Gene Set Linkage Analysis Tool

Now much attention was paid on the relation between the phenotype and genotype, and understanding the pathway between them helps found causal genes. A phenotype could be viewed as a gene set, so it could found how phenotype is regulated by genes through connection between gene sets. There are some gene set analysis methods, such as GSEA, FCS and so on, but they have flaws more or less. So the Gene Set Linkage Analysis is proposed to weight the connection between gene sets. By virtue of protein-protein interaction network, in GSLA the genes within gene set are viewed as a whole to gather the signal and enhance the signal. Lin had proved the effectiveness of GSLA, but there’s no programming library or online analysis service distributed. So we establish an online service and provide service including GSLA, BPLN querying as a practical tool for experimental biologists. The paper introduces the framework of the GSLA platform, and takes protein family, differential express genes, microRNA targets and transcription factor targets as examples to illustrate how to use GSLA platform and show the effectiveness and practicability of GSLA.