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Genome-Wide gene expression of Tetrahymena thermophila conjugation

ABSTRACT: Eleven genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in conjugation cells (C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16, C-18). Combined these eleven microarrays with 50 microarrays described in Miao et al (2009) and other 6 microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient 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, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE26650 | GEO | 2011/06/13

SECONDARY ACCESSION(S): PRJNA136385

REPOSITORIES: GEO

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Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

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Genome-Wide gene expression of Tetrahymena thermophila conjugation

Project description:Eleven genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in conjugation cells (C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16, C-18). Combined these eleven microarrays with 50 microarrays described in Miao et al (2009) and other 6 microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient 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, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human. For conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 200,000 cells/ml, mixed, and samples were collected at 15 min, 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture （referred to as C-0, C-15m, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18).

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Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

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