Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
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M. Amills | Y. Ramayo-Caldas | R. Quintanilla | E. Mármol-Sánchez | R. González-Prendes | J. Tibau | T. F. Cardoso
[1] F. Drabløs,et al. Enhanced identification of significant regulators of gene expression , 2020, BMC Bioinformatics.
[2] J. Jordana,et al. An association analysis for 14 candidate genes mapping to meat quality quantitative trait loci in a Duroc pig population reveals that the ATP1A2 genotype is highly associated with muscle electric conductivity. , 2020, Animal genetics.
[3] C. Postic,et al. Carbohydrate Sensing Through the Transcription Factor ChREBP , 2019, Front. Genet..
[4] Yunxia Zhu,et al. Ets1-Mediated Acetylation of FoxO1 Is Critical for Gluconeogenesis Regulation during Feed-Fast Cycles. , 2019, Cell reports.
[5] Zizhen Yao,et al. MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle , 2019, eLife.
[6] M. Laplante,et al. PGC1A regulates the IRS1:IRS2 ratio during fasting to influence hepatic metabolism downstream of insulin , 2019, Proceedings of the National Academy of Sciences.
[7] L. Silió,et al. Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs , 2018, Front. Genet..
[8] Y. Zhang,et al. MicroRNA‐17 impairs glucose metabolism in insulin‐resistant skeletal muscle via repressing glucose transporter 4 expression , 2018, European journal of pharmacology.
[9] J. Jordana,et al. Analysing the Expression of Eight Clock Genes in Five Tissues From Fasting and Fed Sows , 2018, Front. Genet..
[10] S. Hughes,et al. Myogenin promotes myocyte fusion to balance fibre number and size , 2018, Nature Communications.
[11] R. Eri,et al. Role of Oxidative Stress in the Pathology and Management of Human Tuberculosis , 2018, Oxidative medicine and cellular longevity.
[12] Cong Niu,et al. Bach1: Function, Regulation, and Involvement in Disease , 2018, Oxidative medicine and cellular longevity.
[13] Tieming Ji,et al. Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously , 2018, BMC Bioinformatics.
[14] M. Amills,et al. Role of AMPK signalling pathway during compensatory growth in pigs , 2018, BMC Genomics.
[15] Jan Gorodkin,et al. Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates , 2018, PloS one.
[16] L. Ling,et al. MicroRNA-30e promotes hepatocyte proliferation and inhibits apoptosis in cecal ligation and puncture-induced sepsis through the JAK/STAT signaling pathway by binding to FOSL2. , 2018, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.
[17] Qing Zhu,et al. The Wnt antagonist and secreted frizzled-related protein 5: implications on lipid metabolism, inflammation, and type 2 diabetes mellitus , 2018, Bioscience reports.
[18] D. Bartel. Metazoan MicroRNAs , 2018, Cell.
[19] Alan C. Rupp,et al. Defining the Transcriptional Targets of Leptin Reveals a Role for Atf3 in Leptin Action , 2018, Diabetes.
[20] S. Klein,et al. Diurnal Variation in PDK4 Expression Is Associated With Plasma Free Fatty Acid Availability in People , 2017, The Journal of clinical endocrinology and metabolism.
[21] K. Gopal,et al. FoxO1 regulates myocardial glucose oxidation rates via transcriptional control of pyruvate dehydrogenase kinase 4 expression. , 2017, American journal of physiology. Heart and circulatory physiology.
[22] Jay W. Shin,et al. An integrated expression atlas of miRNAs and their promoters in human and mouse , 2017, Nature Biotechnology.
[23] M. Amills,et al. Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle , 2017, BMC Genomics.
[24] M. Amills,et al. A genome-wide association analysis for carcass traits in a commercial Duroc pig population. , 2017, Animal genetics.
[25] Jianguo Wang,et al. TXNIP overexpression suppresses proliferation and induces apoptosis in SMMC7221 cells through ROS generation and MAPK pathway activation. , 2017, Oncology reports.
[26] M. Hermann,et al. C10ORF10/DEPP-mediated ROS accumulation is a critical modulator of FOXO3-induced autophagy , 2017, Molecular Cancer.
[27] Di Ran,et al. Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq , 2017, Nucleic acids research.
[28] P. Carmeliet,et al. Sex‐specific, reciprocal regulation of ERα and miR‐22 controls muscle lipid metabolism in male mice , 2017, The EMBO journal.
[29] Tingting Li,et al. miR-30e is negatively regulated by myostatin in skeletal muscle and is functionally related to fiber-type composition , 2017, Acta biochimica et biophysica Sinica.
