DAVIDdemo-functionalAnnotationChart: DAVID's website Functional Annotation Chart 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 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

1. The Database for Annotation, Visualization and Integrated Discovery (david.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_annotation.html#E3

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