Open Access Research article

Co-expressed immune and metabolic genes in visceral and subcutaneous adipose tissue from severely obese individuals are associated with plasma HDL and glucose levels: a microarray study

Marcel GM Wolfs1, Sander S Rensen2, Elinda J Bruin-Van Dijk1, Froukje J Verdam2, Jan-Willem Greve2, Bahram Sanjabi3, Marcel Bruinenberg3, Cisca Wijmenga3, Timon W van Haeften14, Wim A Buurman2, Lude Franke35 and Marten H Hofker1*

Author Affiliations

1 Department of Pathology and Medical Biology, Medical Biology Section, Molecular Genetics, University Medical Center Groningen, University of Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands

2 NUTRIM School for Nutrition, Toxicology and Metabolism, Department of General Surgery, Maastricht University Medical Center, Maastricht, the Netherlands

3 Department of Genetics, University Medical Center Groningen, University of Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands

4 Department of Internal Medicine, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, the Netherlands

5 Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK

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BMC Medical Genomics 2010, 3:34  doi:10.1186/1755-8794-3-34

Published: 5 August 2010

Additional files

Additional file 1:

Table S1. Genes picked by random stratified selection and primer sequences used for qRT-PCR. Overview and primer sequences of the genes selected through random stratified selection for the qRT-PCR validation experiment.

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Additional file 2:

Table S2. Correlations between age, BMI, and plasma parameters of the study population. Overview of significant correlations between traits measured in the study population. Both Pearson correlation coefficients (left side of table) and p-values (right side of table) are shown for those correlations that have a p-value <0.01. Correlations significant after Bonferroni correction are marked with an asterisk. Data (except for age and BMI) have been transformed to a natural logarithm to obtain a normal distribution. TG, triglycerides; NEFA, non-esterified fatty acid; ALAT, alanine aminotransaminase; ASAT, aspartate aminotransaminase; CRP, C-reactive protein.

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Additional file 3:

Table S3. Overview of microarray and qRT-PCR results. Comparison of qRT-PCR and microarray data from 20 randomly stratified selected genes in order to validate the quality of the microarray data.

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Additional file 4:

Figure S1. Correlation plot of microarray and qRT-PCR results. Correlation plot of the fold changes in the microarray and the qRT-PCR experiments for 20 randomly stratified selected genes. The y-axis shows the Log2 averaged fold changes for the 20 genes tested as calculated in the qRT-PCR experiment. The x-axis shows Log2 averaged fold changes for these genes as detected in the microarray experiment. The fold changes obtained in the qRT-PCR and microarray experiments are strongly correlated (r = 0.88).

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Additional file 5:

Table S4A and S4B. Genes significantly upregulated in (A) subcutaneous and (B) visceral adipose tissue. List of genes significantly upregulated in subcutaneous and visceral adipose tissue.

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Additional file 6:

Table S5A and S5B. Gene Set Enrichment Analysis of genes differentially expressed in (A) subcutaneous adipose tissue and (B) visceral adipose tissue. Overview of biological processes overrepresented among genes differentially expressed in subcutaneous and visceral adipose tissue.

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Additional file 7:

Table S6A and S6B. Contents of the modules generated in (A) subcutaneous and (B) visceral adipose tissue. For each module, the number of probes in the module, the number of genes corresponding to these probes, and the names of all those genes are listed.

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Additional file 8:

Figure S2. Coloured heatmap of modules in subcutaneous adipose tissue. Pair-wise correlations between probes residing in all the modules identified in SAT were plotted. Probe pairs strongly positively correlated are shown in green and probe pairs strongly negatively correlated are shown in red. Colour intensity represents the strength of the correlation. The modules are indicated by white squares and are ordered in the same way as in Additional file 7, Tables S6A and S6B; thus with the largest module - containing the largest number of probes - in the upper left corner and the smallest module in the lower right corner.

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Additional file 9:

Figure S3. Coloured heatmap of modules in visceral adipose tissue. Pair-wise correlations between probes residing in all the modules identified in VAT were plotted. Probe pairs strongly positively correlated are shown in green and probe pairs strongly negatively correlated are shown in red. Colour intensity represents the strength of the correlation. The modules are indicated by white squares and are ordered in the same way as in Additional file 7, Tables S6A and S6B; thus with the largest module - containing the largest number of probes - in the upper left corner and the smallest module in the lower right corner.

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Additional file 10:

Table S7A and S7B. Gene Set Enrichment Analysis of genes in the modules in (A) subcutaneous adipose tissue and (B) visceral adipose tissue. Overview of biological processes overrepresented among modules identified in subcutaneous and visceral adipose tissue.

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Additional file 11:

Table S8. Relevant medication and menopausal status of the severely obese individuals. Overview of prescribed medication relevant for tested traits, and menopausal status of the severely obese individuals. Patient ID's correspond with the patient ID's deposited in the Gene Expression Omnibus database. Patients that received no relevant medication are not included in the table. Dyslipidemia treatment consists of statins, and treatment of hypertension consists of ACE-inhibitors, Angiotensin Receptor Blockers, and Calcium antagonists.

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Additional file 12:

Table S9A and S9B. Correlations between modules in (A) subcutaneous adipose tissue and (B) visceral adipose tissue, and traits after correction for possible confounding factors. Overview of correlations between modules and traits after correction for confounding factors - menopausal status, hormone treatment and treatment for diabetes, hypertension, dyslipidemia, along with all the other traits we measured: gender, age, BMI, plasma levels of glucose, insulin, HbA1c, triglycerides, non-esterified fatty acids, HDL cholesterol, LDL cholesterol, total cholesterol, CRP, ALAT, and ASAT - in (A) subcutaneous and (B) visceral adipose tissue. The last two columns in the table show Spearman rank correlation coefficients and p-values for the correlation between the module and the associated trait - as shown in columns 2 and 3 - corrected for potential confounders, which are listed in the first column. TG, triglycerides; NEFA, non-esterified fatty acid; ALAT, alanine aminotransaminase; ASAT, aspartate aminotransaminase; CRP, C-reactive protein.

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Additional file 13:

Table S10A, S10B, and S10C. Overlap in genes identified in our study and the study of Capel et al. in subcutaneous adipose tissue. Overview of the overlap between the results of the present study and an earlier microarray study in subcutaneous adipose tissue of severely obese subjects performed by Capel et al. [11].

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