Expander: from expression microarrays to networks and functions
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 f...
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| Veröffentlicht in: | Nature protocols 2010-02, Vol.5 (2), p.303-322 |
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| creator | Ulitsky, Igor Maron-Katz, Adi Shavit, Seagull Sagir, Dorit Linhart, Chaim Elkon, Ran Tanay, Amos Sharan, Roded Shiloh, Yosef Shamir, Ron |
| description | 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 ≈1 h. |
| doi_str_mv | 10.1038/nprot.2009.230 |
| format | Article |
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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. 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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. 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Academic</collection><jtitle>Nature protocols</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ulitsky, Igor</au><au>Maron-Katz, Adi</au><au>Shavit, Seagull</au><au>Sagir, Dorit</au><au>Linhart, Chaim</au><au>Elkon, Ran</au><au>Tanay, Amos</au><au>Sharan, Roded</au><au>Shiloh, Yosef</au><au>Shamir, Ron</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Expander: from expression microarrays to networks and functions</atitle><jtitle>Nature protocols</jtitle><stitle>Nat Protoc</stitle><addtitle>Nat Protoc</addtitle><date>2010-02</date><risdate>2010</risdate><volume>5</volume><issue>2</issue><spage>303</spage><epage>322</epage><pages>303-322</pages><issn>1754-2189</issn><eissn>1750-2799</eissn><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 ≈1 h.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>20134430</pmid><doi>10.1038/nprot.2009.230</doi><tpages>20</tpages></addata></record> |
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| subjects | 631/114/794 631/1647/2017/2079 Algorithms Analytical Chemistry Animals Biological Techniques Biomedical and Life Sciences Chromosome Mapping Clustering Computational Biology/Bioinformatics Computer science Data analysis DNA microarrays Escherichia coli - genetics Gene Expression Gene Expression Regulation Genetic engineering Genetic Techniques Genomics Humans Integrated software Life Sciences Methods Mice Microarrays MicroRNAs MicroRNAs - genetics Multigene Family - genetics Oligonucleotide Array Sequence Analysis Ontology Organic Chemistry Plants - genetics Promoter Regions, Genetic Protocol Rats Saccharomyces cerevisiae - genetics Software Transcription factors Transcription Factors - genetics |
| title | Expander: from expression microarrays to networks and functions |
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