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Huang YH, Wu HY, Wu KM, Liu TT, Liou RF, Tsai SF, Shiao MS, Ho LT, Tzean SS, Yang UC. Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum. PLoS One 2013; 8:e61127. [PMID: 23658685 PMCID: PMC3642047 DOI: 10.1371/journal.pone.0061127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 03/07/2013] [Indexed: 12/24/2022] Open
Abstract
Ganoderma lucidum (G. lucidum) is a medicinal mushroom renowned in East Asia for its potential biological effects. To enable a systematic exploration of the genes associated with the various phenotypes of the fungus, the genome consortium of G. lucidum has carried out an expressed sequence tag (EST) sequencing project. Using a Sanger sequencing based approach, 47,285 ESTs were obtained from in vitro cultures of G. lucidum mycelium of various durations. These ESTs were further clustered and merged into 7,774 non-redundant expressed loci. The features of these expressed contigs were explored in terms of over-representation, alternative splicing, and natural antisense transcripts. Our results provide an invaluable information resource for exploring the G. lucidum transcriptome and its regulation. Many cases of the genes over-represented in fast-growing dikaryotic mycelium are closely related to growth, such as cell wall and bioactive compound synthesis. In addition, the EST-genome alignments containing putative cassette exons and retained introns were manually curated and then used to make inferences about the predominating splice-site recognition mechanism of G. lucidum. Moreover, a number of putative antisense transcripts have been pinpointed, from which we noticed that two cases are likely to reveal hitherto undiscovered biological pathways. To allow users to access the data and the initial analysis of the results of this project, a dedicated web site has been created at http://csb2.ym.edu.tw/est/.
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Affiliation(s)
- Yen-Hua Huang
- Department of Biochemistry, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
| | - Hung-Yi Wu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan, R.O.C.
| | - Keh-Ming Wu
- VYM Genome Research Center, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
| | - Tze-Tze Liu
- VYM Genome Research Center, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
| | - Ruey-Fen Liou
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan, R.O.C.
| | - Shih-Feng Tsai
- VYM Genome Research Center, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
| | - Ming-Shi Shiao
- Medical Research and Education Department, Taipei Veterans General Hospital, Taipei City, Taiwan, R.O.C.
| | - Low-Tone Ho
- Medical Research and Education Department, Taipei Veterans General Hospital, Taipei City, Taiwan, R.O.C.
| | - Shean-Shong Tzean
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan, R.O.C.
| | - Ueng-Cheng Yang
- Institute of Biomedical Informatics, College of Life Science, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei City, Taiwan, R.O.C.
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Milnthorpe AT, Soloviev M. The use of EST expression matrixes for the quality control of gene expression data. PLoS One 2012; 7:e32966. [PMID: 22412959 PMCID: PMC3297614 DOI: 10.1371/journal.pone.0032966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 02/06/2012] [Indexed: 01/10/2023] Open
Abstract
EST expression profiling provides an attractive tool for studying differential gene expression, but cDNA libraries' origins and EST data quality are not always known or reported. Libraries may originate from pooled or mixed tissues; EST clustering, EST counts, library annotations and analysis algorithms may contain errors. Traditional data analysis methods, including research into tissue-specific gene expression, assume EST counts to be correct and libraries to be correctly annotated, which is not always the case. Therefore, a method capable of assessing the quality of expression data based on that data alone would be invaluable for assessing the quality of EST data and determining their suitability for mRNA expression analysis. Here we report an approach to the selection of a small generic subset of 244 UniGene clusters suitable for identification of the tissue of origin for EST libraries and quality control of the expression data using EST expression information alone. We created a small expression matrix of UniGene IDs using two rounds of selection followed by two rounds of optimisation. Our selection procedures differ from traditional approaches to finding "tissue-specific" genes and our matrix yields consistency high positive correlation values for libraries with confirmed tissues of origin and can be applied for tissue typing and quality control of libraries as small as just a few hundred total ESTs. Furthermore, we can pick up tissue correlations between related tissues e.g. brain and peripheral nervous tissue, heart and muscle tissues and identify tissue origins for a few libraries of uncharacterised tissue identity. It was possible to confirm tissue identity for some libraries which have been derived from cancer tissues or have been normalised. Tissue matching is affected strongly by cancer progression or library normalisation and our approach may potentially be applied for elucidating the stage of normalisation in normalised libraries or for cancer staging.
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Affiliation(s)
- Andrew T. Milnthorpe
- School of Biological Sciences, CBMS, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Mikhail Soloviev
- School of Biological Sciences, CBMS, Royal Holloway University of London, Egham, Surrey, United Kingdom
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Maitland NJ, Collins AT. Inflammation as the primary aetiological agent of human prostate cancer: a stem cell connection? J Cell Biochem 2009; 105:931-9. [PMID: 18655194 DOI: 10.1002/jcb.21843] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Inflammation has been implicated for some time as a potential aetiological agent in human prostate cancer. Viral and bacterial infections or even chemical carcinogens such as those found in cooked meat have been proposed as the inflammatory stimuli, but the mechanism of cancer induction is unknown. Recent information about gene expression patterns in normal and malignant epithelial stem cells from human prostate provides a new hypothesis for inflammation-induced carcinogenesis. The hypothesis states that in the stem cells located in the basal cell compartment of the prostate, activated prostate epithelial stem cells acquire a survival advantage, by expressing one of more of the same cytokines such as IL6. The establishment of one or more autocrine signalling loops results in an expansion of these cells in the absence of inflammation, as a potential first stage in the development of the tumour.
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Affiliation(s)
- Norman J Maitland
- YCR Cancer Research Unit, Deparment of Biology, University of York, York YO10 5YW, United Kingdom.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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