Gene expression enrichment in human brain regions

Description

The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The package integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project [1-4]. The statistical analysis is performed by the core function aba_enrich which interfaces the ontology enrichment software FUNC [5]. Additional functions provided in this package like get_expression and plot_expression facilitate exploring the expression data.

Details

Package: ABAEnrichment
Type: Package
Version: 1.3.5
Date: 2016-10-13
License: GPL (>= 2)

For details see vignette("ABAEnrichment",package="ABAEnrichment")

Author(s)

Steffi Grote
Maintainer: Steffi Grote <steffi_grote@eva.mpg.de>

References

[1] Hawrylycz, M.J. et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome, Nature 489: 391-399. doi:10.1038/nature11405
[2] Miller, J.A. et al. (2014) Transcriptional landscape of the prenatal human brain, Nature 508: 199-206. doi:10.1038/nature13185
[3] Allen Institute for Brain Science. Allen Human Brain Atlas [Internet]. Available from: http://human.brain-map.org/
[4] Allen Institute for Brain Science. BrainSpan Atlas of the Developing Human Brain [Internet]. Available from: http://brainspan.org/
[5] Pruefer, K. et al. (2007) FUNC: A package for detecting significant associations between gene sets and ontological annotations, BMC Bioinformatics 8: 41. doi:10.1186/1471-2105-8-41

See Also

vignette("ABAEnrichment",package="ABAEnrichment")
vignette("ABAData",package="ABAData")
aba_enrich
get_expression
plot_expression
get_name
get_sampled_substructures
get_superstructures