蛋白质Geneontology,KEGG分析软件David使用方法介绍.ppt

DAVID;DAVID? provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes ;;Gene List Manager;;;;DAVID Analytic Modules;;Any given gene is associating with a set of annotationterms. If genes share similar set of those terms, they are most likely involved in similar biologicalmechanisms. The algorithm adopts kappa statistics to quantitatively measure the degree of the agreement how genes share the similar annotation terms. Kappa result ranges from 0 to 1. The higher the value of Kappa, the stronger the agreement. Kappa more than 0.7 typically indicates that agreement of two genes are strong. Kappa values greater than 0.9 are considered excellent. ;;Parameter Panel;;;;;;;1;;;;;;;DAVID Gene ID Conversion Tool (DGCT);DAVID Gene Name Batch Viewer;DAVID Gene Functional classification;Similarity Term Overlap (any value =0; default = 4): the minimum number of annotation terms overlapped between two genes in order to be qualified for kappa calculation. Similarity Threshold (any value between 0 to 1; Default = 0.35): the minimum kappa value to be considered biological significant. Initial Group Members (any value =2; default = 4): the minimum gene number in a seeding group, which affects the minimum size of each functional group in the final. Final Group Members (any value =2; default = 4): the minimum gene number in one final group after “cleanup” procedure. Multi-linkage Threshold (any value between 0% to 100%; default = 50%): It controls how seeding groups merge each other, i.e. two groups sharing the same gene members over the percentage will become one group. The higher percentage, in general, gives sharper separation i.e. it generates more final functional groups with more tightly associated genes in each group. In addition, changing the parameter does not contribute extra genes into unclustered group.