Figure 1 | Scientific Reports

Figure 1

From: GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data

Figure 1

Schematic flow diagram of GSAASeqSP.

(A): GSAASeqSP takes as input an experimental count dataset and apriori defined gene sets and first generates permuted datasets based on the experimental dataset; (B): Data is normalized and extremely small and large gene sets are filtered; (C): Differential expression analysis is performed using one of: Signal2Noise, log2Ratio and Signal2Noise_log2Ratio; (D): Gene set association analysis is performed using one of: Weighted_KS, L2Norm, Mean, WeightedSigRatio, SigRatio, GeometricMean, FisherMethod and RankSum; (E): Outputs include 1) ranked summary gene set association table with the name of the gene set, the number of genes (SIZE), association score (AS), normalized association score (NAS), P-VALUE, FDR and FWER; 2) a link to gene set annotation in MSigDB (where applicable); 3) a heat map of the gene expression data for each gene set; and 4) the null distribution of the AS.

Back to article page