leukemiasGO: Gene ontology term enrichment of differential gene expression...
In dieterich-lab/CellPlot: Segmented Bar Chart Plot Methods

Description Usage Format Author(s) References

leukemiasGO is microarray gene expression data from the studies of Kohlmann et al. (2008) and Haferlach et al. (2010). Processed as described in Risueno et al. (2010). Adapted from package leukemiasEset (see leukemiasEset). Differential gene expression was performed using the DESeq2 package comparing the sample classes NoL (no leukemia) against AML, ALL, and CML.

GO annotation was done with the annotate and hu6800.db packages from Bioconductor. The topGO package was utilized to perform a GO enrichment test based on Fisher's exact test using the 'elimScore' method.

1 2	data(golubGO) data(leukemiasGO)

A data.frame that contains the gene ontology enrichment and differential gene expression tests data.

Description of the columns:
GO - character vector with GO ids of the GO terms
Term - character vector with GO terms
Annotated - integer vector with number of GO annotated genes per term
Significant - integer vector with number of significant differential expressed genes per term
Expected - numeric vector with expected number of differential expressed genes per term
pvalCutOff - numeric vector with p values from the GO enrichment test
padj - numeric vector with adjusted p values (FDR) from the GO enrichment test
LogEnrich - numeric vector with the logarithm of the GO term enrichment (significant/expected)
PROBEID/ENSEMBL - list of names of genes differentially expressed per GO term
log2fc/log2FoldChange - list of logarithm of fold changes of all genes per GO term
p/pvalue - list of p values of all differential gene expression

Sven E. Templer [aut]
Authors of the leukemiasEset [ctb]

Kohlmann A, Kipps TJ, Rassenti LZ, Downing JR et al. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Br J Haematol (2008) 142(5):802-7. PMID: 18573112

Haferlach T, Kohlmann A, Wieczorek L, Basso G et al. Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol (2010) 28(15):2529-37. PMID: 20406941

Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics (2010) 11:221. PMID: 20429936.

dieterich-lab/CellPlot documentation built on May 15, 2019, 8:29 a.m.