Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification

Bioinformatics
Itai YanaiOrit Shmueli

Abstract

Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression. To obtain such novel information genome-wide, we have determined the mRNA expression levels for one of the largest hitherto analyzed set of 62 839 probesets in 12 representative normal human tissues. Indeed, when using a newly defined graded tissue specificity index tau, valued between 0 for housekeeping genes and 1 for tissue-specific genes, genes with midrange profiles having 0.15< tau<0.85 were found to constitute >50% of all expression patterns. We developed a binary classification, indicating for every gene the I(B) tissues in which it is overly expressed, and the 12-I(B) tissues in which it shows low expression. The 85 dominant midrange patterns with I(B)=2-11 were found to be bimodally distributed, and to contribute most significantly to the definition of tissue specification dendrograms. Our analyses provide a novel route to infer expression profiles for presumed ancestral nodes in the tissue dendrogram. Such definition has uncovered an unsuspected correlation, whereby de novo enhancement and diminution of gene expression g...Continue Reading

References

Apr 29, 1996·Physical Review Letters·M BlattE Domany
Oct 18, 2000·Proceedings of the National Academy of Sciences of the United States of America·G GetzE Domany
Jan 5, 2002·Physiological Genomics·L L HsiaoS R Gullans
Mar 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Apr 5, 2002·Genome Research·W James Kent
Apr 12, 2002·The American Journal of Pathology·Christine A Iacobuzio-DonahueRalph H Hruban
Apr 25, 2002·Nature Reviews. Genetics·Daniel St Johnston
May 7, 2002·Nature Genetics·Martin J LercherLaurence D Hurst
Jun 12, 2002·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Akihiko Saito-HisaminatoYusuke Nakamura
Aug 30, 2002·Current Opinion in Genetics & Development·Rob BurgessMichael Rosenfeld
Sep 5, 2002·Physiological Genomics·Marc S Halfon, Alan M Michelson
Sep 13, 2002·Genome Biology·Yangrae ChoVirginia Walbot
Nov 9, 2002·Bioinformatics·Marilyn SafranDoron Lancet
Dec 20, 2002·Bioinformatics·Earl HubbellRui Mei
Dec 21, 2002·Trends in Genetics : TIG·Heriberto Cerutti
Jan 10, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Jan 10, 2003·Nucleic Acids Research·Guoying LiuMichael A Siani-Rose
Apr 4, 2003·Current Opinion in Genetics & Development·Cheryl C Hsia, William McGinnis
Jul 10, 2003·Trends in Genetics : TIG·Eli Eisenberg, Erez Y Levanon
Jan 17, 2004·Briefings in Bioinformatics·Vered Chalifa-CaspiDoron Lancet
Jan 28, 2004·Comptes rendus biologies·Orit ShmueliDoron Lancet
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
May 13, 2004·PLoS Biology·Philipp KhaitovichSvante Pääbo

❮ Previous
Next ❯

Citations

Apr 28, 2011·Molecular Neurobiology·John KorenChad A Dickey
Jan 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ziv Bar-JosephItamar Simon
Sep 14, 2011·Proceedings of the National Academy of Sciences of the United States of America·Yang ShenChung-I Wu
Oct 5, 2011·Proceedings of the National Academy of Sciences of the United States of America·Timothy B SacktonBernardo Lemos
Nov 19, 2009·The Journal of Biological Chemistry·Moh'd A SalamehEvette S Radisky
Dec 17, 2009·Omics : a Journal of Integrative Biology·Gil StelzerDoron Lancet
Oct 2, 2008·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Pamela MukhopadhyayTapash Chandra Ghosh
Nov 1, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yousheng RaoXiquan Zhang
Jan 1, 2009·Genome Biology and Evolution·James J CaiDmitri A Petrov
Jan 1, 2009·Genome Biology and Evolution·Richard P MeiselMatthew W Hahn
Oct 5, 2010·Genome Biology and Evolution·Robert EkblomTerry Burke
Mar 3, 2011·Genome Biology and Evolution·Daudi JjingoI King Jordan
Sep 20, 2011·Genome Biology and Evolution·Tanja SlotteMikkel H Schierup
Oct 12, 2011·Genome Biology and Evolution·Vera B KaiserDoris Bachtrog
May 2, 2012·Genome Biology and Evolution·Zhuo-Cheng HouDerek E Wildman
Sep 15, 2012·Genome Biology and Evolution·Colin D Meiklejohn, Daven C Presgraves
Oct 26, 2012·Genome Biology and Evolution·Raquel AssisDoris Bachtrog
Jun 20, 2013·Genome Biology and Evolution·Maria Warnefors, Henrik Kaessmann
Oct 3, 2013·Genome Biology and Evolution·Yuh Chwen G Lee, Hsiao-Han Chang
Sep 29, 2011·Human Molecular Genetics·Jungsun ParkSoojin V Yi
Dec 22, 2011·Human Molecular Genetics·Wenfei JinShuhua Xu
Dec 4, 2009·Molecular Biology and Evolution·Soumita Podder, Tapash C Ghosh
Mar 3, 2010·Molecular Biology and Evolution·Feng-Chi ChenTrees-Juen Chuang
Mar 11, 2011·Molecular Biology and Evolution·Liang Yang, Brandon S Gaut
Sep 24, 2011·Molecular Biology and Evolution·Alex WongCharles F Aquadro
Jan 19, 2013·Molecular Biology and Evolution·Xiangjun TianDavid C Queller
May 21, 2013·Molecular Biology and Evolution·Péter SzövényiAndreas Wagner
Sep 21, 2007·Nucleic Acids Research·Alexander E Vinogradov, Olga V Anatskaya
Nov 13, 2012·Nucleic Acids Research·Frederik Otzen BaggerBo T Porse
Nov 30, 2012·Nucleic Acids Research·Ruth BarshirEsti Yeger-Lotem
May 10, 2013·Nucleic Acids Research·Yi-Ching ChenTrees-Juen Chuang
May 13, 2009·Biology Letters·Judith E Mank, Hans Ellegren
Jan 12, 2013·Genes & Development·Nila Roy ChoudhuryGracjan Michlewski
Aug 2, 2008·Genome Research·Shlomit Farkash-AmarItamar Simon
Apr 14, 2012·Genome Research·Richard P MeiselAndrew G Clark

❮ Previous
Next ❯

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Andrew I SuJohn B Hogenesch
Trends in Genetics : TIG
Eli Eisenberg, Erez Y Levanon
Proceedings of the National Academy of Sciences of the United States of America
Andrew I SuJohn B Hogenesch
© 2021 Meta ULC. All rights reserved