Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

BMC Bioinformatics
Alexandre KuhnMauro Delorenzi

Abstract

The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies.Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models (e.g. relational), they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles. We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation...Continue Reading

References

May 18, 2000·Human Molecular Genetics·R Luthi-CarterJ M Olson
Jan 12, 2001·Human Molecular Genetics·C H LinP J Detloff
Jul 12, 2003·Bioinformatics·Jung Kyoon ChoiOok Joon Yoo
Jan 1, 1955·Annual Review of Microbiology·R E BUCHANAN
May 7, 2004·Genome Biology·Dmitry N GrigoryevJoe G N Garcia
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Dec 21, 2004·Nucleic Acids Research·Donna MaglottTatiana Tatusova
May 13, 2005·Human Molecular Genetics·Andrew D StrandJames M Olson
Sep 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Lu TianPeter J Park
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Oct 7, 2005·Pharmacogenomics·Frank J Steemers, Kevin L Gunderson
Nov 30, 2005·The American Journal of Pathology·Robert S StearmanMark W Geraci
Feb 10, 2006·Human Molecular Genetics·Angela HodgesRuth Luthi-Carter
Nov 28, 2006·Bioinformatics·Zhen Jiang, Robert Gentleman
Dec 7, 2006·Nucleic Acids Research·T J P HubbardE Birney
Dec 7, 2006·Nucleic Acids Research·Donna MaglottTatiana Tatusova
Feb 17, 2007·Bioinformatics·Jelle J Goeman, Peter Bühlmann
Apr 28, 2007·Bioinformatics·Steven A Eschrich, Andrew M Hoerter

❮ Previous
Next ❯

Citations

Nov 26, 2013·Nature Genetics·Mira JeongMargaret A Goodell
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Kazue Hashimoto-ToriiPasko Rakic
Apr 27, 2012·Rejuvenation Research·Kristen FortneyIgor Jurisica
Nov 4, 2010·Seminars in Nephrology·Jeffrey B Hodgin, Clemens D Cohen
Nov 4, 2010·Seminars in Nephrology·Wenjun Ju, Frank C Brosius
Aug 20, 2010·Journal of Neuropathology and Experimental Neurology·Birgit ZuckerRuth Luthi-Carter
Nov 7, 2014·Allergy, Asthma & Immunology Research·Gergely TemesiCsaba Szalai
Nov 16, 2014·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Martine Schroyen, Christopher K Tuggle
Jun 2, 2017·Nature Communications·Andrew E Teschendorff, Tariq Enver
Dec 23, 2015·Bioinformatics and Biology Insights·Peter R LoVerso, Feng Cui
Feb 23, 2020·Cell Metabolism·Marte MolenaarsRiekelt H Houtkooper

❮ Previous
Next ❯

Software Mentioned

R
R package limma
Resourcerer
Bioconductor
Affymetrix
Linux
Windows
getPROBESET
R package
GCOS

Related Concepts

Related Feeds

Alpha-Synuclein Aggregation (MDS)

Alpha-synucleins are small proteins that are believed to restrict the mobility of synpatic vesicles and inhibit neurotransmitter release. Aggregation of these proteins have been linked to several types of neurodegenerative diseases including dementia with Lewy bodies and Parkinson's disease. Here is the latest research on α-synuclein aggregation.