iFad: an integrative factor analysis model for drug-pathway association inference.

Bioinformatics
Haisu Ma, Hongyu Zhao

Abstract

Pathway-based drug discovery considers the therapeutic effects of compounds in the global physiological environment. This approach has been gaining popularity in recent years because the target pathways and mechanism of action for many compounds are still unknown, and there are also some unexpected off-target effects. Therefore, the inference of drug-pathway associations is a crucial step to fully realize the potential of system-based pharmacological research. Transcriptome data offer valuable information on drug-pathway targets because the pathway activities may be reflected through gene expression levels. Hence, it is of great interest to jointly analyze the drug sensitivity and gene expression data from the same set of samples to investigate the gene-pathway-drug-pathway associations. We have developed iFad, a Bayesian sparse factor analysis model to jointly analyze the paired gene expression and drug sensitivity datasets measured across the same panel of samples. The model enables direct incorporation of prior knowledge regarding gene-pathway and/or drug-pathway associations to aid the discovery of new association relationships. We use a collapsed Gibbs sampling algorithm for inference. Satisfactory performance of the propo...Continue Reading

References

Sep 13, 2001·Proceedings of the National Academy of Sciences of the United States of America·J E StauntonT R Golub
Sep 5, 2002·Nature Reviews. Drug Discovery·Andrew L Hopkins, Colin R Groom
Mar 8, 2005·Journal of Bioinformatics and Computational Biology·Jeong-Ho ChangByoung-Tak Zhang
Mar 18, 2005·Protein Science : a Publication of the Protein Society·Maria I Zavodszky, Leslie A Kuhn
Dec 27, 2005·Drug Discovery Today·Andreas P Russ, Stefan Lampel
Dec 31, 2005·Nucleic Acids Research·Gary D BaderChris Sander
Jan 3, 2006·American Journal of Respiratory and Critical Care Medicine·Sina A GharibWilliam A Altemeier
Sep 23, 2006·Nature Reviews. Cancer·Robert H Shoemaker
Nov 8, 2006·Molecular Cancer Therapeutics·Ogechi N IkediobiRichard Wooster
Feb 27, 2007·BMC Bioinformatics·Iosifina Pournara, Lorenz Wernisch
Mar 7, 2007·Molecular Cancer Therapeutics·Uma T ShankavaramJohn N Weinstein
Oct 9, 2007·Nature Biotechnology·Muhammed A YildirimMarc Vidal
Nov 23, 2007·Nucleic Acids Research·Tina Hernandez-BoussardTeri E Klein
Dec 1, 2007·Nucleic Acids Research·David S WishartMurtaza Hassanali
Dec 18, 2007·Nucleic Acids Research·Michael KuhnPeer Bork
Feb 5, 2008·International Journal of Cancer. Journal International Du Cancer·Jing ChenJian-Bing Fan
Apr 15, 2008·Drug Discovery Today·Gerhard F EckerPeter Chiba
Jul 16, 2008·Science·Monica CampillosPeer Bork
Sep 11, 2008·Nucleic Acids Research·Allan Peter DavisCarolyn J Mattingly
Feb 25, 2009·Expert Opinion on Drug Metabolism & Toxicology·Florian NigschDonatas Zmuidinavicius
Feb 25, 2009·Expert Opinion on Drug Metabolism & Toxicology·Paul CzodrowskiThomas Fox
Apr 2, 2009·Nature Reviews. Drug Discovery·Eric E SchadtDavid A Shaywitz
Jun 25, 2009·BMC Genomics·Uma T ShankavaramJohn N Weinstein
Sep 2, 2009·Journal of Medicinal Chemistry·John J IrwinYiqun Cao
Sep 8, 2009·Current Opinion in Biotechnology·Peter KolbBrian K Shoichet
Sep 29, 2009·Journal of Molecular Biology·Sarah E BoyceBrian K Shoichet
Nov 3, 2009·Nucleic Acids Research·Minoru KanehisaMika Hirakawa
Nov 6, 2009·Molecular Systems Biology·Bo-Juen ChenDana Pe'er
Feb 2, 2010·Trends in Pharmacological Sciences·Albert PujolPatrick Aloy
Mar 20, 2010·Nature Reviews. Cancer·Sreenath V SharmaJeff Settleman
Aug 17, 2010·Behavioural Processes·Alan B BondAlan C Kamil

❮ Previous
Next ❯

Citations

Feb 2, 2013·Advanced Drug Delivery Reviews·Haisu Ma, Hongyu Zhao
Aug 15, 2014·Molecular BioSystems·Meiyue SongZhenran Jiang
Jun 23, 2015·Journal of Biopharmaceutical Statistics·Federico MattielloBie Verbist
Aug 5, 2016·Molecular Informatics·Meiyue Song, Zhenran Jiang
Sep 21, 2016·Journal of the American Statistical Association·Lisa M PhamEric D Kolaczyk
Jun 15, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Cong LiHongyu Zhao
Jan 1, 2014·Journal of Bioinformatics and Computational Biology·Henry HanZhou Ji
Apr 10, 2017·Computational Biology and Chemistry·Giovanna Maria Dimitri, Pietro Lió
Oct 13, 2017·Molecular BioSystems·Fan-Shu ChenZhenran Jiang
Aug 24, 2017·Nature Reviews. Gastroenterology & Hepatology·Heitor S P de SouzaDimitrios Iliopoulos
May 18, 2018·Biometrics·Paula J GriffinEric D Kolaczyk
May 13, 2020·Briefings in Bioinformatics·Chun-Chun WangXing Chen
Dec 27, 2018·Journal of Chemical Information and Modeling·José JiménezGianni De Fabritiis
Mar 19, 2021·Journal of Crohn's & Colitis·Claudio FiocchiUNKNOWN Scientific Workshop Steering Committee

❮ Previous
Next ❯

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.