A sample dataset for ENViz Cytoscape plugin (http://apps.cytoscape.org/apps/enviz)

The dataset can be found here and contains:

Primary data file: Enerly_GeneExpression.tab, a tab delimited file containing gene expression data for 13,639 genes and 100 samples from microarray experiments. Gene expression data is taken from gProcessedSignal Agilent Feature Extraction files. The expression levels were log2 transformed and quantile normalized [1].

Pivot data file: Enerly_miRNAExpression.tab, a tab delimited file containing microarray based expression data for 489 miRNAs and the same 100 samples. miRNA expression data is log2 transformed and normalized to the 75^th percentile [1].

Annotation files: GO annotation file Enerly_GO_Annotation.tab.gz, and WikiPathway annotation file Enerly_WikiPathway_Annotation.tab.gz.   The GO annotation file contains gene annotations for 11,177 GO terms. GO annotation is based on GO database release downloaded on 08/22/2013. The pathway annotation file contains gene annotations for 204 pathways [2].

The primary data file, pivot data file and one of the annotation files are all needed to run ENViz enrichment analysis.

Analysis Results files: the following files are also included as examples of the results of running the  enrichment analysis as detailed below. These files can be visualized without running the analysis.

                Pathway enrichment file Enerly_PathwayAnalysisResults.mhg: results of enrichment analysis using the gene annotation file Enerly_WikiPathway_Annotation.tab.gz.

                Pathway enrichment file with Enerly_PathwayAnalysisResults.WithSimulations.1K.mhg: results of enrichment analysis using the gene annotation file Enerly_WikiPathway_Annotation.tab.gz and with ‘filter by permutation test’ option turned ON.

                GO enrichment file Enerly_GOAnalysisResults.mhg: results of enrichment analysis using the gene annotation file Enerly_GO_Annotation.tab.gz

                GO enrichment file Enerly_GOAnalysisResults.WithSimulations.1K.mhg: results of enrichment analysis using the gene annotation file Enerly_GO_Annotation.tab.gz and with ‘filter by permutation test’ option turned ON.

 

References:

1.       Enerly ,E, et al (2011), “miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors”, PLoS One.

2.       Kelder, T, et al (2011) “WikiPathways: building research communities on biological pathways” NAR.