R: DAVID's website Functional Annotation Chart example files
funChart1
R Documentation
DAVID's website Functional Annotation Chart example files
Description
These datasets correspond to the reports obtained using
Functional Annotation Chart Reports 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.
Usage
data(funChart1)
data(funChart2)
Format
funChart1/2 are data.frame for demoList1/2 input ids,
respectively, with the following columns.
Category
factor with the main categories under used in the present
analysis.
Term
character with the name of the term in format id~name (if
available).
Count
integer with the number of ids of the gene list that belong to
this term.
X.
after converting user input gene IDs to corresponding DAVID gene
ID, it refers to the percentage of DAVID genes in the list assoicated with
particular annotation term. Since DAVID gene ID is unique per gene, it is
more accurate to use DAVID ID percentage to present the gene-annotation
association by removing any redundency in user gene list, i.e. two user IDs
represent same gene.
PValue
numeric with the EASE Score of the term (see DAVID Help
page).
Genes
character in comma separated style with the genes present in
the term.
List.Total, Pop.Hits, Pop.Total
integers (in addition to Count) to
build the 2x2 contingency table in order to compute the EASE Score (see
DAVID Help page).
Fold.Enrichment
numeric with the ratio of the two proportions. For
example, if 40/400 (i.e. 10%) of your input genes involved in "kinase
activity" and the background information is 300/30000 genes (i.e. 1%)
associating with "kinase activity", roughly 10%/1%=10 fold enrichment.
Bonferroni, Benjamini, FDR
numerics with p-value adjust different
criterias (see p.adjust)
Author(s)
Cristobal Fresno and Elmer A Fernandez
References
The Database for Annotation,
Visualization and Integrated Discovery
(david.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