4.5 Article

A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis

Related references

Note: Only part of the references are listed.
Review Rheumatology

Ribosome dysfunction in osteoarthritis

Guus G. H. van den Akker et al.

Summary: This review discusses the role of the ribosome in the pathogenesis of osteoarthritis, highlighting the potential importance of ribosome aberrations in the development of the disease. The authors propose the hypothesis of an "acquired ribosomopathy" in osteoarthritis, suggesting novel opportunities for disease-modifying treatments.

CURRENT OPINION IN RHEUMATOLOGY (2022)

Article Biochemistry & Molecular Biology

LncSEA: a platform for long non-coding RNA related sets and enrichment analysis

Jiaxin Chen et al.

Summary: LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users, and supports lncRNA annotations and enrichment analyses.

NUCLEIC ACIDS RESEARCH (2021)

Review Cell Biology

Gene regulation by long non-coding RNAs and its biological functions

Luisa Statello et al.

Summary: Recent studies have shed new light on the biogenesis and functions of long non-coding RNAs (lncRNAs), showcasing their diverse roles in gene regulation and signaling pathways, particularly in the contexts of neuronal disorders, immune responses, and cancer. The discovery of unique biogenesis pathways and subcellular localizations of lncRNAs has opened up potential therapeutic avenues for targeting lncRNAs in various biological and pathophysiological conditions.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Multidisciplinary Sciences

A molecular quantitative trait locus map for osteoarthritis

Julia Steinberg et al.

Summary: Researchers identified molecular trait loci and potential drug targets by analyzing cartilage and synovium from osteoarthritis patients.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Disrupting upstream translation in mRNAs is associated with human disease

David S. M. Lee et al.

Summary: The study investigates genetic variants in upstream open reading frames, finding that they are under high evolutionary constraint and may contribute to disease.

NATURE COMMUNICATIONS (2021)

Editorial Material Rheumatology

Targeting calcium-related mechanotransduction in early OA

Michelle L. Delco et al.

Summary: Mechanical stimuli sensation by chondrocytes is crucial for cartilage homeostasis and osteoarthritis development. The early responses in chondrocyte mechanotransduction pathways involve calcium influx and changes in mitochondrial function, which occur within seconds to minutes. Understanding these events can reveal new therapeutic targets for early intervention to prevent osteoarthritis.

NATURE REVIEWS RHEUMATOLOGY (2021)

Article Multidisciplinary Sciences

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

Tianzhi Wu et al.

Summary: The updated version of clusterProfiler 4.0 is a powerful tool for functional enrichment analysis in a wide range of organisms, offering tidy interfaces for data operation and visualization, as well as new features like gene set enrichment analysis and comparison of results from multiple gene lists.

INNOVATION (2021)

Review Genetics & Heredity

Regulation of gene expression by cis-acting long non-coding RNAs

Noa Gil et al.

NATURE REVIEWS GENETICS (2020)

Article Orthopedics

Macrophages regulate the progression of osteoarthritis

H. Zhang et al.

OSTEOARTHRITIS AND CARTILAGE (2020)

Review Biochemistry & Molecular Biology

RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer

Katharina Jonas et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Review Biochemistry & Molecular Biology

Classifying the Binding Modes of Disordered Proteins

Monika Fuxreiter

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Biotechnology & Applied Microbiology

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Lorena de la Fuente et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

CellMarker: a manually curated resource of cell markers in human and mouse

Xinxin Zhang et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

ensembldb: an R package to create and use Ensembl-based annotation resources

Johannes Rainer et al.

BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

The CH25H-CYP7B1-RORα axis of cholesterol metabolism regulates osteoarthritis

Wan-Su Choi et al.

NATURE (2019)

Article Multidisciplinary Sciences

Assembly and functionality of the ribosome with tethered subunits

Nikolay A. Aleksashin et al.

NATURE COMMUNICATIONS (2019)

Review Cell Biology

TGFβ/BMP Signaling Pathway in Cartilage Homeostasis

Nathalie G. M. Thielen et al.

CELLS (2019)

Article Rheumatology

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

Rodrigo Coutinho de Almeida et al.

ANNALS OF THE RHEUMATIC DISEASES (2019)

Review Biochemistry & Molecular Biology

Function, clinical application, and strategies of Pre-mRNA splicing in cancer

Cuixia Di et al.

CELL DEATH AND DIFFERENTIATION (2019)

Article Biochemistry & Molecular Biology

Identification of differentially expressed long noncoding RNAs in human knee osteoarthritis

Ke Xiao et al.

JOURNAL OF CELLULAR BIOCHEMISTRY (2019)

Article Biochemistry & Molecular Biology

Ensembl 2019

Fiona Cunningham et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Orthopedics

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage

B. Ajekigbe et al.

OSTEOARTHRITIS AND CARTILAGE (2019)

Review Cardiac & Cardiovascular Systems

The Extracellular Matrix Protein ABI3BP in Cardiovascular Health and Disease

Dawn A. Delfin et al.

FRONTIERS IN CARDIOVASCULAR MEDICINE (2019)

Article Genetics & Heredity

Annotation-free quantification of RNA splicing using LeafCutter

Yang I. Li et al.

NATURE GENETICS (2018)

Review Cell Biology

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Kathrin Leppek et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

Alejandro Reyes et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Orthopedics

Bone morphogenetic proteins for articular cartilage regeneration

Z. H. Deng et al.

OSTEOARTHRITIS AND CARTILAGE (2018)

Article Neurosciences

The Neuron-Specific Protein TMEM59L Mediates Oxidative Stress-Induced Cell Death

Qiuyang Zheng et al.

MOLECULAR NEUROBIOLOGY (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Cell & Tissue Engineering

A Three-Dimensional Chondrocyte-Macrophage Coculture System to Probe Inflammation in Experimental Osteoarthritis

Satyavrata Samavedi et al.

TISSUE ENGINEERING PART A (2017)

Review Cell & Tissue Engineering

Osteoarthritis: toward a comprehensive understanding of pathological mechanism

Di Chen et al.

BONE RESEARCH (2017)

Review Genetics & Heredity

RNA mis-splicing in disease

Marina M. Scotti et al.

NATURE REVIEWS GENETICS (2016)

Article Orthopedics

Investigation of candidate genes for osteoarthritis based on gene expression profiles

Shuanghai Dong et al.

ACTA ORTHOPAEDICA ET TRAUMATOLOGICA TURCICA (2016)

Article Rheumatology

Synovitis in knee osteoarthritis: a precursor of disease?

I. Atukorala et al.

ANNALS OF THE RHEUMATIC DISEASES (2016)

Review Biochemistry & Molecular Biology

Chondrocyte Apoptosis in the Pathogenesis of Osteoarthritis

Hyun Sook Hwang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2015)

Article Biochemistry & Molecular Biology

Neighboring Genes Show Correlated Evolution in Gene Expression

Avazeh T. Ghanbarian et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Pharmacology & Pharmacy

mTOR: A Potential Therapeutic Target in Osteoarthritis?

Bandna Pal et al.

DRUGS IN R&D (2015)

Article Rheumatology

Cartilage-specific deletion of mTOR upregulates autophagy and protects mice from osteoarthritis

Yue Zhang et al.

ANNALS OF THE RHEUMATIC DISEASES (2015)

Article Rheumatology

ADAMTS-7 forms a positive feedback loop with TNF-α in the pathogenesis of osteoarthritis

Yongjie Lai et al.

ANNALS OF THE RHEUMATIC DISEASES (2014)

Article Biochemistry & Molecular Biology

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

Stefan Washietl et al.

GENOME RESEARCH (2014)

Article Biochemistry & Molecular Biology

Pfam: the protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

svaseq: removing batch effects and other unwanted noise from sequencing data

Jeffrey T. Leek

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Charity W. Law et al.

GENOME BIOLOGY (2014)

Article Orthopedics

Identification of Long Noncoding RNA Associated with Osteoarthritis in Humans

Dan Xing et al.

ORTHOPAEDIC SURGERY (2014)

Review Mathematical & Computational Biology

biobambam: tools for read pair collation based algorithms on BAM files

German Tischler et al.

SOURCE CODE FOR BIOLOGY AND MEDICINE (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Assessment of transcript reconstruction methods for RNA-seq

Tamara Steijger et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

Software for Computing and Annotating Genomic Ranges

Michael Lawrence et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Review Biotechnology & Applied Microbiology

The Role of Changes in Extracellular Matrix of Cartilage in the Presence of Inflammation on the Pathology of Osteoarthritis

Maricela Maldonado et al.

BIOMED RESEARCH INTERNATIONAL (2013)

Review Biochemistry & Molecular Biology

S100 proteins in cartilage: Role in arthritis

Raghunatha R. Yammani

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2012)

Article Biochemistry & Molecular Biology

Detecting differential usage of exons from RNA-seq data

Simon Anders et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

Molecular signatures database (MSigDB) 3.0

Arthur Liberzon et al.

BIOINFORMATICS (2011)

Review Biochemistry & Molecular Biology

Mechanotransduction by TRP Channels: General Concepts and Specific Role in the Vasculature

Jun Yin et al.

CELL BIOCHEMISTRY AND BIOPHYSICS (2010)

Article Rheumatology

Interleukin-6 Is a Significant Predictor of Radiographic Knee Osteoarthritis The Chingford Study

Gregory Livshits et al.

ARTHRITIS AND RHEUMATISM (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Osteopontin promotes pathologic mineralization in articular cartilage

Ann K. Rosenthal et al.

MATRIX BIOLOGY (2007)

Article Multidisciplinary Sciences

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramanian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Rheumatology

Type II collagen degradation and its regulation in articular cartilage in osteoarthritis

AR Poole et al.

ANNALS OF THE RHEUMATIC DISEASES (2002)