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Prediction of p53 target genes based on integrative analysis of chromatin immunoprecipitated and sequenced tags,by using Galaxy,a web-based interactive platform for large-scale genome analysis
https://doi.org/10.15114/tr.43.1
https://doi.org/10.15114/tr.43.172e42b68-2504-4b62-91dd-4d4370f515bb
名前 / ファイル | ライセンス | アクション |
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n00414093431.pdf (1.9 MB)
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Item type | 紀要論文 / Departmental Bulletin Paper(1) | |||||
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公開日 | 2019-07-31 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Prediction of p53 target genes based on integrative analysis of chromatin immunoprecipitated and sequenced tags,by using Galaxy,a web-based interactive platform for large-scale genome analysis | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Tags | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Transcription factor binding site | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Transcription start site | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Genome database | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Genome browse | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | departmental bulletin paper | |||||
ID登録 | ||||||
ID登録 | 10.15114/tr.43.1 | |||||
ID登録タイプ | JaLC | |||||
著者 |
Hiroaki, Mita
× Hiroaki, Mita× Yasushi, Sasaki× Hiromu, Suzuki× Masashi, Idogawa× Lisa, Kashima× Naoki, Anbo× Hirofumi, Akashi× Haruyuki, Tatsumi× Minoru, Toyota |
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抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | Chromatin immunoprecipitation (ChIP) followed by sequencing of immunoprecipitated DNA fragments is the high throughput method for identifying transcription factor binding sites. In one such method, ChIP PET, paired end ditags (PETs) derived from both ends of the immunoprecipitated DNA fragments are sequenced and mapped to the genome. We report here the prediction of p53 target genes by meta analyzing tags of p53 ChIP PET and by combining with other genomic annotations, using Galaxy, a web based platform for large scale genome analysis. We found 327 of p53 binding sites on the genome of 5-fluorouracil (5-FU)-treated HCT116 colon cancer cells by searching the total 65,509 PETs for PET clusters. The search for p53 target gene, which focused on PET clusters with computationally-predicted p53 binding motif, identified 20 of putative p53 target genes as well as 11 of known p53 targets. Another search for p53 target genes, which focused on PET clusters located within 50-kb flanking regions of transcription start sites of genes, identified 278 of Refseq genes, 79 of non-coding RNAs and 5 of microRNAs as p53 targets which included lots of known validated targets. Our results indicate that sequencing-based ChIP analysis combined with the existing genome annotation is effective method to predict p53 binding loci and target genes, and also show that the Galaxy platform is well-suited for multiple-type analyses and visualization of ChIP data, leading to functional annotation of transcription factor binding sites. | |||||
書誌情報 |
Tumor Research en : Tumor Research 巻 43, p. 1-23, 発行日 2008 |
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ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 0041-4093 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||
出版者 | ||||||
出版者 | Sapporo Medical University |