Meta-analysis of kindling-induced gene expression in hippocampus

Supplement to Meta-Analysis of Kindling-Induced Gene Expression Changes in the Rat Hippocampus.
Rogic S, Pavlidis P pubmed reprint

Abstract

Numerous studies have been performed to examine gene expression patterns in the rodent hippocampus in the kindling model of epilepsy. However, recent reviews of this literature have revealed limited agreement among studies. Because this conclusion was based on retrospective comparison of reported “hit lists” from individual studies, we hypothesized that re-analysis of the original expression data would help address this concern. In this paper, we reanalyzed four genome-wide expression studies of excitotoxin-induced kindling in rat and performed a statistical meta-analysis. The meta-analysis revealed over 800 genes which show significant change in expression 24 h after initial seizure induction, and 59 genes altered after 10 days. To evaluate our results in light of previous work, we assembled a reference list of genes formed from a consensus of the published literature. Our profiles include most of the genes in this reference list, and most of the additional genes are from pathways or biological processes previously recognized to be altered in kindling. In addition our results emphasized expression changes in lipid metabolism and protein degradation pathways. We conclude that a cautious re-analysis of published expression data can help illuminate genes and pathways underling kindling.

Publication

Frontiers in NeuroGenomics

Contact

paul@chibi.ubc.ca

Supplement

  1. 24-hour gene list – The complete list of genes identified to be significant with FEM method at 24 hours after the excitotoxic insult. Meaning of columns:
    • Gene Symbol – official gene symbol for Rattus norvegicus
    • FEM q-val – q-value from FEM method
    • Fisher’s q-val – q-value from Fisher’s method
    • GSE4236 q-val – q-value from individual analysis of GSE4236 dataset
    • Tang q-val – q-value from individual analysis of Tang dataset
    • Direction – direction of expression; + if gene is upregulated after ecitotoxic insult and – if it’s downregulated
    • Reference Set – x indicates if the genes is also in the reference gene set
    • Epilepsy – x indicates if the genes is also in the CarpeDB epilepsy database
    • 240h – x indicates if the genes is also on the 240-hour gene list
  2. 240-hour gene list – The complete list of genes identified to be significant with FEM method at 240 hours after the excitotoxic insult. Meaning of columns is similar to above.
  3. reference genes – The complete list of the reference genes. The first column is the official gene symbol for Rattus norvegicus and x in the second column indicates if the gene is mapped by a probe from the microarray platforms used in the study.
  4. A graph of significant biological functions for the 24-hour dataset computed by the Ingenuity Pathway Analysis (IPA) software. reprint
  5. A graph of significant canonical pathways for the 24-hour dataset computed by IPA software. reprint
  6. A graph of significant biological functions for the 240-hour dataset computed by IPA software. reprint
  7. A graph of significant canonical pathways for the 240-hour dataset computed by IPA software. reprint
  8. GSE4236 dataset in Gemma
  9. GSE1833 dataset in Gemma
  10. Tang dataset in Gemma
  11. Elliott dataset in Gemma