Exploring the transcriptome of ciliated cells using in silico dissection of human tissues.

PloS One
Alexander E IvlievM G Sergeeva

Abstract

Cilia are cell organelles that play important roles in cell motility, sensory and developmental functions and are involved in a range of human diseases, known as ciliopathies. Here, we search for novel human genes related to cilia using a strategy that exploits the previously reported tendency of cell type-specific genes to be coexpressed in the transcriptome of complex tissues. Gene coexpression networks were constructed using the noise-resistant WGCNA algorithm in 12 publicly available microarray datasets from human tissues rich in motile cilia: airways, fallopian tubes and brain. A cilia-related coexpression module was detected in 10 out of the 12 datasets. A consensus analysis of this module's gene composition recapitulated 297 known and predicted 74 novel cilia-related genes. 82% of the novel candidates were supported by tissue-specificity expression data from GEO and/or proteomic data from the Human Protein Atlas. The novel findings included a set of genes (DCDC2, DYX1C1, KIAA0319) related to a neurological disease dyslexia suggesting their potential involvement in ciliary functions. Furthermore, we searched for differences in gene composition of the ciliary module between the tissues. A multidrug-and-toxin extrusion tran...Continue Reading

References

Apr 2, 2003·Human Molecular Genetics·Inés Ibañez-TallonHeymut Omran
Apr 1, 2004·BMC Bioinformatics·Dominic J AlloccoAtul J Butte
Jun 3, 2004·Genome Research·Homin K LeePaul Pavlidis
Oct 21, 2004·The Journal of Pathology·B A Afzelius
Mar 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Viktor StolcWallace F Marshall
Mar 26, 2005·Development·Evgeni EfimenkoPeter Swoboda
Jul 7, 2005·The Journal of Cell Biology·Gregory J PazourGeorge B Witman
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Jul 11, 2006·Developmental Cell·Erica E DavisNicholas Katsanis
Jul 25, 2006·Trends in Genetics : TIG·Peter N InglisMichel R Leroux
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael C OldhamDaniel H Geschwind
Jan 24, 2007·Traffic·Søren T ChristensenPeter Satir
Apr 7, 2007·American Journal of Respiratory Cell and Molecular Biology·Andrea J RossRobert B Devlin
May 18, 2007·Annual Review of Cell and Developmental Biology·Jonathan T Eggenschwiler, Kathryn V Anderson
Oct 13, 2007·Science·Sabeeha S MerchantArthur R Grossman
Nov 1, 2007·Physiological Genomics·Timothy S McClintockDaniel A Bergman
Nov 21, 2007·Bioinformatics·Peter LangfelderSteve Horvath
Jan 9, 2008·The Journal of Cell Biology·Wallace F Marshall
Feb 8, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Jeremy A MillerDaniel H Geschwind
Mar 20, 2008·Journal of Cell Science·Juha M TorkkoKai Simons
Jun 14, 2008·Genome Biology·Rob JelierJan A Kors
Aug 16, 2008·PLoS Computational Biology·Steve Horvath, Jun Dong
Oct 14, 2008·Nature Neuroscience·Michael C OldhamDaniel H Geschwind
Oct 23, 2008·Nucleic Acids Research·Tanya BarrettRon Edgar
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 24, 2009·Current Psychiatry Reports·Tracey L Petryshen, David L Pauls
Oct 16, 2009·Nature·Daniel H Geschwind, Genevieve Konopka
Oct 27, 2009·Developmental Biology·Andrew M GlazerPeter W Reddien
Dec 22, 2009·Acta Neuropathologica·Marc R Del Bigio
Apr 17, 2010·Nature Reviews. Genetics·Sarah C Goetz, Kathryn V Anderson
Jan 1, 2009·Database : the Journal of Biological Databases and Curation·Olivier ArnaizJean Cohen
Jun 17, 2010·BMC Bioinformatics·Emidio Capriotti, Marc A Marti-Renom
Dec 3, 2010·Nucleic Acids Research·Christopher P ChildersChristine G Elsik

❮ Previous
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Citations

Apr 8, 2014·Genes·Dianne F NewburySilvia Paracchini
Jul 23, 2013·Nature Genetics·Aarti TarkarHeymut Omran
Oct 8, 2015·Annual Review of Genetics·Sarah A Graham, Simon E Fisher
Oct 18, 2013·Dyslexia : the Journal of the British Dyslexia Association·Amaia Carrion-CastilloSimon E Fisher
May 28, 2014·Birth Defects Research. Part C, Embryo Today : Reviews·Sukanya LodhNorann A Zaghloul
Mar 10, 2015·American Journal of Respiratory Cell and Molecular Biology·Luke R BonserDavid J Erle
Aug 12, 2014·Stem Cells·Jie-Hong PanSteven L Brody
Aug 1, 2014·Biochemical and Biophysical Research Communications·Juha Kere
Feb 27, 2013·Biological Psychiatry·Joseph J LoTurco, Aarti Tarkar
Aug 12, 2016·Brain Structure & Function·Isabel Martinez-GarayAntonio Velayos-Baeza
Apr 8, 2018·Nature Reviews. Nephrology·Joanne Y-C SooMelissa H Little
Sep 16, 2018·The European Journal of Neuroscience·Luiz G GuidiZoltán Molnár
Mar 18, 2016·PLoS Biology·Chunmei LiMichel R Leroux
May 17, 2019·PloS One·Teunis J P van DamMartijn A Huynen
Jul 28, 2016·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Kristiina TammimiesPeter Swoboda
Nov 9, 2016·PloS One·Alexander E IvlievMarina G Sergeeva
Mar 16, 2017·Journal of Medical Genetics·Ange-Line BruelChristel Thauvin-Robinet
Dec 5, 2013·Stem Cells Translational Medicine·Brendan A S McIntyreMickie Bhatia
May 24, 2020·Molecular Neurobiology·Andrea BiederIsabel Tapia-Páez
Feb 21, 2018·Cancer Research·Venkata ManemBenjamin Haibe-Kains
Mar 28, 2021·Fertility and Sterility·Jessica A LentscherGregory E Chow
Sep 8, 2018·Journal of Proteome Research·Paula DuekLydie Lane
Oct 8, 2021·Science·Tobias PriemelMatthew J Harrington

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Datasets Mentioned

BETA
GSE15745
GSE11882
GSE7307

Methods Mentioned

BETA
dissection

Software Mentioned

DAVID
R
affy
R package “ multtest ”
deepSplit
WGCNA
DNAMR
Anni
CilDB
Protein Atlas

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