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 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.
Ulitsky
Igor
I
Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
Maron-Katz
Adi
A
Shavit
Seagull
S
Sagir
Dorit
D
Linhart
Chaim
C
Elkon
Ran
R
Tanay
Amos
A
Sharan
Roded
R
Shiloh
Yosef
Y
Shamir
Ron
R
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping; D004926:Escherichia coli / Q000235:genetics; D015870:Gene Expression; D005786:Gene Expression Regulation; D005821:Genetic Techniques; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D014157:Transcription Factors / Q000235:genetics
D035683:MicroRNAs; D014157:Transcription Factors