Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package

Sogand Sajedi; Ghazal Ebrahimi; Raheleh Roudi; Isha Mehta; Amirreza Heshmat; Hanie Samimi; Shiva Kazempour; Aamir Zainulabadeen; Thomas Roderick Docking; Sukeshi Patel Arora; Francisco Cigarroa; Sudha Seshadri; Aly Karsan; Habil Zare

doi:10.1038/s41598-023-48237-8

Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package

Sci Rep. 2023 Dec 8;13(1):21721. doi: 10.1038/s41598-023-48237-8.

Authors

Sogand Sajedi^#^{1

2}, Ghazal Ebrahimi^#³, Raheleh Roudi⁴, Isha Mehta⁵, Amirreza Heshmat⁶, Hanie Samimi⁷, Shiva Kazempour^{1

2}, Aamir Zainulabadeen⁸, Thomas Roderick Docking⁹, Sukeshi Patel Arora¹⁰, Francisco Cigarroa¹¹, Sudha Seshadri^{2

12

13}, Aly Karsan⁹, Habil Zare^{14

15

16}

Affiliations

¹ Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
² Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA.
³ Bioinformatics Program, The University of British Columbia, Vancouver, BC, Canada.
⁴ Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
⁵ Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
⁶ Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
⁷ School of Architecture, University of Utah, Salt Lake City, UT, 84112, USA.
⁸ Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA.
⁹ Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
¹⁰ Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
¹¹ Malu and Carlos Alvarez Center for Transplantation, Hepatobiliary Surgery and Innovation, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
¹² Department of Neurology, University of Texas, San Antonio, TX, 78229, USA.
¹³ Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, 02139, USA.
¹⁴ Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, 78229, USA. zare@uthscsa.edu.
¹⁵ Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, San Antonio, TX, 78229, USA. zare@uthscsa.edu.
¹⁶ Department of Cell Systems & Anatomy, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA. zare@uthscsa.edu.

^# Contributed equally.

Abstract

Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. 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.

MeSH terms

DNA Methylation*
Gene Expression
Gene Regulatory Networks
Humans
Software*

Abstract

MeSH terms

Grants and funding