DESCRIPTION:
The complete differential gene expression geneset was made available at NCBI GEO (NAc accession no.: GSE62699) and obtained using the GEO2R tool. Gene expression was assayed using Affymetrix GeneChip Human Genome U133A 2.0 (HG-U133A 2.0) on 22,214 probe sets spanning ~ 18,400 mRNA transcripts, and the Affymetrix GeneChip miRNA 3.0 microarray interrogating the expression of 1733 mature miRNAs as previously described [24]. None of the mRNA or miRNA probes were excluded based on quality control criteria outlined in previous studies [18]. Raw probe data were GCRMA background corrected, log2 transformed, and quantile normalized using Partek Genomics Suite v6.23 (PGS; Partek Inc., St. Louis, MO) to obtain relative gene expression values. A principal component analysis was used to identify potential outlier samples. Only one case sample was removed from the analyses, leaving 18 controls and 17 cases (n = 35) for both brain regions. It has become widely accepted to verify a subset of microarray-generated gene expression changes via an independent platform such as qPCR. Considering limited tissue availability and our extensive use of the Affymetrix platform in the past, we did not include microarray validation in this study which is similar to what other groups have done in the past [25]. We have previously ‘validated’ the same array and platform in independent qPCR experiments with a concordance between microarray and qPCR platforms exceeding 80% in the past [18].
LABEL:
DEG NAc AD cases vs control_pvalue
SCORE TYPE:
P-Value
THRESHOLD:
<= 0.5
GENES IN THRESHOLD:
8861
DATE ADDED:
DATE UPDATED:
SPECIES:
AUTHORS:
TITLE:
JOURNAL:
ABSTRACT:
Genes in threshold: 8861
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