蛋白质Geneontology,KEGG分析软件David使用方法介绍（课堂PPT）

1、1DAVIDDatabase for Annotation, Visualization and Integrated Discovery2DAVID provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes l Identify enriched biological themes, particularly GO terms l Discover enriched funct

2、ional-related gene groups l Cluster redundant annotation termsl Visualize genes on BioCarta & KEGG pathway maps l Display related many-genes-to-many-terms on 2-D view. l Search for other functionally related genes not in the list l List interacting proteinsl Explore gene names in batch l Link ge

3、ne-disease associations l Highlight protein functional domains and motifs l Redirect to related literatures l Convert gene identifiers from one type to another. 34Gene List Manager5678DAVID Analytic Modules910Any given gene is associating with a set of annotationterms. If genes share similar set of

4、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 agree

5、ment. Kappa more than 0.7 typically indicates that agreement of two genes are strong. Kappa values greater than 0.9 are considered excellent. 1112Parameter PanelGene Clusters Identified by DAVIDUsers gene IDs & Names1314151617181912View and select annotation categories of your interests333Percen

6、tage,e.g.44/163Genes from the list involved in this annotation categorySingle chart report only for this Annotation categories 20Table report for all Selected annotation categories2122Linear or redundant chart report of annotation terms for all selected annotation categories above2324Clustered or no

7、n-redundant chart report of annotation terms for all selected annotation categories above2526DAVID Gene ID Conversion Tool (DGCT)If a significant portion (20%) of input gene IDs fail to bemapped to an internal DAVID ID, a specially designed module, the DAVID Gene ID Conversion Tool, will start up to

8、 help map such IDs.27DAVID Gene Name Batch ViewerThe gene name batch viewer is able to quickly attach meaning to a list of gene IDs by rapidly translating them into their corresponding gene names. before proceeding to analysis with other more comprehensive analytic tools, investigators can quickly g

9、lance at the gene names to further gain insight about their study and to answer questions.28DAVID Gene Functional classification The Functional Classification Tool generates a gene-to-gene similarity matrix based shared functional annotation using over 75,000 terms from 14 functional annotation sour

10、ces. The novel clustering algorithms classifies highly related genes into functionally related groups. 29Similarity 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

11、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

12、=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 separat