Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: Four genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in starved cells (Starvation 0 hour and Starvation 9 hour, each two replicates). Combined these four microarrays with 50 microarrays described in Miao et al (2009, PMID: 19204800; GSE11300) and other 13 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 starvation, CU427 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 9 hours (referred to as S-0 and S-9, respectively).

ORGANISM(S): Tetrahymena thermophila

SUBMITTER: Yifan Liu

PROVIDER: E-GEOD-26385 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene network landscape of the ciliate Tetrahymena thermophila.

Xiong Jie J Yuan Dongxia D Fillingham Jeffrey S JS Garg Jyoti J Lu Xingyi X Chang Yue Y Liu Yifan Y Fu Chengjie C Pearlman Ronald E RE Miao Wei W

PloS one 20110526 5

<h4>Background</h4>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 thermoph ...[more]

PMID: 21637855

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Project description:A genome wide microarray platform containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila is described, validated and used to study gene expression in growing, starved and conjugating cells. Of the ~27,400 predicted open reading frames in Tetrahymena, transcripts homologous to 5876 are not detectable in one or more of these life cycle stages, indicating that this organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels 5X background and 95 genes are expressed at 250X background in all stages. Transcripts homologous to 94 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, and 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1073 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the previously described developmental stages of meiosis, nuclear differentiation and DNA elimination. Genes encoding proteins known to be complexed show similar expression patterns, indicating that co-ordinate expression with putative genes of known function should identify new genes with related functions. Keywords: growth (three cell densities); Starvation (seven time points); Conjugation (ten time points) For growth, CU428 cells at low, medium and high cell densities (~100Kcells/ml, ~350Kcells/ml and ~1000Kcells/ml; referred to as L-l, L-m and L-h) were collected. For starvation, CU428 cells were starved at 2x105 cells/ml in 10 mM Tris (pH 7.5) for 3, 6, 9, 12, 15 and 24 hours ï¼referred to as S-0, S-3, S-6, S-9, S-12, S-15 and S-24. For conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 2x105 cells/ml, mixed, and samples were collected at 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture ï¼referred to as C-0, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18). For each growing and starved Tetrahymena sample, hybridizations were performed on three independent microarrays (e.g. L1, L2 and L3; S1, S2 and S3). For analysis of conjugation, hybridizations were performed on two independent microarrays (e.g. C1 and C2). Each individual microarray represents a separate experiment; total RNA was isolated from independent cell cultures then independently labeled and hybridized.

Dataset Information

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

Publications

Gene network landscape of the ciliate Tetrahymena thermophila.

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