These datasets correspond to the Functional Annotation Clustering or Gene Functional Classification report obtained in the Database for Annotation, Visualization and Integrated Discovery (DAVID) website, using as input file the ones provided for demo purposes (demoList1 or demoList2) with GOTERM_BP_ALL, GOTERM_MF_ALL and GOTERM_CC_ALL categories.
geneCluster1/2 or termCluster1/2 are tab delimitate unstructured files with DAVID format where:
TypeGene Cluster or Annotation Cluster.
Numberinteger to indicate the cluster label.
Enrichment Scorenumeric with the geometric mean (in -log scale) of members p-values in a corresponding annotation cluster, is used to rank their biological significance. Thus, the top ranked annotation groups most likely have consistent lower p-values for their annotation members.
according to the type of cluster it can be:
Genethe character vector with "ID", "Gene" and "Name".
Annotationthe same columns of a Functional Annotation Chart (see getFunctionalAnnotationChart).
member data per line according to the respective type of cluster.
Cristobal Fresno and Elmer A Fernandez
The Database for Annotation, Visualization and Integrated Discovery (davidgeneList.abcc.ncifcrf.gov)
Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C.; Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175
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