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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
TLDR
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. Expand
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
TLDR
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. Expand
Mechanisms Controlling Mitochondrial Biogenesis and Respiration through the Thermogenic Coactivator PGC-1
TLDR
PGC-1, a cold-inducible coactivator of nuclear receptors, stimulates mitochondrial biogenesis and respiration in muscle cells through an induction of uncoupling protein 2 (UCP-2) and through regulation of the nuclear respiratory factors (NRFs). Expand
Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter
TLDR
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. Expand
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
TLDR
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). Expand
mTOR controls mitochondrial oxidative function through a YY1–PGC-1α transcriptional complex
TLDR
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. Expand
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins
TLDR
The improved MitoCarta 2.0 inventory provides a molecular framework for system-level analysis of mammalian mitochondria and helps to understand mitochondrial pathways in health and disease. Expand
MICU1 encodes a mitochondrial EF hand protein required for Ca2+ uptake
TLDR
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. Expand
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
TLDR
It is reported that uORFs correlate with significantly reduced protein expression of the downstream ORF, based on analysis of 11,649 matched mRNA and protein measurements from 4 published mammalian studies, and that 5 uORF-altering mutations, detected within genes previously linked to human diseases, dramatically silence expression ofThe downstream protein. Expand
Defects in Adaptive Energy Metabolism with CNS-Linked Hyperactivity in PGC-1α Null Mice
TLDR
A central role for PGC-1alpha in the control of energy metabolism is illustrated but also novel systemic compensatory mechanisms and pathogenic effects of impaired energy homeostasis are revealed. Expand
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