Gene network landscape of the ciliate Tetrahymena thermophila.

PloS One
Jie XiongWei Miao

Abstract

Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated ...Continue Reading

References

Feb 14, 1992·Biochemical and Biophysical Research Communications·F ZindyC Bréchot
Mar 1, 1992·Molecular and Cellular Biology·Q J HuE Harlow
Mar 1, 1994·Cancer Metastasis Reviews·M E Ewen
Jul 1, 1993·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·K G Wiman
Jan 1, 1996·Annual Review of Biochemistry·O CouxA L Goldberg
Sep 1, 1996·Journal of Cellular Biochemistry·M G PaggiA Giordano
Jul 1, 1996·Research in Microbiology·A H Romano, T Conway
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·K Collins, L Gandhi
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jul 3, 1999·Trends in Microbiology·M A HuynenP Bork
Jan 27, 2000·Cell·D Hanahan, R A Weinberg
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Jun 5, 2002·The Journal of Eukaryotic Microbiology·Jeffrey S FillinghamRonald E Pearlman
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·M Girvan, M E J Newman
Jul 23, 2002·Nature Genetics·Lars M SteinmetzRonald W Davis
Dec 4, 2002·Nature Reviews. Drug Discovery·Atul Butte
May 16, 2003·Proceedings of the National Academy of Sciences of the United States of America·Oliver LauleMarkus Lange
Feb 7, 2004·Science·Amy Hin Yan TongCharles Boone
Jun 3, 2004·Genome Research·Homin K LeePaul Pavlidis
Sep 30, 2004·Bioinformatics·David J Bakewell, Ernst Wit
Nov 30, 2004·Science·Insuk LeeEdward M Marcotte
Dec 22, 2004·Molecular Cell·Nevan J KroganJack F Greenblatt
May 12, 2005·Current Biology : CB·Kathleen Collins, Martin A Gorovsky
Jul 15, 2005·The Journal of Eukaryotic Microbiology·Grant R BowmanAaron P Turkewitz
Nov 16, 2005·Annual Review of Genetics·Meng-Chao Yao, Ju-Lan Chao
Dec 31, 2005·Nucleic Acids Research·Feng ChenDavid S Roos
Dec 31, 2005·Nucleic Acids Research·Nicholas A StoverJ Michael Cherry
Mar 25, 2006·The British Journal of Ophthalmology·A MohanS Krishnakumar
Aug 4, 2006·PLoS Computational Biology·Chad HaynesLilia M Iakoucheva
Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden

❮ Previous
Next ❯

Citations

Dec 12, 2013·BioMed Research International·Jun LiPatrick Xuechun Zhao
Mar 14, 2013·Database : the Journal of Biological Databases and Curation·Jie XiongWei Miao
Jan 9, 2015·PLoS Genetics·Po-Hsuen LeeGeoffrey M Kapler
Jan 23, 2020·Journal of Cell Science·Daniela SparvoliAaron P Turkewitz
Jul 23, 2020·Frontiers in Cell and Developmental Biology·Suzanne WahabJeffrey Fillingham

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE26385
GSE26650

Methods Mentioned

BETA
RNA-Seq
pull down

Software Mentioned

OrthoMCL
Perl scripts
TGN
BLAST
Perl script
Blast2GO
YeastNet
ArrayStar
DB
MCL

Related Concepts

Related Feeds

Cell Cycle Control & Proteolysis

Key regulators of cell cycle, including cyclins, cyclin dependent kinase inhibitors, DNA replication factors, are controlled by proteolysis. Discover the latest research on cell cycle control and proteolysis.

ATP Synthases

ATP synthases are enzymes located in the inner mitochondrial membrane that catalyze the synthesis of ATP during cellular respiration. Discover the latest research on ATP synthases here.

African Trypanosomiasis

African trypanosomiasis, also known as sleeping sickness, is an insect-borne parasitic disease of humans and other animals. It is caused by protozoa of the species Trypanosoma brucei and almost invariably progresses to death unless treated. Discover the latest research on African trypanosomiasis here.