus of p15 is a coiled coil that assembles as a parallel tetramer. Mutation of Lys22 into Asp destabilized the tetramer and put forward the presence of a salt bridge between Lys22 and Asp24 in a model building of the stalk.