Open Access Research

The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum

Marcin Piechota1, Michal Korostynski1, Wojciech Solecki1, Agnieszka Gieryk1, Michal Slezak1, Wiktor Bilecki1, Barbara Ziolkowska1, Elzbieta Kostrzewa1, Iwona Cymerman2, Lukasz Swiech2, Jacek Jaworski2 and Ryszard Przewlocki1*

Author Affiliations

1 Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland

2 Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, Warsaw, 02-109, Poland

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Genome Biology 2010, 11:R48  doi:10.1186/gb-2010-11-5-r48

Published: 4 May 2010

Additional files

Additional file 1:

A figure presenting ANOVA results of gene expression profiling of drug effects in mouse striatum. The upper panel shows the relationship between the number of true positive results and the proportion of false positives for (a) time and (b) drug factors and (c) their interaction in ANOVA. The lower panel presents the relationship between the obtained P-values (y-axis) for both the factors and their interaction and the theoretically expected P-values (x-axis).

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Additional file 2:

A table listing the results of two-way ANOVA (followed by correction for multiple comparisons or Tukey's post-hoc test). The lists include: those genes altered by drug treatment, by time and with interaction between the factors; those genes regulated by each particular drug (P < 0.05, versus saline); and the expression levels of genes from patterns A and B. Each of these is available as a separate spreadsheet. P-values obtained from two-way ANOVA were further corrected using Bonferroni or Benjamini and Hochberg (percent FDR) corrections.

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Additional file 3:

A data file providing the results from the qPCR validation of the microarray data. Results for selected genes are presented as the mean (± standard error) compared with the saline control group (n = 3 to 10). A list of TaqMan assays used in the qPCR experiments with IDs and exon boundaries is included as a separate sheet.

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Additional file 4:

A figure showing hierarchical clustering of drug-induced gene expression alterations in mouse striatum. Microarray results are shown as a heat map and include genes with a significance obtained from two-way analysis of variance of the drug factor at (a) 5% and (b) 29% of FDR. Colored rectangles represent the transcript abundance (Additional file 5) of the gene and are labeled on the right. The intensity of the color is proportional to the standardized values (between -2 and 2) from each microarray, as indicated on the bar below the heat map image.

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Additional file 5:

A figure showing chromosome localizations of drug-responsive genes.

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Additional file 6:

A figure showing comparison of drug-induced effects in mouse striatum. (a-g) Average activity of time-dependent, drug-induced gene expression patterns. The results are presented as mean changes in gene expression (measured using z-values, in the extended A, B1, B2 and B3 groups of genes). The values are relative to the level of transcript abundance in naïve animals (at each of the time points 1, 2, 4 and 8 h). The thickness of the line is proportional to the number of genes in each cluster. (h,i) Matrices of correlation between all compared drug-induced gene expression profiles. The results were obtained using (h) DNA microarrays and (i) qPCR. The qPCR analysis was used to validate microarray results (Additional file 3).

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Additional file 7:

A table listing the complete results of the GO analysis presented in the manuscript. The analyses were performed on lists of genes that correspond to patterns A, B1, B2 and B3. The genes are listed in Additional file 2. Selected results are presented in Table 1.

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Additional file 8:

A table listing the complete results of the literature mining presented in the manuscript. The analyses were performed on lists of genes that correspond to patterns A, B1, B2 and B3. The genes are listed in Additional file 2. Selected results are presented in Table 1.

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Additional file 9:

A table providing the results of correlation analysis between the transcriptional response to drugs of abuse and behavioral traits related to drug abuse (see Materials and methods). Behavioral data and the matrix of correlations are available as separate sheets. Gene expression data from each pattern were normalized using z-score transformation and summarized as a function of time. Associations were computed using Pearson's correlation.

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