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Muscle project

...some intro/description ..

General scheme of the project

Experiments Rat ..experiment description .. ..reference to GEO... Human GSE164081 Description of experiment GEO References

Bioinformatic analysis Human data analysis Differentially expressed genes Ontology analysis CAGE-seq analysis GTRD database Skeletal muscle specific signalling pathways Skeletal muscle specific signalling pathways in human TSS and DEGs Key master regulators of co-expressed genes Gene set enrichment analysis (GSEA) Unique intergenic TSS Alternative usage of dominating TSS Enhancers Merging CAGE experiments Methods References

Mathematical modelling Linkage of metabolic pathways and gene expression MetGeneConjugation Pathways and key proteins AMPK Ca-CaM-AMPK signaling models CaMKII CaMKKβ LKB1 SBGN diagrams Models Muscle models DataSets Integrated modular models Integrated model description Integrated model validation

Publications of the project

• GTRD: a database on gene transcription regulation
• Modular Visual Model of Energy Metabolism in Human Skeletal Muscle
• A mathematical model linking signalling pathway and gene expression regulation in Human Skeletal Muscle
• Integrated Modular Model Linking Metabolism, Signaling Transduction and Gene Expression Regulation in Human Skeletal Muscle.
• Regulation of Proteins in Human Skeletal Muscle: The Role of Transcription
• Transcriptomic Signatures and Upstream Regulation in Human Skeletal Muscle Adapted to Disuse and Aerobic Exercise
• Genome-wide atlas of promoters expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy, under review