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Giovanni Coppola

Kellen Winden

Genevieve Konopka

Fuying Gao

Daniel Geschwind

Expression and network analysis of Illumina microarray data

Microarrays are commonly used tools for assessing changes in gene expression between two populations.  Many algorithms exist for analyzing the hybridization signals from theses arrays.  Here, we present our code for assessing changes in expression from samples hybridized to Illumina whole genome microarrays.  We also include our code for building weighted gene coexpression networks.  Finally, we present how we determined the overlap from two independent microarray studies.

1.  Requires a personal computer running R/Bioconductor.

Smyth, G.K., Gentleman, R., Carey, V., Dudoit, S., Irizarry, R., and Huber, W. \(2005). Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor \(Springer), pp. 397-420.





Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. \(2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol, 5.





Zhang, B., and Horvath, S.  \(2005)  A general framework for weighted gene co-expression network analysis.  Stat Appl Genet Mol Biol, 4: Article 17.





Langfelder, P., Zhang, B., and Horvath, S.  \(2008)  Defining clusters from a hierarchical cluster tree:  the Dynamic Tree Cut package for R.  Bioinformatics, 24\(5): 719-20.

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Method Article

Expression and network analysis of Illumina microarray data

Giovanni Coppola, Kellen Winden, Genevieve Konopka, Fuying Gao, Daniel Geschwind

Giovanni Coppola

UCLA

Kellen Winden

UCLA

Genevieve Konopka

UCLA

Fuying Gao

UCLA

Daniel Geschwind

UCLA

DOI:

10.1038/nprot.2009.215

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Human-specific transcriptional regulation of CNS development genes by FOXP2

by Genevieve Konopka, Jamee M. Bomar, Kellen Winden, +6

Nature (20 October, 2009)

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This is a preprint. It has not completed peer review.

Method Article

Expression and network analysis of Illumina microarray data

Giovanni Coppola, Kellen Winden, Genevieve Konopka, Fuying Gao, Daniel Geschwind

Giovanni Coppola

UCLA

Kellen Winden

UCLA

Genevieve Konopka

UCLA

Fuying Gao

UCLA

Daniel Geschwind

UCLA

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