Expander: from expression microarrays to networks and functions.

Nature Protocols
Igor UlitskyRon Shamir

Abstract

A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks. The microarray analysis described in this protocol starts with importing the data into Expander 5.0 and is followed by normalization and filtering. Then, clustering and network-based analyses are performed. The gene groups identified are tested for enrichment in function (based on Gene Ontology), co-regulation (using transcription factor and microRNA target predictions) or co-location. The results of each analysis step can be visualized in a number of ways. The complete protocol can be executed in approximately 1 h.

References

Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·E WingenderF Schacherer
Jan 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·C Li, W H Wong
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Jun 5, 2001·Nature Reviews. Genetics·J Quackenbush
Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Feb 12, 2002·Bioinformatics·Alexander SturnZlatko Trajanoski
Feb 14, 2002·Journal of Cellular Biochemistry. Supplement·E E SchadtW H Wong
Aug 10, 2002·Bioinformatics·Amos TanayRon Shamir
Aug 10, 2002·Bioinformatics·Daniel HanischThomas Lengauer
Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Mar 5, 2003·BioTechniques·A I SaeedJ Quackenbush
Dec 19, 2003·Nucleic Acids Research·Henning HermjakobRolf Apweiler
Feb 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Amos TanayRon Shamir
Sep 17, 2004·Nature·Nicholas M LuscombeMark Gerstein
Sep 24, 2005·BMC Bioinformatics·Ron ShamirRan Elkon
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 26, 2005·Science·Kyle Kai-How FarhDavid P Bartel
Feb 24, 2006·International Journal of Cancer. Journal International Du Cancer·Roy BlumYoel Kloog
Jun 1, 2006·Nature Genetics·Nikolaus Rajewsky
Mar 3, 2007·BMC Bioinformatics·Dimos GaidatzisMihaela Zavolan
Apr 6, 2007·BMC Systems Biology·Igor Ulitsky, Ron Shamir
Apr 25, 2007·Molecular Systems Biology·Shay SternErez Braun
Apr 28, 2007·Science·Antony RodriguezAllan Bradley
Jul 7, 2007·Molecular Cell·Andrew GrimsonDavid P Bartel
Sep 18, 2007·RNA·Cydney B NielsenChristopher B Burge
Sep 22, 2007·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Doron RosenzweigDan Zilberstein
Oct 20, 2007·Nature Protocols·Melissa S ClineGary D Bader
Apr 23, 2008·Current Protocols in Bioinformatics·Anne Kristin StavrumBjarte Dysvik
May 30, 2008·Nucleic Acids Research·Joaquín TárragaJoaquín Dopazo
Jun 14, 2008·Current Protocols in Bioinformatics·Heidi KuehnJill P Mesirov

❮ Previous
Next ❯

Citations

Oct 27, 2011·Nature Communications·Nicolas LéveilléReuven Agami
Dec 16, 2011·Proceedings of the National Academy of Sciences of the United States of America·Moon-Suhn RyuRobert J Cousins
Mar 21, 2013·Journal of Neurotrauma·Jacob D FealaJaques Reifman
Jan 26, 2011·Briefings in Bioinformatics·Yijun MengMing Chen
Nov 26, 2010·Nucleic Acids Research·Arnon PazRon Shamir
Jun 26, 2010·Nucleic Acids Research·Igor UlitskyRon Shamir
Jan 1, 2013·Nucleic Acids Research·Hiroshi I SuzukiKohei Miyazono
Jun 8, 2013·American Journal of Respiratory Cell and Molecular Biology·Sean E GillWilliam C Parks
Oct 6, 2010·The Journal of Clinical Investigation·Kirsten M L HertoghsRené A W van Lier
Oct 30, 2012·BMC Bioinformatics·Darya FilippovaCarl Kingsford
May 29, 2010·Algorithms for Molecular Biology : AMB·Burton Kuan Hui Chia, R Krishna Murthy Karuturi
Jun 14, 2013·Genome Biology·Silvia Dal SantoMario Pezzotti
Mar 19, 2013·PLoS Computational Biology·David AmarRon Shamir
Dec 29, 2010·PLoS Genetics·Luis B BarreiroYoav Gilad
Mar 1, 2014·Nature Protocols·Uri Ben-David, Nissim Benvenisty
Feb 6, 2014·Nucleic Acids Research·David Amar, Ron Shamir
Mar 5, 2014·Bioinformatics·Rodrigo SantamaríaLuis Quintales
Nov 17, 2014·Archives of Toxicology·Marianna GrinbergJan G Hengstler
Jan 18, 2013·American Journal of Physiology. Cell Physiology·Gabriela CampanholleJeremy S Duffield
Feb 15, 2012·Cellular and Molecular Life Sciences : CMLS·Floriane Nicol-BenoîtDenis Michel
Feb 18, 2016·Cellular and Molecular Life Sciences : CMLS·Aloysius DomingoAna Westenberger
Feb 10, 2016·Scientific Reports·Orr Friedman-MazurskyShimon Efrat
Feb 24, 2016·Scientific Reports·Adi Maron-KatzRon Shamir
Dec 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Rafael D MesquitaPedro L Oliveira

❮ 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.

Related Papers

Journal of the Association for Research in Otolaryngology : JARO
Ronna HertzanoScott E Strome
Proceedings of the National Academy of Sciences of the United States of America
Lilach M FriedmanKaren B Avraham
© 2021 Meta ULC. All rights reserved