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  1. 紀要
  2. Tumor Research
  3. Vol.43

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.43.1
72e42b68-2504-4b62-91dd-4d4370f515bb
名前 / ファイル ライセンス アクション
n00414093431.pdf n00414093431.pdf (1.9 MB)
Item type 紀要論文 / Departmental Bulletin Paper(1)
公開日 2019-07-31
タイトル
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 en
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

Hiroaki, Mita

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Yasushi, Sasaki

× Yasushi, Sasaki

Yasushi, Sasaki

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Hiromu, Suzuki

× Hiromu, Suzuki

Hiromu, Suzuki

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Masashi, Idogawa

× Masashi, Idogawa

Masashi, Idogawa

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Lisa, Kashima

× Lisa, Kashima

Lisa, Kashima

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Naoki, Anbo

× Naoki, Anbo

Naoki, Anbo

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Hirofumi, Akashi

× Hirofumi, Akashi

Hirofumi, Akashi

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Haruyuki, Tatsumi

× Haruyuki, Tatsumi

Haruyuki, Tatsumi

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Minoru, Toyota

× Minoru, Toyota

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
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
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Cite as

Hiroaki, Mita, Yasushi, Sasaki, Hiromu, Suzuki, Masashi, Idogawa, Lisa, Kashima, Naoki, Anbo, Hirofumi, Akashi, Haruyuki, Tatsumi, Minoru, Toyota, 2008, 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: Sapporo Medical University, 1–23 p.

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