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Table 1 Functional classes, results from literature, and transcription factor binding sites associated with drug-regulated patterns of gene expression

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

Gene pattern

Gene ontology

Literature mining

TFBS over-representation

 

Term

Fold (P)a

Dataset

P a

Binding sitesb

Fold (P)c

A

Protein phosphatase activity

32.4 (0.0036)

Rodriguez et al. [108], cocaine 1 h

1.33E-36

SRF (MA0083)

5.7 (0.095)

 

Rhythmic process

14.7 (0.0166)

Jayanthi et al. [40], methampethamine 2 h

1.04E-13

CREB1 (MA0018)

3.9 (0.0068)

 

Phosphotransferase activity

10.7(<0.0001)

Lemberger et al. [41], kainic acid 1 h

5.88E-13

  
 

Protein dimerization activity

3.6 (0.0203)

Ryan et al. [42], domoic acid 0.5 and 1 h

3.52E-12

  
 

Regulation of transcription

3 (0.0001)

Impey et al. [43], forskolin 1 h

3.87E-12

  

B1

Small GTPase mediated signal transduction

5.9 (0.0085)

Sanchis-Segura et al. [44], morphine 4 h

8.96E-29

Foxd3 (MA0041)

4.4 (0.02)

 

Apoptosis

5 (0.0018)

Treadwell et al. [46], ethanol 6 h

1.87E-11

Foxa2 (MA0047)

4.2 (0.043)

 

Cell cycle

4.7 (0.0025)

Sato et al. [47], dexamethasone 2 h

1.57E-08

FOXF2 (MA0030)

4 (0.025)

 

Intracellular signaling cascade

3.2 (0.0079)

Lemberger et al. [41], kainic acid 1 h

9.51E-07

Evi1 (MA0029)

3.8 (0.036)

 

Intracellular

1.5 (0.0017)

Ryan et al. [42], domoic acid 4 h

8.90E-07

  

B2

Enzyme inhibitor activity

8.9 (0.041)

Korostynski et al. [45], morphine 4 h

1.15E-29

NR1H2 (MA0115)

3.5 (0.288)

 

Apoptosis

5.9 (0.0007)

Ryan et al. [42], domoic acid 4 h

1.41E-18

Ar (MA0007)

3.3 (0.074)

 

Response to stress

4.2 (0.01)

McClung et al. [27], morphine withdrawal

4.23E-17

NR2F1 (MA0017)

3.3 (0.0428)

 

Cell differentiation

2.5 (0.026)

Treadwell et al. [46], ethanol 6 h

3.58E-13

  
 

Intracellular

1.4 (0.0074)

Chen et al. [109], heart failure left ventricular assist device (LVAD)

1.47E-07

  

B3

Regulation of developmental process

9.1 (0.0364)

Korostynski et al. [45], morphine 4 h

3.75E-15

Fos (MA0099)

6.7 (0.0103)

 

Magnesium ion binding

8.5 (0.0416)

McClung et al. [27], morphine withdrawal

3.52E-10

NR3C1 (MA0113)

5.6 (0.0058)

 

Anatomical structure morphogenesis

3.9 (0.0261)

Ryan et al. [42], domoic acid 4 h

3.22E-08

Ar (MA0007)

4.7 (0.0021)

 

Calcium ion binding

3.5 (0.1894)

Treadwell et al. [46], ethanol 6 h

9.56E-06

TEAD1 (MA0090)

3.9 (0.0302)

 

Transmembrane transporter activity

3.4 (0.1973)

Hasan et al. [110], chronic oxycodone

7.61E-05

  
  1. The complete results of data-mining are presented in Additional files 7 and 8. aStatistical significance of gene enrichment was computed using algorithms implemented in DAVID 2008 database and ErmineJ software. bConserved promoter regions +5,000/-1,000 bp from the transcription start site were analyzed (see Materials and methods). cFold change of the detected number of identified transcription factor binding sites (TFBSs) compared to the number expected by chance. dStatistical significance of over-representation of TFBS-containing genes compared to a number expected by chance was computed using a z-score test.
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Genome Biology

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