DAVIDdemo-clusterReport: DAVID's website gene/term cluster report example files

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description

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.

Format

geneCluster1/2 or termCluster1/2 are tab delimitate unstructured files with DAVID format where:

Cluster header

1. TypeGene Cluster or Annotation Cluster.

2. Numberinteger to indicate the cluster label.

3. 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.

Members Header

according to the type of cluster it can be:

1. Genethe character vector with "ID", "Gene" and "Name".

2. Annotationthe same columns of a Functional Annotation Chart (see getFunctionalAnnotationChart).

Members Body

member data per line according to the respective type of cluster.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (davidgeneList.abcc.ncifcrf.gov)

2. 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

3. DAVID Help page http://david.abcc.ncifcrf.gov/helps/functional_classification.html#textmode

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.