Analysis of gene expression during neurite outgrowth and regeneration

Moriah L Szpara¹^,2^,3 , Karen Vranizan³ , Yu Chuan Tai³^,4 , Corey S Goodman¹^,2 , Terence P Speed³^,5 and John Ngai¹^,2^,3

¹Department of Molecular and Cell Biology, University of California, Berkeley, California, USA

²Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA

³Functional Genomics Laboratory, University of California, Berkeley, California, USA

⁴Division of Biostatistics, University of California, Berkeley, California, USA

⁵Department of Statistics, University of California, Berkeley, California, USA

author email corresponding author email

BMC Neuroscience 2007, 8:100doi:10.1186/1471-2202-8-100


Published:	23 November 2007

Additional files

Additional file 1:

Additional Figures and Additional Methods. Contains Additional Figures 1–5, figure legends and Additional Methods.

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Additional file 2:

Abbreviations. Lists the abbreviations and corresponding gene names used in the Sema3A pathway of Figure 4 and in the annotation of regeneration-associated genes (shown on Figure 1 and in Additional file 1). Meta-analysis. Lists the genes extracted from the meta-analysis of our data with three published studies of genes changed during in vivo neurite regeneration. The table indicates where matching probesets were found in the present data, as well as if those genes were significantly changed in the present study. Top 5% intersection. Lists the top 5%, 2% and 1% intersection of genes with the highest intensity, or expression level, in both DRG and SCG. The table includes the median intensity for each gene in DRG and SCG, as well as the Affymetrix probeset for each gene. Q-RT-PCR. Lists the genes used for qRT-PCR analysis, the main reference sequence from NCBI used to design each set of primers, and the sequences of each forward, probe, and reverse primer. The table also lists the Affymetrix probesets matching each of these genes. Sema3A effects. Lists the genes observed by microarray to be significantly affected by exposure to Sema3A. The table includes the maximum fold difference after Sema3A exposure, as well as the quadratic analysis p-value for significance of this difference.

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Additional file 3:

DRG-SCG dataset. Lists all 11,268 probe sets found in the DRG-SCG dataset, along with relevant annotation and microarray data. Statistics and measures of maximum change over time are listed for all genes. This list contains the data and criteria used to generate HOPACH clusters and GenMAPP filters.

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Additional file 4:

DRG SCG gMAPP.gex. GenMAPP expression database of the 712 genes jointly affected during neurite outgrowth by DRG and SCG. Includes HOPACH cluster levels and other criteria for analyzing and visualizing affected genes and pathways in GenMAPP. GenMAPP software is available online [104].

Format: GEX Size: 2MB Download file