[30] C. Kühn,et al. Increased expression of thyroid hormone responsive protein (THRSP) is the result but not the cause of higher intramuscular fat content in cattle , 2017, International journal of biological sciences.
[31] C. Óvilo,et al. Nutrigenomics in farm animals , 2017 .
[32] D. Gilot,et al. Definition and identification of small RNA sponges: Focus on miRNA sequestration. , 2017, Methods.
[33] K. Nakayama,et al. A Bach2-Cebp Gene Regulatory Network for the Commitment of Multipotent Hematopoietic Progenitors. , 2017, Cell reports.
[34] M. Amills,et al. RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles , 2017, Scientific Reports.
[35] Shuli Yang,et al. Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig , 2016, PloS one.
[36] Daiwen Chen,et al. From Nutrient to MicroRNA: a Novel Insight into Cell Signaling Involved in Skeletal Muscle Development and Disease , 2016, International journal of biological sciences.
[37] Yan Li,et al. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.
[38] A. B. Reddy,et al. The Pentose Phosphate Pathway Regulates the Circadian Clock , 2016, Cell metabolism.
[39] V. Pialoux,et al. Transition from physical activity to inactivity increases skeletal muscle miR‐148b content and triggers insulin resistance , 2016, Physiological reports.
[40] L. Goedeke,et al. microRNAs in lipoprotein metabolism and cardiometabolic disorders. , 2016, Atherosclerosis.
[41] C. Óvilo,et al. Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism , 2015, PloS one.
[42] Pardis C Sabeti,et al. Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis , 2015, Nature Medicine.
[43] Philippe Salembier,et al. NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference , 2015, BMC Bioinformatics.
[44] R. de Cabo,et al. Identification of miR-148a as a novel regulator of cholesterol metabolism , 2015, Nature Medicine.
[45] J. Baenziger,et al. Nicotinic acetylcholine receptor-lipid interactions: Mechanistic insight and biological function. , 2015, Biochimica et biophysica acta.
[46] T. Duchaine,et al. On the availability of microRNA-induced silencing complexes, saturation of microRNA-binding sites and stoichiometry , 2015, Nucleic acids research.
[47] D. Bartel,et al. Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.
[48] Min Zhang,et al. miR-148a is Associated with Obesity and Modulates Adipocyte Differentiation of Mesenchymal Stem Cells through Wnt Signaling , 2015, Scientific Reports.
[49] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[50] S. Salzberg,et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.
[51] Jun Liu,et al. Characterization of the mammalian miRNA turnover landscape , 2015, Nucleic acids research.
[52] Weidong Wei,et al. miR-22 as a prognostic factor targets glucose transporter protein type 1 in breast cancer. , 2015, Cancer letters.
[53] S. Dhanasekaran,et al. The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.
[54] Vishal R. Patel,et al. Erratum to "Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock" [Mol Metab 3 (2014) 29-41]. , 2014, Molecular metabolism.
[55] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[56] M. Lazar,et al. Nuclear receptor Rev-erbα: up, down, and all around , 2014, Trends in Endocrinology & Metabolism.
[57] L. Goedeke,et al. microRNA regulation of lipoprotein metabolism , 2014, Current opinion in lipidology.
[58] K. Zen,et al. Argonaute 2 in Cell-Secreted Microvesicles Guides the Function of Secreted miRNAs in Recipient Cells , 2014, PloS one.
[59] J. Estellé,et al. Differences in Muscle Transcriptome among Pigs Phenotypically Extreme for Fatty Acid Composition , 2014, PloS one.
[60] C. Óvilo,et al. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics , 2014, BMC Genomics.
[61] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[62] M. Hulver,et al. The pivotal role of pyruvate dehydrogenase kinases in metabolic flexibility , 2014, Nutrition & Metabolism.
[63] J. Svaren,et al. Bach2 Regulates Homeostasis of Foxp3+ Regulatory T Cells and Protects against Fatal Lung Disease in Mice , 2014, The Journal of Immunology.
[64] Pierre Baldi,et al. Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock , 2013, Molecular metabolism.
[65] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[66] J. Miyoshi,et al. Hypothalamic ATF3 is involved in regulating glucose and energy metabolism in mice , 2013, Diabetologia.
[67] Qing Xu,et al. A regulatory circuit of miR-148a/152 and DNMT1 in modulating cell transformation and tumor angiogenesis through IGF-IR and IRS1. , 2013, Journal of molecular cell biology.
[68] Paul J Thornalley,et al. Glucose-Induced Down Regulation of Thiamine Transporters in the Kidney Proximal Tubular Epithelium Produces Thiamine Insufficiency in Diabetes , 2012, PloS one.
