A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis
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E. Zeggini | L. Southam | R. D. de Almeida | J. Steinberg | D. Swift | I. Meulenbelt | M. Tuerlings | J. Wilkinson | G. Katsoula | R. C. de Almeida | J. M. Wilkinson
[1] M. Peffers,et al. Ribosome dysfunction in osteoarthritis , 2021, Current opinion in rheumatology.
[2] Xiaochen Bo,et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data , 2021, Innovation.
[3] L. Bonassar,et al. Targeting calcium-related mechanotransduction in early OA , 2021, Nature Reviews Rheumatology.
[4] D. Rader,et al. Disrupting upstream translation in mRNAs is associated with human disease , 2021, Nature Communications.
[5] E. Zeggini,et al. A molecular quantitative trait locus map for osteoarthritis , 2021, Nature Communications.
[6] L. Clement,et al. satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications , 2021, bioRxiv.
[7] Maite Huarte,et al. Gene regulation by long non-coding RNAs and its biological functions , 2020, Nature reviews. Molecular cell biology.
[8] M. Fuxreiter. Classifying the Binding Modes of Disordered Proteins , 2020, International journal of molecular sciences.
[9] Jian Zhang,et al. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis , 2020, Nucleic Acids Res..
[10] L. Jia,et al. Long non-coding RNA MIR22HG promotes osteogenic differentiation of bone marrow mesenchymal stem cells via PTEN/ AKT pathway , 2020, Cell Death & Disease.
[11] H. Suchiman,et al. Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage , 2020, Arthritis & rheumatology.
[12] G. Calin,et al. RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer , 2020, International journal of molecular sciences.
[13] X. Bai,et al. Macrophages regulate the progression of osteoarthritis. , 2020, Osteoarthritis and cartilage.
[14] I. Ulitsky,et al. Regulation of gene expression by cis-acting long non-coding RNAs , 2019, Nature Reviews Genetics.
[15] G. Collins,et al. Global, regional and national burden of osteoarthritis 1990-2017: a systematic analysis of the Global Burden of Disease Study 2017 , 2019, Annals of the Rheumatic Diseases.
[16] P. M. van der Kraan,et al. TGFβ/BMP Signaling Pathway in Cartilage Homeostasis , 2019, Cells.
[17] Jeremy R. B. Newman,et al. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing , 2019, bioRxiv.
[18] Dawn A. Delfín,et al. The Extracellular Matrix Protein ABI3BP in Cardiovascular Health and Disease , 2019, Front. Cardiovasc. Med..
[19] D. Klepacki,et al. Assembly and functionality of the ribosome with tethered subunits , 2019, Nature Communications.
[20] Hojung Nam,et al. The CH25H–CYP7B1–RORα axis of cholesterol metabolism regulates osteoarthritis , 2019, Nature.
[21] Laurent Gatto,et al. ensembldb: an R package to create and use Ensembl-based annotation resources , 2019, Bioinform..
[22] Yaobo Xu,et al. Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage , 2019, Osteoarthritis and cartilage.
[23] M. Reinders,et al. RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage , 2018, Annals of the rheumatic diseases.
[24] Astrid Gall,et al. Ensembl 2019 , 2018, Nucleic Acids Res..
[25] J. Hoheisel,et al. Function, clinical application, and strategies of Pre-mRNA splicing in cancer , 2018, Cell Death & Differentiation.
[26] J. Parvizi,et al. Novel mutation in Teneurin 3 found to co‐segregate in all affecteds in a multi‐generation family with developmental dysplasia of the hip , 2018, Journal of orthopaedic research : official publication of the Orthopaedic Research Society.
[27] Zhihong Wu,et al. Identification of differentially expressed long noncoding RNAs in human knee osteoarthritis , 2018, Journal of cellular biochemistry.
[28] Joshua F. McMichael,et al. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer , 2018, bioRxiv.
[29] Feng Li,et al. CellMarker: a manually curated resource of cell markers in human and mouse , 2018, Nucleic Acids Res..
[30] J. Huard,et al. Bone morphogenetic proteins for articular cartilage regeneration. , 2018, Osteoarthritis and cartilage.
[31] A. Su,et al. Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. , 2018, Osteoarthritis and cartilage.
[32] J. Schwartz,et al. Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage , 2017, Annals of the rheumatic diseases.
[33] Wolfgang Huber,et al. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues , 2017, Nucleic acids research.
[34] Rhiju Das,et al. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them , 2017, Nature Reviews Molecular Cell Biology.
[35] David A. Knowles,et al. Annotation-free quantification of RNA splicing using LeafCutter , 2017, Nature Genetics.
[36] M. Robinson,et al. stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage , 2017, Genome Biology.
[37] Xing Fu,et al. The Neuron-Specific Protein TMEM59L Mediates Oxidative Stress-Induced Cell Death , 2016, Molecular Neurobiology.
[38] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.
[39] Di Chen,et al. Osteoarthritis: toward a comprehensive understanding of pathological mechanism , 2017, Bone Research.
[40] E. Zeggini,et al. Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis , 2016, Scientific Reports.
[41] Qing-hua Zhao,et al. Investigation of candidate genes for osteoarthritis based on gene expression profiles , 2016, Acta orthopaedica et traumatologica turcica.
[42] S. Samavedi,et al. A Three-Dimensional Chondrocyte-Macrophage Coculture System to Probe Inflammation in Experimental Osteoarthritis. , 2016, Tissue engineering. Part A.
[43] D. Zheng,et al. MYOSLID Is a Novel Serum Response Factor–Dependent Long Noncoding RNA That Amplifies the Vascular Smooth Muscle Differentiation Program , 2016, Arteriosclerosis, thrombosis, and vascular biology.
[44] J. Schwartz,et al. Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses , 2016, Osteoarthritis and cartilage.
[45] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.
[46] M. Swanson,et al. RNA mis-splicing in disease , 2015, Nature Reviews Genetics.
[47] H. Hwang,et al. Chondrocyte Apoptosis in the Pathogenesis of Osteoarthritis , 2015, International journal of molecular sciences.
[48] A. Su,et al. Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes. , 2015, Osteoarthritis and cartilage.
[49] L. Hurst,et al. Neighboring Genes Show Correlated Evolution in Gene Expression , 2015, Molecular biology and evolution.
[50] F. Meng,et al. Expression profile of long noncoding RNAs in cartilage from knee osteoarthritis patients. , 2015, Osteoarthritis and cartilage.
[51] B. Pal,et al. mTOR: A Potential Therapeutic Target in Osteoarthritis? , 2015, Drugs in R&D.
[52] Raphael Gottardo,et al. Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.
[53] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[54] Y. Rampersaud,et al. PPARγ deficiency results in severe, accelerated osteoarthritis associated with aberrant mTOR signalling in the articular cartilage , 2015, Annals of the rheumatic diseases.
[55] C. Kwoh,et al. Synovitis in knee osteoarthritis: a precursor of disease? , 2014, Annals of the rheumatic diseases.
[56] Li-Yan Xu,et al. Identification of Long Noncoding RNA Associated with Osteoarthritis in Humans , 2014, Orthopaedic surgery.
[57] J. Goeman,et al. Genes Involved in the Osteoarthritis Process Identified through Genome Wide Expression Analysis in Articular Cartilage; the RAAK Study , 2014, PloS one.
[58] J. Leek. svaseq: removing batch effects and other unwanted noise from sequencing data , 2014, bioRxiv.
[59] Andrew B. Conley,et al. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression , 2014, Mobile DNA.
[60] Xin Zhang,et al. Long Noncoding RNA Related to Cartilage Injury Promotes Chondrocyte Extracellular Matrix Degradation in Osteoarthritis , 2014, Arthritis & rheumatology.
[61] J. Pelletier,et al. Cartilage-specific deletion of mTOR upregulates autophagy and protects mice from osteoarthritis , 2014, Annals of the rheumatic diseases.
[62] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[63] A. Carr,et al. A gene expression study of normal and damaged cartilage in anteromedial gonarthrosis, a phenotype of osteoarthritis , 2014, Osteoarthritis and cartilage.
