RN+ : A Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein-Protein Interaction Network

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Jaegyoon AhnJibum Kim

Abstract

Biclustering is a process of finding groups of genes that behave similarly under a subset of conditions. In this article, we propose an efficient biclustering algorithm, namely RN+, to identify biologically meaningful biclusters in gene expression data. The RN+ algorithm finds biologically meaningful biclusters through a novel gene filtering using protein-protein interaction network, gene searching, gene grouping, and queuing process. It also efficiently removes duplicate biclusters. We tested the proposed RN+ on five real microarray datasets, and compared its performance with seven competitive biclustering algorithms. The experimental results show that RN+ efficiently finds functionally enriched and biologically meaningful biclusters for large gene expression datasets, and outperforms the other tested biclustering algorithms on real datasets.

References

Feb 23, 2000·The Journal of Adolescent Health : Official Publication of the Society for Adolescent Medicine
Aug 10, 2002·Bioinformatics·Amos TanayRon Shamir
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Amir Ben-DorZohar Yakhini
Jun 11, 2009·Nucleic Acids Research·Guojun LiYing Xu
Jul 10, 2012·Briefings in Bioinformatics·Kemal ErenÜmit V Çatalyürek
Jan 25, 2017·BMC Bioinformatics·Victor A Padilha, Ricardo J G B Campello
Nov 27, 2018·Nucleic Acids Research·Rose OughtredMike Tyers

❮ Previous
Next ❯

Methods Mentioned

BETA
ISA

Software Mentioned

SAMBA
UniBIC
OPSM
Bimax
QUBIC
RN
DeclareMathSizes
Plaid

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.

Related Papers

Algorithms for Molecular Biology : AMB
Burton Kuan Hui Chia, R Krishna Murthy Karuturi
Journal of Bioinformatics and Computational Biology
Anirban MukhopadhyaySanghamitra Bandyopadhyay
Advances and Applications in Bioinformatics and Chemistry : AABC
Sawannee SutheeworapongKengo Kinoshita
© 2022 Meta ULC. All rights reserved