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實用生物資訊研習課程 2008/04/09 - FastSNP

實用生物資訊研習課程 2008/04/09 - FastSNP. 生物醫學資訊所 博士班 邱振傑. 生物資訊校內推廣. 主辦單位： 生 物醫學資訊研究所 推廣宗旨： 有效解決生物資訊問題、實用工具推廣 預期目標： 真正協助各領域的研究 互動方式： 實用生物資訊研習課程 – 面對面推廣 「生物資訊論壇」 （免註冊帳號） - 線上互動. What is FastSNP?. An website – http://fastsnp.ibms.sinica.edu.tw IIS & IBMS , Academia Sinica

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實用生物資訊研習課程 2008/04/09 - FastSNP

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  1. 實用生物資訊研習課程2008/04/09 - FastSNP 生物醫學資訊所 博士班 邱振傑

  2. 生物資訊校內推廣 • 主辦單位：生物醫學資訊研究所 • 推廣宗旨：有效解決生物資訊問題、實用工具推廣 • 預期目標：真正協助各領域的研究 • 互動方式： • 實用生物資訊研習課程–面對面推廣 • 「生物資訊論壇」（免註冊帳號）- 線上互動

  3. What is FastSNP? • An website – http://fastsnp.ibms.sinica.edu.tw • IIS & IBMS, Academia Sinica • 進階生物資訊核心設施, 基因體國家型計畫 • Nucleic Acids Research 2006 34(Web Server issue):W635-W641; doi:10.1093/nar/gkl236 • Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data (2nd edition) • Website traffic

  4. Genome related info 資訊科學技術 Information Technology IT 比較生物資訊 Comparative Bioinformatics 許鈞南Hsu, Chun-Nan 張傳雄Chang, Chuan-Hsiung CB FB 李國彬Li, Kuo-Bin 功能生物資訊 Functional Bioinformatics GS 楊永正Yang, Ueng-Cheng 陳珍信 Chen, Chen-Hsin 陳君厚 Chen, Chun-houh 基因體研究統計 Genomic Statistics Preventive & personal medicine Advanced Bioinformatics Core (ABC)進階生物資訊核心設施 http://abc.binfo.org.tw/

  5. Website traffic

  6. Purpose of FastSNP Millions of SNPs deposited in public SNP databases, only a very small proportion may contribute to disease phenotypes • to approach functional variation in a disease in association studies. • to helpselecting SNPs more efficiently • to generate a Completely Function Report for a SNP  “A Functional Analysis and Selection Tool for SNP".

  7. Strategy for SNP selection • Specific disease or phenotype • Select candidate genes, regions (PubMed, OMIM…etc) • Retrieve SNP data from public domain databases (dbSNP, Ensembl…etc) • SNP selection work! • It depends on your criterion • To get SNP list, Flanking sequence • Primer design for genotyping • Basic information of selected SNPs • “SNP functional effects” for example • Many on-line tools can do different analysis • But hard to integrate all results from out source

  8. Query Module Function Analysis Module Seq. ESEfinder EnsemblMart RESCUE-ESE Gene HUGO Aliases FAS-ESS NCBI Gene Symbol PolyPhen coding ? TFSearch SNP set non-coding SNP Ensembl Protein Domain dbSNP SNP Seq. SNP prediction Info. SNP basic Info. SNP functional effects Function Report Module Prioritization Module UCSC Seq. Check SNP Function Report Classification Link out query HapMap Haplotype Ranking SwissProt’s Feature Generate SNP function report GenBank Protein Domain

  9. ESEfinder RESCUE-ESE Function Report TFSEARCH dbSNP PolyPhen Swiss-prot Ensembl NCBI GenBank Real-Time SNP Data Analysis Gene Symbol SNP rsID Candidate Gene Approach SNP Search Single SNP (batch) Chromosome Novel SNP Agent Starter Prioritization Decision tree

  10. Functional effect for coding SNP

  11. Functional effect for non-coding SNP

  12. Decision tree

  13. FastSNP user guide • http://fastsnp.ibms.sinica.edu.tw/userguide/UserGuide.jsp • A result example: • http://fastsnp.ibms.sinica.edu.tw/pages/PrioritizeResult.jsp?taskid=TK14938&Submit=ENST00000272895

  14. Result - SNP list Click here to export SNP list to Excel format Click here to get “Function Report”

  15. Function Report

  16. Click here to get detail information

  17. Hands on session • 任意挑選Coding region與Non-coding region的SNP各三個進行FastSNP分析。 • 取得SNP周圍的DNA序列 • 寫下這三個SNP分別被預測屬於產生哪種Functional effects？ • 以一個您正在研究的疾病為例，輸入Candidate gene，看看是否FastSNP能找到資料並進行分析？ • 如果我所輸入的Gene Symbol出現多筆Transcription資訊，我該如何判斷選擇哪一個？ • 我分析完成的結果，要如何回去看呢？

  18. 謝謝您的參與關於本課程後續相關討論，可上「生物資訊論壇」（免註冊）謝謝您的參與關於本課程後續相關討論，可上「生物資訊論壇」（免註冊）

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