"iNETgrate": integrating DNA methylation and gene expression data in a single gene network.


Journal

Research square
Titre abrégé: Res Sq
Pays: United States
ID NLM: 101768035

Informations de publication

Date de publication:
18 Aug 2023
Historique:
pubmed: 30 8 2023
medline: 30 8 2023
entrez: 30 8 2023
Statut: epublish

Résumé

Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package (https://bioconductor.org/packages/iNETgrate/) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.

Identifiants

pubmed: 37645739
doi: 10.21203/rs.3.rs-3246325/v1
pmc: PMC10462231
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NIA NIH HHS
ID : P30 AG072975
Pays : United States
Organisme : NIA NIH HHS
ID : U01 AG046152
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG017917
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG057896
Pays : United States
Organisme : NIA NIH HHS
ID : RF1 AG063507
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG068293
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG015819
Pays : United States
Organisme : NIA NIH HHS
ID : U01 AG061356
Pays : United States
Organisme : NIA NIH HHS
ID : RF1 AG065301
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG036042
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG010161
Pays : United States
Organisme : NINDS NIH HHS
ID : U19 NS115388
Pays : United States
Organisme : NINDS NIH HHS
ID : RF1 NS112391
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG066546
Pays : United States
Organisme : NIA NIH HHS
ID : RF1 AG057473
Pays : United States
Organisme : NIA NIH HHS
ID : RF1 AG059082
Pays : United States

Déclaration de conflit d'intérêts

Competing interests The authors declare no competing interests.

Auteurs

Sogand Sajedi (S)

Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.
Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, Texas 78229, USA.

Ghazal Ebrahimi (G)

Bioinformatics Program, the University of British Columbia, Vancouver, BC, Canada.

Raheleh Roudi (R)

Department of Radiology, Stanford University School of Medicine, Stanford, California 94305, USA.

Isha Mehta (I)

Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

Hanie Samimi (H)

School of Architecture, University of Utah, Salt Lake City, Utah 84112, USA.

Shiva Kazempour (S)

Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.
Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, Texas 78229, USA.

Aamir Zainulabadeen (A)

Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.

Thomas Roderick Docking (TR)

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.

Sukeshi Patel Arora (SP)

Mays Cancer Center, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.

Francisco Cigarroa (F)

Malu and Carlos Alvarez Center for Transplantation, Hepatobiliary Surgery and Innovation, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.

Sudha Seshadri (S)

Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, Texas 78229, USA.
Department of Neurology, University of Texas, San Antonio, Texas 78229, USA.
Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02139,USA.

Aly Karsan (A)

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.

Habil Zare (H)

Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.
Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, Texas 78229, USA.

Classifications MeSH