Integrating human omics data to prioritize candidate genes

BMC Medical Genomics
Yong ChenRui Jiang

Abstract

The identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a protein-protein interaction network for the prioritization of candidate genes, other valuable omics data sources have been largely overlooked in these methods. With this understanding, we proposed a method called BRIDGE to prioritize candidate genes by integrating disease phenotypic similarities with such omics data as protein-protein interactions, gene sequence similarities, gene expression patterns, gene ontology annotations, and gene pathway memberships. BRIDGE utilizes a multiple regression model with lasso penalty to automatically weight different data sources and is capable of discovering genes associated with diseases whose genetic bases are completely unknown. We conducted large-scale cross-validation experiments and demonstrated that more than 60% known disease genes can be ranked top one by BRIDGE in simulated linkage intervals, suggesting the superior performance of this method. We further performed two comprehensive case studies by applying BRIDGE to predict novel genes and transcriptional networks involved in obe...Continue Reading

References

Aug 1, 1993·Nature Genetics·M S BoguskiC M Tolstoshev
May 15, 2002·Nature Genetics·Carolina Perez-IratxetaMiguel A Andrade
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Martin OlbrotArun Sharma
Jan 10, 2003·Nucleic Acids Research·V MatysE Wingender
Sep 26, 2003·Pathology International·Tatsuo Tomita
Nov 13, 2003·Genome Biology·Frances S TurnerColin A M Semple
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Jun 8, 2004·Nucleic Acids Research·Núria López-Bigas, Christos A Ouzounis
Jun 24, 2004·Nature Reviews. Genetics·Han G Brunner, Marc A van Driel
Aug 31, 2004·Nature Immunology·Daniel L Mueller
Mar 16, 2005·BMC Bioinformatics·Euan A AdieBen S Pickard
Mar 29, 2005·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Suheeta RoyDavid E Cohen
Jun 28, 2005·Nucleic Acids Research·Stein AertsBart De Moor
Feb 24, 2006·European Journal of Human Genetics : EJHG·Marc A van DrielJack A M Leunissen
May 9, 2006·Nature Biotechnology·Stein AertsYves Moreau
Jun 20, 2006·Physiology & Behavior·Yi Zhang, Philip J Scarpace
Jan 24, 2007·Bioinformatics·Kyle J GaultonTodd J Vision
Mar 9, 2007·Bioinformatics·James Z WangChin-Fu Chen
Mar 9, 2007·Nature Biotechnology·Kasper LageSøren Brunak
Mar 16, 2007·American Journal of Human Genetics·Victor A McKusick
Apr 13, 2007·The New England Journal of Medicine·Kristina I Rother
May 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kwang-Il GohAlbert-László Barabási
Jul 27, 2007·The New England Journal of Medicine·Albert-László Barabási
Sep 14, 2007·Clinical Pharmacology and Therapeutics·J A BatsisF Lopez-Jimenez
Oct 9, 2007·Bioinformatics·Sergey A ShiryevRicha Agarwala
Oct 13, 2007·Science·Laura D WoodBert Vogelstein
Nov 17, 2007·Nature Reviews. Genetics·Günter P WagnerJames M Cheverud
Mar 18, 2008·Nature·Valur EmilssonKari Stefansson
May 9, 2008·Molecular Systems Biology·Xuebing WuShao Li
Oct 23, 2008·Nucleic Acids Research·Sarah HunterCorin Yeats
Dec 17, 2008·Nature Genetics·Cristen J WillerUNKNOWN Genetic Investigation of ANthropometric Traits Consortium
Jan 16, 2009·BMC Genomics·Damian SmedleyArek Kasprzyk

❮ Previous
Next ❯

Citations

Apr 8, 2014·BioMed Research International·Quan ZouXiangxiang Zeng
Jun 26, 2014·Computational and Mathematical Methods in Medicine·Mingxin Gan
Mar 5, 2015·Computational Biology and Chemistry·Zhi-Qin ZhaoJinyan Li
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Dongdong LinYu-Ping Wang
Oct 12, 2016·Journal of Biomedical Informatics·Zahra Razaghi-MoghadamMorteza Ebrahimi
Dec 23, 2017·Briefings in Bioinformatics·Giulia TiniMarie-Pier Scott-Boyer
Sep 9, 2019·Journal of Integrative Bioinformatics·Olga Zolotareva, Maren Kleine
Oct 1, 2019·Briefings in Bioinformatics·Pingjian DingChee-Keong Kwoh
Sep 19, 2019·Scientific Reports·Shuaichao WangShuangge Ma
Dec 5, 2020·Briefings in Bioinformatics·Sezin Kircali AtaXiao-Li Li
Aug 13, 2021·PLoS Computational Biology·Ran DuanSongwei Jia

❮ Previous
Next ❯

Software Mentioned

AlignPI
Ensemble
CIPHER
GeneCards
GOSemSim
BRIDGE Identify GEnes
Matlab
DAVID
BioMart
BRIDGE

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.