Open Access Research article

Reciprocal regulation of metabolic and signaling pathways

Andreas S Barth1, Ami Kumordzie1, Carlo Colantuoni2, Kenneth B Margulies3, Thomas P Cappola3 and Gordon F Tomaselli1*

Author Affiliations

1 Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, Maryland, USA

2 Department of Biostatistics, The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA

3 Penn Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA

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BMC Genomics 2010, 11:197  doi:10.1186/1471-2164-11-197

Published: 24 March 2010

Additional files

Additional file 1:

Graphical representation of 200 KEGG pathways sorted based on their similarity to OXPHOS expression. For 20 different human tissues, KEGG pathways were compared between the ten samples displaying the highest and the lowest values of OXPHOS gene expression (each study-ID with sample characteristics are listed in the tables in Additional Files 2 and 3). The directional regulation of 200 major KEGG pathways (number of up- minus down-regulated genes in a given KEGG pathway normalized to the total number of regulated genes within a study) was color-coded with yellow and blue representing low and high expression of the pathways, respectively. KEGG pathways were then sorted according to their similarity to "oxidative phosphorylation" which is represented by the top row in Additional File 1A. Metabolic pathways were consistently positively correlated with each other and negatively correlated with the expression of cell signaling pathways.

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Additional file 2:

List of gene expression datasets used in the present study. The study-ID, tissue type, Gene Expression Omnibus (GEO) accession number, species, sample characteristics, comparison, microarray type and methods of normalization are given for each dataset.

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Additional file 3:

List of human tissues samples with high vs. low OXPHOS gene activity. The tissue type, study-ID (Gene Expression Omnibus (GEO) accession number), sample-ID and clinical characteristics are given for samples with high and low OXPHOS gene activity.

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