title: Gene network landscape of the ciliate Tetrahymena thermophila.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human.
  
  
  CONCLUSIONS
  This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xiong
authors.forename: Dongxia
authors.initials: D
authors.lastname: Yuan
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Fillingham
authors.forename: Jyoti
authors.initials: J
authors.lastname: Garg
authors.forename: Xingyi
authors.initials: X
authors.lastname: Lu
authors.forename: Yue
authors.initials: Y
authors.lastname: Chang
authors.forename: Yifan
authors.initials: Y
authors.lastname: Liu
authors.forename: Chengjie
authors.initials: C
authors.lastname: Fu
authors.forename: Ronald E
authors.initials: RE
authors.lastname: Pearlman
authors.forename: Wei
authors.initials: W
authors.lastname: Miao
mesh_terms: D000818:Animals; D016770:Ciliophora Infections / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D017125:Genes, Protozoan / Q000235:genetics; D006801:Humans; D008018:Life Cycle Stages / Q000235:genetics; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D016808:Tetrahymena thermophila / Q000235:genetics* / Q000254:growth & development
chemical_list: D046988:Proteasome Endopeptidase Complex