[69] Michael Q. Zhang,et al. Novel Foxo1-dependent transcriptional programs control Treg cell function , 2012, Nature.
[70] In-kyu Lee,et al. Transcriptional Regulation of Pyruvate Dehydrogenase Kinase , 2012, Diabetes & metabolism journal.
[71] B. Dalrymple,et al. Beyond differential expression: the quest for causal mutations and effector molecules , 2012, BMC Genomics.
[72] Ling Tian,et al. MicroRNA‐7 inhibits tumor growth and metastasis by targeting the phosphoinositide 3‐kinase/Akt pathway in hepatocellular carcinoma , 2012, Hepatology.
[73] L. Aravind,et al. Interplay between gene expression noise and regulatory network architecture. , 2012, Trends in genetics : TIG.
[74] Saptarsi M. Haldar,et al. Kruppel-like factor 15 regulates skeletal muscle lipid flux and exercise adaptation , 2012, Proceedings of the National Academy of Sciences.
[75] S. Moore,et al. Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. , 2012, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.
[76] E. Wagner,et al. FOSL2 promotes leptin gene expression in human and mouse adipocytes. , 2012, The Journal of clinical investigation.
[77] Davis J. McCarthy,et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.
[78] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[79] C. Dani,et al. Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis , 2011, Genome Biology.
[80] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[81] Kakajan Komurov,et al. Patterns of human gene expression variance show strong associations with signaling network hierarchy , 2010, BMC Systems Biology.
[82] Phillip A. Sharp,et al. Emerging Roles for Natural MicroRNA Sponges , 2010, Current Biology.
[83] Anindya Dutta,et al. MiR-322/424 and -503 Are Induced during Muscle Differentiation and Promote Cell Cycle Quiescence and Differentiation by Down-Regulation of Cdc25A , 2010, Molecular biology of the cell.
[84] M. Band,et al. Jcb: Article , 2022 .
[85] Loyal A Goff,et al. Differential regulation of microRNA stability. , 2010, RNA.
[86] Brian P. Dalrymple,et al. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data , 2010, Bioinform..
[87] M. Robinson,et al. A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.
[88] Antonio Reverter,et al. PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches , 2010, Bioinform..
[89] Davis J. McCarthy,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[90] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[91] Pornpimol Charoentong,et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..
[92] S. O’Rahilly,et al. The transcription factors Egr1 and Egr2 have opposing influences on adipocyte differentiation , 2009, Cell Death and Differentiation.
[93] S. Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[94] Antonio Reverter,et al. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks , 2008, Bioinform..
[95] Yunqing Li,et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. , 2008, Cancer research.
[96] P. Watkins,et al. Fatty Acid Transport Protein 4 Is the Principal Very Long Chain Fatty Acyl-CoA Synthetase in Skin Fibroblasts* , 2007, Journal of Biological Chemistry.
[97] H. Aburatani,et al. Increased hepatic expression of ganglioside-specific sialidase, NEU3, improves insulin sensitivity and glucose tolerance in mice. , 2007, Metabolism: clinical and experimental.
[98] M. Oliver,et al. Increasing the amount of n-3 fatty acid in meat from young Holstein bulls through nutrition. , 2006, Journal of animal science.
[99] M. Holness,et al. Regulation of pyruvate dehydrogenase complex activity by reversible phosphorylation. , 2003, Biochemical Society transactions.
[100] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[101] J. Ros,et al. Simultaneous HPLC Analysis of α-Tocopherol and Cholesterol in Fresh Pig Meat , 2003 .
[102] Y. Benjamini,et al. THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .
[103] J. Keele,et al. Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. , 2000, Journal of animal science.
[104] G. Lienhard,et al. The glucose transporter GluT4 and secretory carrier membrane proteins (SCAMPs) colocalize in rat adipocytes and partially segregate during insulin stimulation. , 1993, The Journal of biological chemistry.
[105] Gebert Lfr,et al. Regulation of microRNA function in animals , 2019 .
[106] N. Turner,et al. Altered feeding differentially regulates circadian rhythms and energy metabolism in liver and muscle of rats. , 2013, Biochimica et biophysica acta.
[107] S. Archer,et al. FOXO1-mediated upregulation of pyruvate dehydrogenase kinase-4 (PDK4) decreases glucose oxidation and impairs right ventricular function in pulmonary hypertension: therapeutic benefits of dichloroacetate , 2012, Journal of Molecular Medicine.
[108] Gábor Csárdi,et al. The igraph software package for complex network research , 2006 .
[109] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .