title: Chondrocyte channel transcriptomics: do microarray data fit with expression and functional data?
abstract: To date, a range of ion channels have been identified in chondrocytes using a number of different techniques, predominantly electrophysiological and/or biomolecular; each of these has its advantages and disadvantages. Here we aim to compare and contrast the data available from biophysical and microarray experiments. This letter analyses recent transcriptomics datasets from chondrocytes, accessible from the European Bioinformatics Institute (EBI). We discuss whether such bioinformatic analysis of microarray datasets can potentially accelerate identification and discovery of ion channels in chondrocytes. The ion channels which appear most frequently across these microarray datasets are discussed, along with their possible functions. We discuss whether functional or protein data exist which support the microarray data. A microarray experiment comparing gene expression in osteoarthritis and healthy cartilage is also discussed and we verify the differential expression of 2 of these genes, namely the genes encoding large calcium-activated potassium (BK) and aquaporin channels.
authors.affiliation: Musculoskeletal Biology; Institute of Ageing and Chronic Disease; Faculty of Health & Life Sciences; University of Liverpool; Liverpool, UK; The D-BOARD European Consortium for Biomarker Discovery.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Lewis
authors.affiliation: Musculoskeletal Biology; Institute of Ageing and Chronic Disease; Faculty of Health & Life Sciences; University of Liverpool; Liverpool, UK.
authors.forename: Hannah
authors.initials: H
authors.lastname: May
authors.affiliation: Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis; Arthritis Research UK Pain Centre; Medical Research Council and Arthritis Research UK Centre for Musculoskeletal Ageing Research; The University of Nottingham; Queen's Medical Centre; Nottingham, UK; School of Life Sciences; University of Bradford; Bradford, UK; Center for Excellence in Genomic Medicine Research (CEGMR); King Fahad Medical Research Center (KFMRC); King AbdulAziz University; Jeddah, Saudi Arabia; The D-BOARD European Consortium for Biomarker Discovery.
authors.forename: Ali
authors.initials: A
authors.lastname: Mobasheri
authors.affiliation: Musculoskeletal Biology; Institute of Ageing and Chronic Disease; Faculty of Health & Life Sciences; University of Liverpool; Liverpool, UK; The D-BOARD European Consortium for Biomarker Discovery.
authors.forename: Richard
authors.initials: R
authors.lastname: Barrett-Jolley
mesh_terms: D000818:Animals; D019902:Chondrocytes / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007473:Ion Channels / Q000235:genetics* / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010003:Osteoarthritis / Q000235:genetics
chemical_list: D007473:Ion Channels
keywords: biomarker; biophysics; cartilage; chondrocyte; electrophysiology; ion channel; osteoarthritis; transcriptomics