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"Functional and Evolutionary Insights Into Human Brain Development Through Global Transcriptome Analysis," Johnson et al., Neuron 2009.

Weighted Gene Co-expression Network Analysis

Weighted gene co-expression network analysis (WGCNA) was performed as described previously (Oldham et al., PNAS 103(47):1793-8, 2006) using gene-level expression values for all core probesets from the Affymetrix Exon Arrays. Two separate analyses were performed, the first using all five brain regions sampled (NCTX, HIP, STR, THM, CBL) and the second restricted to nine areas of neocortex (NCTX). PDFs contain clustering dendrograms used to define the modules, as well as heatmaps and eigengenes (first principal component values) for all modules. Excel files list the genes in each module sorted by Kin, which represents the within-module connectivity or “hub status” of each gene. In addition, the total connectivity of the gene to the entire network is given (“kTotal”), as well as the correlation of the gene’s expression data to the module eigengene (“eigencorr”) and the significance of this correlation (“eigenpval”). Finally, at the right of these tables are appended the corrected p-values for module genes that were also differentially expressed (DEX) or alternatively spliced (DAS) in conventional comparative expression analyses.

For more information about WGCNA, visit:
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/.

Exon Array data at the UCSC Genome Browser

Exon-level expression data from these studies are viewable at the UCSC Human Genome Browser using the "Sestan Brain" expression track (http://genome.ucsc.edu).

NCBI GEO Accession for Affymetrix Exon Array Data

The raw and processed Affymetrix Exon Array data used for these analyses are available through the NCBI Gene Expression Omnibus (GEO), accession number GSE13344: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13344.