TITLE

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

AUTHOR(S)
Dutilh, Bas E; Huynen, Martijn A; Snel, Berend
PUB. DATE
January 2006
SOURCE
BMC Genomics;2006, Vol. 7, p10
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: The massive scale of microarray derived gene expression data allows for a global view of cellular function. Thus far, comparative studies of gene expression between species have been based on the level of expression of the gene across corresponding tissues, or on the coexpression of the gene with another gene. Results: To compare gene expression between distant species on a global scale, we introduce the "expression context". The expression context of a gene is based on the co-expression with all other genes that have unambiguous counterparts in both genomes. Employing this new measure, we show 1) that the expression context is largely conserved between orthologs, and 2) that sequence identity shows little correlation with expression context conservation after gene duplication and speciation. Conclusion: This means that the degree of sequence identity has a limited predictive quality for differential expression context conservation between orthologs, and thus presumably also for other facets of gene function.
ACCESSION #
28858592

 

Related Articles

  • The Regulation and Biological Significance of Genomic Imprinting in Mammals. Kaneko-Ishino, Tomoko; Kohda, Takashi; Ishino, Fumitoshi // Journal of Biochemistry;Jun2003, Vol. 133 Issue 6, p699 

    Genomic imprinting is a system of non-Mendelian inheritance that is unique to mammals. Two types of imprinted genes show parent-of-origin-specific expression patterns: the paternally expressed genes (Pegs), and the maternally expressed genes (Megs). Parental genomic imprinting memory is...

  • Genes Induced by Reovirus Infection Have a Distinct Modular Cis- Regulatory Architecture. Lapadat, R.; DeBiasi, R. L.; Johnson, G. L.; Tyler, K. L.; Shah, I. // Current Genomics;Nov2005, Vol. 6 Issue 7, p501 

    The availability of complete genomes and global gene expression profiling has greatly facilitated analysis of complex genetic regulatory systems. We describe the use of a bioinformatics strategy for analyzing the cis-regulatory design of genes diferentially regulated during viral infection of a...

  • Germline Expression Influences Operon Organization in the Gaenorhabditis elegans Genome. Reinke, Valerie; Cutter, Asher D. // Genetics;Apr2009, Vol. 181 Issue 4, p1219 

    Operons are found across multiple kingdoms and phyla, from prokaryotes to chordates. In the nematode Caenor/iabditis elegans, the genome contains >1000 operons that compose ∼15% of the protein-coding genes. However, determination of the force(s) promoting the origin and maintenance of...

  • Major aging-associated RNA expressions change at two distinct age-positions. Gheorghe, Marius; Snoeck, Marc; Emmerich, Michael; Bäck, Thomas; Goeman, Jelle J.; Raz, Vered // BMC Genomics;2014, Vol. 15 Issue 1, p1 

    Background Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to...

  • Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue. Goulter, Andrew B; Harmer, Daniel W; Clark, Kenneth L // BMC Genomics;2006, Vol. 7, p34 

    Background: Low density arrays (LDAs) have recently been introduced as a novel approach to gene expression profiling. Based on real time quantitative RT-PCR (QRT-PCR), these arrays enable a more focused and sensitive approach to the study of gene expression than gene chips, while offering higher...

  • MECANISMO DE INFECCIÓN Y TRANSFORMACIÓN NEOPLÁSICA PRODUCIDO POR VIRUS PAPILOMA HUMANO EN EL EPITELIO CERVICAL. Rivera, Z. René; Delgado, D. Jorge; Painel, P. Vicente; Barrero, P. Raúl; Larraín, H. Angélica // Revista Chilena de Obstetricia y Ginecología;2006, Vol. 71 Issue 2, p135 

    A bibliographical revision of the infection mechanism and neoplastic transformation produced by human papilloma virus of high risk in cervical epithelium is presented. The capside receptor interaction, internalization, early genes expression, integration of genoma to the host cell and mechanisms...

  • Understanding the Epigenetic Interface Between the Cell and the Genome: A Supplemental Issue of DNA and Cell Biology on Epigenetics. Kasinski, Andrea L.; Pincus, Zachary // DNA & Cell Biology;Oct2012 Supplement, Vol. 31, pS-1 

    An introduction to the journal is presented in which the guest editors discuss ways to regulate the expression state of the genome by the biological environment of the cell.

  • Update on human genome completion and annotations: Gene nomenclature. Nebert, Daniel W.; Wain, Hester M. // Human Genomics;Nov2003, Vol. 1 Issue 1, p66 

    Why is agreeing on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression. gene-gene and gene-product interactions and evolutionary relatedness across species. To...

  • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. Bullard, James H.; Purdom, Elizabeth; Hansen, Kasper D.; Dudoit, Sandrine // BMC Bioinformatics;2010, Vol. 11, p94 

    Background: High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and...

Share

Read the Article

Courtesy of

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics