Dataset Information

MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes.

ABSTRACT: Microbe induced cardiovascular diseases (CVDs) are less studied at present. Host-pathogen interactions (HPIs) between human proteins and microbial proteins associated with CVD can be found dispersed in existing molecular interaction databases. MorCVD database is a curated resource that combines 23,377 protein interactions between human host and 432 unique pathogens involved in CVDs in a single intuitive web application. It covers endocarditis, myocarditis, pericarditis and 16 other microbe induced CVDs. The HPI information has been compiled, curated, and presented in a freely accessible web interface ( http://morcvd.sblab-nsit.net/About ). Apart from organization, enrichment of the HPI data was done by adding hyperlinked protein ID, PubMed, gene ontology records. For each protein in the database, drug target and interactors (same as well as different species) information has been provided. The database can be searched by disease, protein ID, pathogen name or interaction detection method. Interactions detected by more than one method can also be listed. The information can be presented in tabular form or downloaded. A comprehensive help file has been developed to explain the various options available. Hence, MorCVD acts as a unified resource for retrieval of HPI data for researchers in CVD and microbiology.

SUBMITTER: Singh N

PROVIDER: S-EPMC6411875 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Publications

MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes.

Singh Nirupma N Bhatia Venugopal V Singh Shubham S Bhatnagar Sonika S

Scientific reports 20190311 1

Microbe induced cardiovascular diseases (CVDs) are less studied at present. Host-pathogen interactions (HPIs) between human proteins and microbial proteins associated with CVD can be found dispersed in existing molecular interaction databases. MorCVD database is a curated resource that combines 23,377 protein interactions between human host and 432 unique pathogens involved in CVDs in a single intuitive web application. It covers endocarditis, myocarditis, pericarditis and 16 other microbe induc ...[more]

PMID: 30858555

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Project description:MotivationAn important aspect of infectious disease research involves understanding the differences and commonalities in the infection mechanisms underlying various diseases. Systems biology-based approaches study infectious diseases by analyzing the interactions between the host species and the pathogen organisms. This work aims to combine the knowledge from experimental studies of host-pathogen interactions in several diseases to build stronger predictive models. Our approach is based on a formalism from machine learning called 'multitask learning', which considers the problem of building models across tasks that are related to each other. A 'task' in our scenario is the set of host-pathogen protein interactions involved in one disease. To integrate interactions from several tasks (i.e. diseases), our method exploits the similarity in the infection process across the diseases. In particular, we use the biological hypothesis that similar pathogens target the same critical biological processes in the host, in defining a common structure across the tasks.ResultsOur current work on host-pathogen protein interaction prediction focuses on human as the host, and four bacterial species as pathogens. The multitask learning technique we develop uses a task-based regularization approach. We find that the resulting optimization problem is a difference of convex (DC) functions. To optimize, we implement a Convex-Concave procedure-based algorithm. We compare our integrative approach to baseline methods that build models on a single host-pathogen protein interaction dataset. Our results show that our approach outperforms the baselines on the training data. We further analyze the protein interaction predictions generated by the models, and find some interesting insights.AvailabilityThe predictions and code are available at: http://www.cs.cmu.edu/∼mkshirsa/ismb2013_paper320.html .Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes.

Publications

MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes.

Similar Datasets

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