Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms.

TheScientificWorldJournal
Cheng-Yu YehVon-Wun Soo

Abstract

With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set. The comparisons of our method with other existing methods on known yeast MAPK pathways in terms of precision and recall show that we can find maximum number of the proteins and perform comparably well. On the other hand, our method is more efficient than previous ones and detects the paths of length 10 within 40 seconds using CPU Intel 1.73 GHz and 1 GB main memory running under windows operating system.

References

May 1, 1996·The Journal of Cell Biology·Y MatsuiA Toh-e
Mar 6, 1999·Microbiology and Molecular Biology Reviews : MMBR·D I Johnson
Mar 24, 1999·The Journal of Cell Biology·A Nern, R A Arkowitz
Dec 11, 1999·Nucleic Acids Research·I XenariosD Eisenberg
Jan 11, 2000·Nucleic Acids Research·G SherlockJ M Cherry
May 3, 2001·Nature·H JeongZ N Oltvai
Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Nov 5, 2002·BMC Bioinformatics·Martin SteffenGeorge Church
Jan 10, 2003·Nucleic Acids Research·Long-Cheng LiRajvir Dahiya
Sep 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Zhuo ZhangRuiwen Zhang
Dec 19, 2003·Nucleic Acids Research·H W MewesA Ruepp
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Jan 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jacques LapointeJonathan R Pollack
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Jun 10, 2005·Microbiology and Molecular Biology Reviews : MMBR·David E Levin
Jun 18, 2005·Bioinformatics·Mary E DolanJudith A Blake
Apr 12, 2006·BMC Bioinformatics·Tomer ShlomiRoded Sharan
Jul 18, 2006·Nucleic Acids Research·Carlos Prieto, Javier De Las Rivas
Dec 8, 2006·Nucleic Acids Research·Itay MayroseTal Pupko
Mar 10, 2007·Microbiology and Molecular Biology Reviews : MMBR·Hay-Oak Park, Erfei Bi
Oct 10, 2008·Nucleic Acids Research·Joanna AmbergerAda Hamosh

❮ Previous
Next ❯

Citations

Jan 20, 2012·BMC Systems Biology·Liang-Chun ChenVon-Wun Soo
Oct 9, 2014·TheScientificWorldJournal·Francisco Gómez-Vela, Norberto Díaz-Díaz
Oct 18, 2015·Briefings in Functional Genomics·Jie HouJianlin Cheng
Dec 4, 2019·BMC Bioinformatics·Ibrahim YoussefAnna Ritz
Dec 7, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Baofang HuWeihua Yuan

❮ Previous
Next ❯

Methods Mentioned

BETA
two-hybrid
nucleotide exchange

Software Mentioned

NetSearch
Pathfinder
Ontologizer
windows
Tree
java
Search

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.

© 2021 Meta ULC. All rights reserved