[64] Manolis Kellis,et al. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals , 2014, Genome research.
[65] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[66] J. Harrow,et al. Assessment of transcript reconstruction methods for RNA-seq , 2013, Nature Methods.
[67] J. Nam,et al. The Role of Changes in Extracellular Matrix of Cartilage in the Presence of Inflammation on the Pathology of Osteoarthritis , 2013, BioMed research international.
[68] Brendan H. Lee,et al. ADAMTS-7 forms a positive feedback loop with TNF-α in the pathogenesis of osteoarthritis , 2013, Annals of the rheumatic diseases.
[69] Robert Gentleman,et al. Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..
[70] German Tischler,et al. biobambam: tools for read pair collation based algorithms on BAM files , 2013, Source Code for Biology and Medicine.
[71] W. Huber,et al. Detecting differential usage of exons from RNA-seq data , 2012, Genome research.
[72] R. Yammani. S100 proteins in cartilage: role in arthritis. , 2012, Biochimica et biophysica acta.
[73] Helga Thorvaldsdóttir,et al. Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..
[74] R. Dreier. Hypertrophic differentiation of chondrocytes in osteoarthritis: the developmental aspect of degenerative joint disorders , 2010, Arthritis research & therapy.
[75] M. Brenner,et al. Fibroblast‐like synoviocytes in inflammatory arthritis pathology: the emerging role of cadherin‐11 , 2010, Immunological reviews.
[76] W. B. van den Berg,et al. TGF-beta signaling in chondrocyte terminal differentiation and osteoarthritis: modulation and integration of signaling pathways through receptor-Smads. , 2009, Osteoarthritis and cartilage.
[77] T. Spector,et al. Interleukin-6 is a significant predictor of radiographic knee osteoarthritis: The Chingford study , 2009, Arthritis and rheumatism.
[78] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[79] C. Gohr,et al. Osteopontin promotes pathologic mineralization in articular cartilage. , 2007, Matrix biology : journal of the International Society for Matrix Biology.
[80] K. Paul-Pletzer. Tocilizumab: blockade of interleukin-6 signaling pathway as a therapeutic strategy for inflammatory disorders. , 2006, Drugs of today.
[81] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[82] John M. Squire,et al. Fibrous Proteins: Coiled-Coils, Collagen and Elastomers , 2005 .
[83] L. Bridgewater,et al. A type XI collagen mutation leads to increased degradation of type II collagen in articular cartilage. , 2004, Osteoarthritis and cartilage.
[84] T. Yokota,et al. A novel chordin-like BMP inhibitor, CHL2, expressed preferentially in chondrocytes of developing cartilage and osteoarthritic joint cartilage , 2004, Development.
[85] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[86] P. Bullough,et al. Histological Assessment of Cartilage Repair: A Report by the Histology Endpoint Committee of the International Cartilage Repair Society (ICRS) , 2003, The Journal of bone and joint surgery. American volume.
[87] A R Poole,et al. Type II collagen degradation and its regulation in articular cartilage in osteoarthritis , 2002, Annals of the rheumatic diseases.
[88] A. Perraud,et al. TRPM4 Is a Ca2+-Activated Nonselective Cation Channel Mediating Cell Membrane Depolarization , 2002, Cell.
[89] H. Li,et al. Whole-transcriptome sequencing of knee joint cartilage from osteoarthritis patients , 2019, Bone & joint research.
[90] Florian Hahne,et al. Visualizing Genomic Data Using Gviz and Bioconductor , 2016, Statistical Genomics.
[91] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[92] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[93] G. Lei,et al. Elevated osteopontin level of synovial fluid and articular cartilage is associated with disease severity in knee osteoarthritis patients. , 2010, Osteoarthritis and cartilage.
[94] W. Kuebler,et al. Mechanotransduction by TRP Channels: General Concepts and Specific Role in the Vasculature , 2009, Cell Biochemistry and Biophysics.
[95] A. Persikov,et al. Molecular structure of the collagen triple helix. , 2005, Advances in protein chemistry.
[96] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .