NDLI: Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems

Content Provider	Springer Nature : BioMed Central
Author	Shu, Le Zhao, Yuqi Kurt, Zeyneb Byars, Sean Geoffrey Tukiainen, Taru Kettunen, Johannes Orozco, Luz D. Pellegrini, Matteo Lusis, Aldons J. Ripatti, Samuli Zhang, Bin Inouye, Michael Mäkinen, Ville-Petteri Yang, Xia
Abstract	Background Complex diseases are characterized by multiple subtle perturbations to biological processes. New omics platforms can detect these perturbations, but translating the diverse molecular and statistical information into testable mechanistic hypotheses is challenging. Therefore, we set out to create a public tool that integrates these data across multiple datasets, platforms, study designs and species in order to detect the most promising targets for further mechanistic studies. Results We developed Mergeomics, a computational pipeline consisting of independent modules that 1) leverage multi-omics association data to identify biological processes that are perturbed in disease, and 2) overlay the disease-associated processes onto molecular interaction networks to pinpoint hubs as potential key regulators. Unlike existing tools that are mostly dedicated to specific data type or settings, the Mergeomics pipeline accepts and integrates datasets across platforms, data types and species. We optimized and evaluated the performance of Mergeomics using simulation and multiple independent datasets, and benchmarked the results against alternative methods. We also demonstrate the versatility of Mergeomics in two case studies that include genome-wide, epigenome-wide and transcriptome-wide datasets from human and mouse studies of total cholesterol and fasting glucose. In both cases, the Mergeomics pipeline provided statistical and contextual evidence to prioritize further investigations in the wet lab. The software implementation of Mergeomics is freely available as a Bioconductor R package. Conclusion Mergeomics is a flexible and robust computational pipeline for multidimensional data integration. It outperforms existing tools, and is easily applicable to datasets from different studies, species and omics data types for the study of complex traits.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-016-3198-9.pdf
Ending Page	16
Page Count	16
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-016-3198-9
Journal	BMC Genomics
Issue Number	1
Volume Number	17
Language	English
Publisher	BioMed Central
Publisher Date	2016-11-04
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Mergeomics Integrative genomics Multidimensional data integration Functional genomics Gene networks Key drivers Cholesterol Blood glucose
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration

Genomics Portals: integrative web-platform for mining genomics data

Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems

Dintor: functional annotation of genomic and proteomic data

Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia

Synergistic use of plant-prokaryote comparative genomics for functional annotations

A novel method to identify gene interaction patterns

iMarmot: an integrative platform for comparative and functional genomics of marmots

Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems

Similar Documents

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration

Genomics Portals: integrative web-platform for mining genomics data

Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems

Dintor: functional annotation of genomic and proteomic data

Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia

Synergistic use of plant-prokaryote comparative genomics for functional annotations

A novel method to identify gene interaction patterns

iMarmot: an integrative platform for comparative and functional genomics of marmots

Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems