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Figure 7 | BMC Bioinformatics

Figure 7

From: CLEAN: CLustering Enrichment ANalysis

Figure 7

Integrated software package. CLEAN was implemented as an add-on R package [36]. The package integrates routines for calculating gene specific functional coherence scores and the interactive Java-based viewer Functional TreeView (FTreeView). The figure shows a screenshot of the fTreeView session displaying CLEAN results for one breast cancer dataset GSE3494 [28]. fTreeView was developed from the original Java TreeView [38] by adding panel 3, which displays functional cluster annotations generated by the CLEAN R package. This functionality enables seamless integration and browsing of functional categories associated with each cluster of genes (panel 2), which in turn can be selected based on the functional coherence scores (panel 1). The selected cluster of genes (panel 2) which we identified based on the overall high CLEAN scores (panel 1) is highly enriched for genes associate with immunity related Gene Ontology terms (FDR < 10-60) as well as two KEGG pathways, and putative targets of the Interferon Consensus Sequence-binding protein (ICSBP) transcription factor. These Results can be viewed interactively at http://Clusteranalysis.org using the Java web-start version of FTreeView.

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