EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data.It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis It seamlessly integrates in one package all analysis steps, including:
- Data preprocessing and normalization
- Identification of differential genes
- Clustering and biclustering;
- Down-stream enrichment analyses of:
– GO functional categories
– TF binding sites in promoter regions
– MicroRNA sites in 3′-UTRs and
– Chromosomal locations
- Network-based analysis of the expression data.
EXPANDER provides support for analysis of human, mouse, rat, chicken, fly, zebrafish, C. elegans, yeast (s.cerevisiaeand s. pombe), arabidopsis, tomato, listeria, A. fumigatus and E. coli.
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Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.
Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230.