In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

BMC Genomics
Sheng-Ying PaoMing-Jing Hwang

Abstract

Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies using bioinformatic approaches because of the rich libraries and tremendous amount of data now available in the public domain. However, any large-scale EST-based bioinformatics analysis must deal with the heterogeneous, and often ambiguous, tissue and organ terms used to describe EST libraries. To deal with the issue of tissue source, in this work, we carefully screened and organized more than 8 million human and mouse ESTs into 157 human and 108 mouse tissue/organ categories, to which we applied an established statistic test using different thresholds of the p value to identify genes differentially expressed in different tissues. Further analysis of the tissue distribution and level of expression of human and mouse orthologous genes showed that tissue-specific orthologs tended to have more similar expression patterns than those lacking significant tissue specificity. On the other hand, a number of orthologs were found to ha...Continue Reading

References

Oct 20, 1995·Science·V E VelculescuK W Kinzler
Aug 1, 1993·Nature Genetics·M S BoguskiC M Tolstoshev
Oct 23, 1997·Genome Research·S Audic, J M Claverie
Jun 1, 1996·Nature Biotechnology·W Bains
Dec 1, 1996·Nature Biotechnology·D J LockhartE L Brown
Mar 24, 1999·Trends in Biotechnology·D H Kozian, B J Kirschbaum
Dec 11, 1999·Nucleic Acids Research·T HishikiK Okubo
Feb 17, 2000·Trends in Endocrinology and Metabolism : TEM·E P DiamandisC V Obiezu
Jul 13, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Z ZhangW Miller
Mar 17, 2001·Journal of Immunological Methods·M YamamotoA Ryo
Mar 30, 2001·The Journal of Biological Chemistry·S J WilliamsM A McGuckin
Sep 1, 2001·Trends in Cardiovascular Medicine·L W Stanton
Nov 3, 2001·Nucleic Acids Research·L Skrabanek, F Campagne
Dec 6, 2001·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·C InoueR Kageyama
Mar 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Oct 23, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nicholas KatsanisJames R Lupski
Jan 10, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Aug 2, 2003·Nature·Diane Gershon
Aug 13, 2003·Bioinformatics·Stephen F MaddenPeter P Doran
Jan 17, 2004·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Lisa KalmanRebecca Buckley
Feb 14, 2004·Genomics·Aaron C BrownDerry C Roopenian
Jan 1, 1998·Journal of Cellular Biochemistry·John P CarulliPeter T Lomedico

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Citations

Nov 21, 2007·Bioinformatics·Athanasia C TzikaMichel C Milinkovitch
Jun 8, 2010·BMC Plant Biology·Adam C EnglishAnn E Loraine
Mar 14, 2012·PloS One·Andrew T Milnthorpe, Mikhail Soloviev
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jeremy A MillerDaniel H Geschwind
Mar 25, 2010·Genome Biology and Evolution·Michel C MilinkovitchAthanasia C Tzika
Aug 8, 2021·Biochemical and Biophysical Research Communications·Mahdi AalikhaniZahra Bazi

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Methods Mentioned

BETA
pull-down

Software Mentioned

MegaBlast
ExQuest
TissueInfo
BodyMap
ExQuest ( Expressional Quantification of ESTs
HomoloGene
TissuDB
Digital Differential Display ( DDD )

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