Co-expressed yeast genes cluster over a long range but are not regularly spaced.

Journal of Molecular Biology
Martin J Lercher, Laurence D Hurst

Abstract

Analysis in yeast of the relationship between a gene's genomic position and its expression profile, derived from chip array data, suggests that both closely linked genes and genes spaced at regular intervals show correlated expression profiles. Unfortunately, yeast arrays are often printed in genomic order. The above results may hence reflect little more than known spatial biases within arrays. To circumvent this problem, we analyse spatially unbiased expression data derived from a large Northern blot study. We find that local domains of co-expressed genes range up to 30 genes (100 kb), and are thus much larger than previously considered. There is, by contrast, no evidence for periodicity of co-expression in yeast. We likewise find no convincing evidence for periodicity in the human or mouse genome. Further, analysis of yeast transcription factor binding data sets suggests that there is currently no statistical evidence for chromosomal periodicity of co-regulation.

References

Jul 1, 1990·Statistics in Medicine·Y Hochberg, Y Benjamini
Oct 25, 1996·Science·G D SchulerT J Hudson
Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Feb 26, 2000·Trends in Genetics : TIG·S Kruglyak, H Tang
Jul 19, 2000·Genome Research·A E LashS F Altschul
Dec 5, 2000·Molecular Biology of the Cell·A P GaschP O Brown
Dec 26, 2001·Nature Biotechnology·Anuj KumarMichael Snyder
Apr 6, 2002·Bioinformatics·Heikki MannilaJuha Kere
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
May 7, 2002·Nature Genetics·Martin J LercherLaurence D Hurst
Oct 19, 2002·Bioinformatics·Marko SalmenkiviHeikki Mannila
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Feb 15, 2003·Genetics·Elizabeth A WinzelerDaniel L Hartl
Jul 31, 2003·Nucleic Acids Research·Gábor BalázsiZoltán N Oltvai
Aug 14, 2003·Human Molecular Genetics·Martin J LercherLaurence D Hurst
Dec 25, 2003·Bioinformatics·Sofia WichertKorbinian Strimmer
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
May 8, 2004·Nature Reviews. Genetics·Laurence D HurstMartin J Lercher
May 21, 2004·BMC Bioinformatics·Tristan Mary-HuardPierre Hilson
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Mar 1, 2005·Trends in Genetics : TIG·Ruth HershbergHanah Margalit

❮ Previous
Next ❯

Citations

Jul 9, 2011·Genome Biology and Evolution·Guang-Zhong WangMartin J Lercher
Apr 29, 2008·Molecular Biology and Evolution·Ben-Yang Liao, Jianzhi Zhang
Oct 2, 2012·BMC Bioinformatics·Danielle G LemayKatherine S Pollard
Jan 9, 2008·BMC Evolutionary Biology·Jason G MezeyCorbin D Jones
Nov 7, 2007·Genome Biology·Juan F Poyatos, Laurence D Hurst
Jan 30, 2010·International Journal of Molecular Sciences·Huai-Kuang TsaiDaryi Wang
Feb 8, 2014·Molecular Biology and Evolution·Zhiming DaiXianhua Dai
Nov 19, 2008·Journal of Theoretical Biology·Leonid HaninAndrei Yakovlev
Sep 8, 2007·Trends in Genetics : TIG·Nizar N BatadaLaurence D Hurst
Mar 2, 2016·Molecular Biology and Evolution·Samina NaseebDaniela Delneri
Mar 7, 2015·Molecular Biology and Evolution·Avazeh T Ghanbarian, Laurence D Hurst
Feb 6, 2015·BMC Genomics·Ting XieHong-Yu Zhang
Nov 4, 2016·G3 : Genes - Genomes - Genetics·Porfirio Quintero-Cadena, Paul W Sternberg
Sep 17, 2019·PLoS Genetics·Mengyi Sun, Jianzhi Zhang
Jul 8, 2020·International Journal of Molecular Sciences·Zhuanzhuan JiangXin Hou
Mar 17, 2019·Interdisciplinary Sciences, Computational Life Sciences·Shuaibin LianLin Cheng
Aug 23, 2006·Human Molecular Genetics·Hong SunRunsheng Chen
Sep 12, 2020·Genome Biology and Evolution·Darci A GiacominiPatrick J Tranel
Aug 12, 2021·Trends in Genetics : TIG·Oriana Q H ZinaniErtuğrul M Özbudak

❮ 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.