geneCluster1: DAVID's website gene/term cluster report example files
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
-
- 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.
- Members Header
- 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).
- Members Body
- member data per line according to the respective type
of cluster.
References
- 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
-
DAVID Help page
http://david.abcc.ncifcrf.gov/helps/functional_classification.html#textmode