A framework using topological pathways for deeper analysis of transcriptome data

BMC Genomics
Yue ZhaoDong-Guk Shin

Abstract

Pathway analysis is one of the later stage data analysis steps essential in interpreting high-throughput gene expression data. We propose a set of algorithms which given gene expression data can recognize which portion of sub-pathways are actively utilized in the biological system being studied. The degree of activation is measured by conditional probability of the input expression data based on the Bayesian Network model constructed from the topological pathway. We demonstrate the effectiveness of our pathway analysis method by conducting two case studies. The first one applies our method to a well-studied temporal microarray data set for the cell cycle using the KEGG Cell Cycle pathway. Our method closely reproduces the biological claims associated with the data sets, but unlike the original work ours can produce how pathway routes interact with each other above and beyond merely identifying which pathway routes are involved in the process. The second study applies the method to the p53 mutation microarray data to perform a comparative study. We show that our method achieves comparable performance against all other pathway analysis systems included in this study in identifying p53 altered pathways. Our method could pave a new...Continue Reading

References

Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Jan 11, 2000·Nucleic Acids Research·G SherlockJ M Cherry
Jan 4, 2001·Nature Genetics·R J ChoD J Lockhart
Feb 16, 2002·Bioinformatics·Debashis Ghosh, Arul M Chinnaiyan
May 15, 2002·Human Mutation·Magali OlivierPierre Hainaut
Jun 12, 2002·Molecular Biology of the Cell·Michael L WhitfieldDavid Botstein
Jun 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Alexander C ZambonPaul A Insel
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 14, 2006·Bioinformatics·S Falcon, R Gentleman
Nov 8, 2008·Bioinformatics·Adi Laurentiu TarcaRoberto Romero
Apr 18, 2009·BMC Bioinformatics·Sung Bum ChoJu Han Kim
Sep 29, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Dong-Guk ShinDavid Rowe
Dec 1, 2011·Statistical Methods in Medical Research·Jun Li, Robert Tibshirani
Nov 19, 2013·Nucleic Acids Research·David CroftPeter D'Eustachio
Jul 19, 2014·PloS One·Melike KorucuogluHasan H Otu
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Oct 21, 2015·Nucleic Acids Research·Martina KutmonAlexander R Pico
May 18, 2016·Nucleic Acids Research·Sasha BabickiDavid S Wishart
Mar 14, 2017·Oncogene·M Fischer
Jun 26, 2017·Methods : a Companion to Methods in Enzymology·Yue ZhaoDong-Guk Shin

❮ Previous
Next ❯

Software Mentioned

SPH
ORA
SPIA
Wikipathways
GSNCA
PWEA
PARADIM
GOStat
PARADIGM
DAVID

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.