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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
- A. Subramanian, P. Tamayo, J. Mesirov
- BiologyProceedings of the National Academy of Sciences…
- 30 September 2005
It is demonstrated how the GSEA method yields insights into several cancer-related data sets, including leukemia and lung cancer, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer.
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
An analytical strategy is introduced, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes, which identifies a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle.
Mechanisms Controlling Mitochondrial Biogenesis and Respiration through the Thermogenic Coactivator PGC-1
Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter
Genome phylogenetic profiling, genome-wide RNA co-expression analysis and organelle-wide protein coexpression analysis are used to predict proteins functionally related to MICU1, establishing MCU as an essential component of the mitochondrial Ca2+ uniporter.
Metabolite profiles and the risk of developing diabetes
Findings underscore the potential key role of amino acid metabolism early in the pathogenesis of diabetes and suggest that amino acid profiles could aid in diabetes risk assessment.
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
A comparative analysis of the human, mouse, rat and dog genomes is presented to create a systematic catalogue of common regulatory motifs in promoters and 3′ untranslated regions (3′ UTRs).
A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology
mTOR controls mitochondrial oxidative function through a YY1–PGC-1α transcriptional complex
- John T. Cunningham, J. T. Rodgers, Daniel H Arlow, F. Vazquez, V. Mootha, P. Puigserver
- 29 November 2007
A mechanism by which a nutrient sensor (mTOR) balances energy metabolism by means of the transcriptional control of mitochondrial oxidative function is identified, which has important implications for the understanding of how these pathways might be altered in metabolic diseases and cancer.
MICU1 encodes a mitochondrial EF hand protein required for Ca2+ uptake
An integrative strategy is used to predict human genes involved in mitochondrial calcium entry based on clues from comparative physiology, evolutionary genomics and organelle proteomics, and finds MICU1 represents the founding member of a set of proteins required for high-capacity mitochondrial calcium uptake.
EMRE Is an Essential Component of the Mitochondrial Calcium Uniporter Complex
Sancak et al. complete the molecular characterization of the mitochondrial calcium uniporter (MCU), the multicomponent channel that allows concentration of calcium within the organelle, and identify a small protein termed “essential MCU regulator”—or EMRE—which was required for calcium transport activity of the fully assembled uniporters.