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APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.

ABSTRACT: APID (Agile Protein Interactomes DataServer) is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes. This resource is a new, fully redesigned server that includes a comprehensive collection of protein interactomes for more than 400 organisms (25 of which include more than 500 interactions) produced by the integration of only experimentally validated protein-protein physical interactions. For each protein-protein interaction (PPI) the server includes currently reported information about its experimental validation to allow selection and filtering at different quality levels. As a whole, it provides easy access to the interactomes from specific species and includes a global uniform compendium of 90,379 distinct proteins and 678,441 singular interactions. APID integrates and unifies PPIs from major primary databases of molecular interactions, from other specific repositories and also from experimentally resolved 3D structures of protein complexes where more than two proteins were identified. For this purpose, a collection of 8,388 structures were analyzed to identify specific PPIs. APID also includes a new graph tool (based on Cytoscape.js) for visualization and interactive analyses of PPI networks. The server does not require registration and it is freely available for use at http://apid.dep.usal.es.

SUBMITTER: Alonso-Lopez D

PROVIDER: S-EPMC4987915 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectiveTo evaluate the effect of a specific communication training for neurologists on how to provide complex information about treatment options to patients with multiple sclerosis (MS).DesignSingle-centre, single-blind, randomised controlled trial.SettingOne university hospital in Norway.ParticipantsThirty-four patients with early-stage MS.InterventionA 3-hour training for neurologists on how to provide complex information about MS escalation therapy.Main outcome measuresPatient recall rate, measured with a reliable counting system of provided and recalled information about drugs.Secondary outcome measuresNumber of information units provided by the physicians. Effects on patient involvement through questionnaires.MethodsPatients with MS were instructed to imagine a disease development and were randomised and blinded to meet a physician to receive information on escalation therapy, before or after the physician had participated in a 3-hour training on how to provide complex information. Consultations and immediate patient recall interviews were video-recorded and transcribed verbatim.ResultsPatient recall rate was 0.37 (SD=0.10) pre-intervention and 0.39 (SD=0.10) post-intervention. The effect of the intervention on recall rate predicted with a general linear model covariate was not significant (coefficient parameter 0.07 (SE 0.04, 95% CI (-0.01 to 0.15)), p=0.099).The physicians tended to provide significantly fewer information units after the training, with an average of 91.0 (SD=30.3) pre-intervention and 76.5 (SD=17.4) post-intervention; coefficient parameter -0.09 (SE 0.02, 95% CI (-0.13 to -0.05)), p<0.001. There was a significant negative association between the amount of provided information and the recall rate (coefficient parameter -0.29 (SE 0.05, 95% CI (-0.39 to -0.18)), p<0.001). We found no significant effects on patient involvement using the Control Preference Scale, Collaborate or Four Habits Patient Questionnaire.ConclusionA brief course for physicians on providing complex information reduced the amount of information provided, but did not improve patient recall rate.Trial registration numberISRCTN42739508.

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APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.

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