Network motif-based analysis of regulatory patterns in paralogous gene pairs.

Journal of Bioinformatics and Computational Biology
Gatis MelkusJuris Viksna

Abstract

Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focus is the analysis of S. cerevisiae gene interaction graphs, which are of particular interest due to the ancestral whole-genome duplication (WGD) that allows to distinguish between paralogous transcription factors that are traceable to this duplication event and other paralogues. Similar analysis is also applied to E. coli and C. elegans networks. We compare paralogous gene pairs according to the presence and size of bi-fan arrays, classically associated in the literature with gene duplication, within other network motifs. We further extend thi...Continue Reading

References

Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Oct 25, 1996·Science·A GoffeauS G Oliver
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Jun 15, 2004·Current Opinion in Structural Biology·M Madan BabuSarah A Teichmann
May 14, 2005·Journal of Molecular Biology·Michael E WallWilliam S Hlavacek
Aug 11, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·I IspolatovA Yuryev
May 9, 2006·BMC Genomics·Piers J IngramJaroslav Stark
May 19, 2007·Nature Reviews. Genetics·Uri Alon
Sep 2, 2009·BMC Systems Biology·Javier MacíaRicard Solé
Jan 24, 2014·Molecular Biology and Evolution·Patricia S SoriaAntonis Rokas
May 6, 2014·Bioinformatics·Connor Clark, Jugal Kalita
Feb 28, 2015·Current Opinion in Biotechnology·Karin VoordeckersKevin J Verstrepen
May 11, 2015·Cell·Trevor R Sorrells, Alexander D Johnson
Aug 21, 2015·Scientific Reports·Joshua L Payne, Andreas Wagner
Oct 22, 2016·Trends in Genetics : TIG·Michael R Brent
Oct 14, 2016·Scientific Reports·Anida SarajlićNataša Pržulj
Jun 4, 2015·EURASIP Journal on Bioinformatics & Systems Biology·Fazle E FaisalTijana Milenković
Apr 30, 2017·Molecular Systems Biology·Alba JiménezJames Sharpe
Nov 22, 2018·Nucleic Acids Research·Simon J LarsenJan Baumbach

❮ Previous
Next ❯

Citations

Jun 27, 2020·Journal of Bioinformatics and Computational Biology·Elisabetta De Maria, Morgan Magnin
Feb 23, 2021·Biosemiotics·Mykola Husev, Andrij Rovenchak

❮ 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.

Related Papers

Trends in Genetics : TIG
Ximena Escalera-FanjulAlicia González
Mammalian Genome : Official Journal of the International Mammalian Genome Society
J H Nadeau, M Kosowsky
© 2021 Meta ULC. All rights reserved