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Bioinformatics Modules: Gene Function Prediction and Data Mining

Bioinformatics Modules: Gene Function Prediction and Data Mining. Bioinformatics Modules: Gene Function Prediction and Data Mining. and Example ORFs. Modules. 1. Basic Information 2. Structure-Based Evidence (Part 1) 3. Structure-Based Evidence (Part II) 4. Multiple Sequence Alignment

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Bioinformatics Modules: Gene Function Prediction and Data Mining

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  1. Bioinformatics Modules: Gene Function Prediction and Data Mining

  2. Bioinformatics Modules: Gene Function Prediction and Data Mining and Example ORFs

  3. Modules 1. Basic Information 2. Structure-Based Evidence (Part 1) 3. Structure-Based Evidence (Part II) 4. Multiple Sequence Alignment 5. Cellular Localization Data – Part I 6. Cellular Localization Data – Part II 7. Gene Deletion Phenotypes 8. Genetic and Physical Interactors and Expression Data

  4. Modules • Guide and Worksheet for each module • Word documents • Guides have: • information on the tool • instructions on how to use the tool • hyperlink to the webpage • instructions on interpreting the data • Worksheets have places to copy and interpret data

  5. Basic Information • Intro to Saccharomyces cerevisiae • Saccharomyces Genome Database • Basic Info: • Description • Coordinates • DNA and Protein Sequences • Sequence-Based Similarity • BLAST

  6. Basic Information Example ORF: ANY VERIFIED ORF SHOULD HAVE ALL OF THIS INFORMATION • Intro to Saccharomyces cerevisiae • Saccharomyces Genome Database • Basic Info: • Description • Coordinates • DNA and Protein Sequences • Sequence-Based Similarity • BLAST

  7. Structure-Based Evidence • Conserved Domain Database Search (CDD) • TIGRFAM • PFAM • Protein Data Bank (PDB) • SUPERFAMILY • SMART • GENE3D • PANTHER

  8. Structure-Based Evidence Example ORF • Conserved Domain Database Search (CDD) • TIGRFAM • PFAM • Protein Data Bank (PDB) • SUPERFAMILY • SMART • GENE3D • PANTHER MEC1 (1 cd, 1 COG) MEC1 (4 TIGR) MEC1 (4 PFAM) MEC1 (186 structures) MEC1 (3 Superfamily) MEC1 (5 SMART) MEC1 (7 CATH Structural Domains MEC1 (1 PANTHER)

  9. Multiple Sequence Alignment • Amino Acid Properties • T-COFFEE: (Tree-based Consistency Objective Function for Alignment Evaluation) • WEBLOGO • Gene Context (neighborhoods)

  10. Multiple Sequence Alignment Example ORFs MEC1 DUN1 or MEC1 • Amino Acid Properties • T-COFFEE: (Tree-based Consistency Objective Function for Alignment Evaluation) • WEBLOGO • Gene Context (neighborhoods)

  11. Cellular Localization Data • TMHMM: (Transmembrane Helices HMM) • Signal P • PSORT II • Phobius • Philius • TargetP • NucPred • Yeast Protein Localization Database (YPL) • Hypothesis

  12. Cellular Localization Data Example ORFs TMN2 (9 TMH) “Example proteins” button below submission box! Not Applicable TMN2 (9 TMH) TMN2 (9 TMH) TMN2 (SP), MGE1 (mTP) MEC1 Images from workshop can be used as examples of GFP in different locations • TMHMM: (Transmembrane Helices HMM) • Signal P • PSORT II • Phobius • Philius • TargetP • NucPred • Yeast Protein Localization Database (YPL)

  13. Gene Deletion Phenotypes • S. cerevisiae Morphological Database • PROPHECY: (PROfiling of PHEnotypic Characteristics in Yeast) • Yeast Fitness Database

  14. Gene Deletion Phenotypes Example ORF: Most Non-Essential ORFs Should be Data Minable Example ORFs • S. cerevisiae Morphological Database • PROPHECY: (PROfiling of PHEnotypic Characteristics in Yeast) • Yeast Fitness Database 4782 ORFs analyzed

  15. Genetic and Physical Interactors and Expression Data • GeneMania • SGD Interactors Tab • SPELL

  16. Example ORF: Most ORFs Should be Data Minable Genetic and Physical Interactors and Expression Data • GeneMania • SGD Interactors Tab • SPELL

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