Wiki-Pi version 2

This is a resource centered on protein-protein interactions (PPIs), built over Wiki-Pi, extending it to present the PPIs that are predicted HiPPIP program. In addition to previously known PPIs of human genes, collected from BioGRID and HPRD, this resource presents novel PPIs of genes linked to a few of the diseases that we studied (Neuropsychiatric Disorders (Schizophrenia, Major Depressive Disorder, ADHD, Autism Spectrum Disorder and Bipolar Disorder), COVID-19, mesotheliomas, congenital heart disease, and rheumatoid arthritis, and the organelle cilia. The novel PPIs are predicted with HiPPIP: a High-confidence Protein-Protein Interaction Prediction model that we presented previously. The website will have functionality to retrieve and discover interactions effectively, through simple queries such as associations to diseases or pathways, or complex queries conditioned on annotations of one or both proteins in the interaction. We propose to update the backend database once a month to reflect recently-assembled annotations of the proteins. Each interaction will be provided with automatically updated annotations of individual proteins from databases such as Gene Ontology, KEGG, REACTOM, Pubmed2ENSEMBL, and DrugBank. Most importantly, we will enable “wiki-style” capabilities to allow registered users to discuss the PPIs, especially the novel PPIs that hold a potential for translational impact.

Please cite the following papers when referring to each of these components:

HiPPIP: Ganapathiraju MK, et al (2016) Schizophrenia interactome with 504 novel protein–protein interactions. npj Schizophrenia 2, Article number: 16012, doi:10.1038/npjschz.2016.12.

Wiki-Pi: Orii N, Ganapathiraju MK (2012) Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function. PLoS ONE 7(11): e49029. doi:10.1371/journal.pone.0049029.

Disease-specific interactomes are described in the following publications

Schizophrenia Interactome: Ganapathiraju MK, et al (2016) Schizophrenia interactome with 504 novel protein–protein interactions. npj Schizophrenia 2, Article number: 16012, doi:10.1038/npjschz.2016.12.
Rheumatoid Arthritis Interactome: Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data, npj Schizophrenia, 3 (11), 2017.
MPM Interactome: Karunakaran KB, Yanamala N, Boyce G, Becich MJ and Ganapathiraju MK. Mesothelioma Interactome with 364 Novel Protein-Protein Interactions. Cancers. 13 (7), 1660, 2020.
Cilia Interactome: Cilia interactome with predicted protein–protein interactions reveals connections to Alzheimer’s disease, aging and other neuropsychiatric processes, Scientific Reports, 10 (15629 ), 2017.

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