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Figure 1 | BMC Bioinformatics

Figure 1

From: Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

Figure 1

Schematic work flow of Pathway pattern extraction Pipeline (PPEP) in WPS. The input of the analysis pipeline can be a set of gene lists derived from the same or even different study in terms of biological contexts, applied technologies and methodologies. Examples of the lists are differential gene lists from class contrasts obtained from microarray data analysis, proteomic profiling, or genome-wide post-transcriptional modification scan. Then the first step is to batch compute the Fisher's exact test to evaluate the enrichment levels for each gene lists for annotated terms or pathways in WPS database (e.g., GOBP, Biocarta pathway). The Fisher's exact test for enrichment levels was described previously [4]. Step 2 is to collect the batch computation results and merging them into an enrichment score (ES) matrix. Then at step 3, the ES matrix can be subjected to pattern analysis using different methods under user's choice: clustering analysis, Pavlidis template matching, and pathway pattern extraction. Clustering analysis and Pavlidis template matching can be done with external tools such as TM4 package from TIGR. The pathway pattern extraction is a newly designed feature in PPEP specifically for pattern extraction using ES score matrix. Then the next step or step 4, obtained terms or pathways after pattern analysis, usually as in a matrix or as a list, can be used to retrieve the associated genes using the interface of the analysis pipeline in WPS. Then at the final step, the data and association relation of the terms and genes can be viewed under GTAN display in WPS using WPS visualization capacity.

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