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Introduction Online Databases and Web Tools of miRNAs

Introduction Online Databases and Web Tools of miRNAs. Speaker: Wen-Ching Chan (wcchan@iis.sinica.edu.tw) Advisor: Dr. Wenchang Lin (wenlin@ibms.sinica.edu.tw). Outlines. Online Databases miRBase (In the 1 st lecture) CoGemiR ZooMir miRGen Web Tools miRNAminer CID-miRNA miRNAgent.

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Introduction Online Databases and Web Tools of miRNAs

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  1. Introduction Online Databases and Web Tools of miRNAs Speaker: Wen-Ching Chan (wcchan@iis.sinica.edu.tw) Advisor: Dr. Wenchang Lin (wenlin@ibms.sinica.edu.tw) Transcriptome Discovery Laboratory

  2. Outlines • Online Databases • miRBase (In the 1st lecture) • CoGemiR • ZooMir • miRGen • Web Tools • miRNAminer • CID-miRNA • miRNAgent Transcriptome Discovery Laboratory

  3. Online Databases: CoGemiR (1) • http://cogemir.tigem.it/ • Comparative Genomics Analysis of MicroRNA • CoGeMiR is a publicily available microRNA-centered database whose aim is to offer an overview of the conservation of microRNAs during evolution in different animal species. This database collects information on genomic location, conservation and expression data of both known and predicted microRNAs. • CoGemiR: a comparative genomics microRNA database Vincenza Maselli, Diego Di Bernardo and Sandro Banfi BMC Genomics 2008, 9:457 (6 October 2008) Transcriptome Discovery Laboratory

  4. Online Databases: CoGemiR Transcriptome Discovery Laboratory

  5. Online Databases: CoGemiR (2) • search by a specific precursor miRNA (e.g. mir-196) Transcriptome Discovery Laboratory

  6. Online Databases: CoGemiR (3) • Show an overview of the conservation of microRNAs during evolution in different animal species and/or precursor miRNA families. • Click one of them to see the detail info. (ex. gga-mir-196-2) Transcriptome Discovery Laboratory

  7. Online Databases: CoGemiR (4) Transcriptome Discovery Laboratory

  8. Online Databases: CoGemiR (5) Transcriptome Discovery Laboratory

  9. Online Databases: ZooMir (1) • http://insr.ibms.sinica.edu.tw/ZooMir/ • ZooMir is an online database of homologous microRNA search in animal genomes. • Li SL, Chan WC, Hu LY, Hsu CN and Lin WC, Identification of homologous microRNAs in 56 animal genomes, Genomics, In Press, Accepted Manuscript, Available online 27 March 2010. Transcriptome Discovery Laboratory

  10. Online Databases: ZooMir (2) Transcriptome Discovery Laboratory

  11. Online Databases: ZooMir (3) • We have analyzed the genomes of 56 animal species, 34 of which have known miRNA entries in miRBase (Release 13.0). In addition, another 30 species also have known miRNA entries in. Transcriptome Discovery Laboratory

  12. Online Databases: ZooMir (4)-Browse by SPECIES Transcriptome Discovery Laboratory

  13. Online Databases: ZooMir (5)- Browse by precursor miRNA CLASS Transcriptome Discovery Laboratory

  14. Online Databases: ZooMir (6) • Evo_source • “Evo_source” column indicates that whether this record is a known miRNA from miRBase 13.0, an orthologous pre-miRNA highly similar to miRNAs from other species or a paralogous pre-miRNA highly similar to miRNAs from own species. • Species_No • In “Species_No” column, the value “a/b” indicates that there are a and b species encoding the known precursor miRNA class and the mature miRNA candidate, respectively. • Distribution • In “Distribution” column, the value “c/d” indicates that there are c pre-miRNAs belonging to the precursor miRNA class and that there are d pre-miRNAs in 64 (50+14) species belonging to this precursor miRNA class. Transcriptome Discovery Laboratory

  15. Online Databases: ZooMir (7)-Evolution Pattern • http://insr.ibms.sinica.edu.tw/miR_Distri/miR_EvoPtnF.php • An overview of the conservation of microRNAs during evolution in different animal species. Transcriptome Discovery Laboratory

  16. Online Databases: ZooMir (8) -Evolution Pattern Transcriptome Discovery Laboratory

  17. Online Databases: ZooMir (8) -Evolution Pattern • Blue blocks represent the species with only known pre-miRNAs. • Red blocks represent the species with both known and novel pre-miRNAs. • Green blocks represent the species with only novel pre-miRNAs. • White (blank) blocks represent the species with neither known nor novel pre-miRNAs. Transcriptome Discovery Laboratory

  18. Web Tools: miRNAminer (1) • http://groups.csail.mit.edu/pag/mirnaminer/ • miRNAminer is a web-based tool used for homologous miRNA gene search in several species. • Shay Artzi, Adam Kiezun and Noam Shomron. miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics 2008, 9:39 Transcriptome Discovery Laboratory

  19. Web Tools: miRNAminer (2) Transcriptome Discovery Laboratory

  20. Web Tools: miRNAminer (3) You need precursor miRNA and mature miRNA for a request. Transcriptome Discovery Laboratory

  21. Web Tools: miRNAminer (4) Transcriptome Discovery Laboratory

  22. Web Tools: CID-miRNA(1) • CIDmiRNA is the tool for computer-assisted identification of micro-RNA using an SCFG model and has been designed to analyze either a single sequence or complete genome. • Current version only supports human miRNA detection • CID-miRNA: A web server for prediction of novel miRNA precursors in human genome, Sonika Tyagi, Candida Vaz, Vipin Gupta, Rohit Bhatia, Sachin Maheshwari, Ashwin Srinivasan and Alok Bhattacharya, Biochemical and Biophysical Research Communications, Volume 372, Issue 4, 8 August 2008, Pages 831-834 Transcriptome Discovery Laboratory

  23. Web Tools: CID-miRNA(2) Transcriptome Discovery Laboratory

  24. Web Tools: CID-miRNA(3) Transcriptome Discovery Laboratory

  25. Web Tools: miRNAgent (1) • http://fgfr.ibms.sinica.edu.tw/miRNAgent/ • miRNAgent is a fully automated server performed a homologus search against mature miRNAs reported in public database. Transcriptome Discovery Laboratory

  26. Web Tools: miRNAgent (2) Transcriptome Discovery Laboratory

  27. Web Tools: miRNAgent (3) • Submit your request by typing query sequence(s) or uploading a FASTA format file w/ query sequence(s) • we will send the results to you via Email • jobId.csv Transcriptome Discovery Laboratory

  28. Web Tools: miRNAgent (4) • Check the STATUS list to monitor the process of your request Transcriptome Discovery Laboratory

  29. Web Tools: miRNAgent (5) • You could also check the tutorial to know how to use miRNAgent • http://fgfr.ibms.sinica.edu.tw/miRNAgent/tutorial.php Transcriptome Discovery Laboratory

  30. Welcome to contact us! • Dr. Wenchang Lin • wenlin@ibms.sinica.edu.tw • Wen-Ching Chan • wcchan@iis.sinica.edu.tw • Sung-Chou Li • pinus@ibms.sinica.edu.tw Transcriptome Discovery Laboratory

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