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Gene function analysis

Gene function analysis . Stem Cell Network Microarray Course, Unit 5 May 2007. Sections. Introduction to Gene Ontology GOstat Example. Gene Ontology. Michael Ashburner Annotate genes or proteins. Started for Drosophila melanogaster (fly). Now expanded for all taxa.

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Gene function analysis

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  1. Gene function analysis Stem Cell Network Microarray Course, Unit 5 May 2007

  2. Sections • Introduction to Gene Ontology • GOstat • Example

  3. Gene Ontology Michael Ashburner Annotate genes or proteins Started for Drosophila melanogaster (fly). Now expanded for all taxa http://www.geneontology.org

  4. Gene Ontology Biological process A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products. Molecular function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. Cellular component The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally copurify under all except extreme conditions.

  5. http://www.geneontology.org/GO_nature_genetics_2000.pdf Gene Ontology Biological process

  6. http://www.geneontology.org/GO_nature_genetics_2000.pdf Gene Ontology

  7. http://www.geneontology.org/GO_nature_genetics_2000.pdf Gene Ontology

  8. Gene Ontology Evidence codes http://www.geneontology.org/GO.evidence.shtml IC: Inferred by Curator IDA: Inferred from Direct Assay IEA: Inferred from Electronic Annotation IEP: Inferred from Expression Pattern (2006) IGC: Inferred from Genomic Context (2007) IGI: Inferred from Genetic Interaction IMP: Inferred from Mutant Phenotype IPI: Inferred from Physical Interaction ISS: Inferred from Sequence or Structural Similarity NAS: Non-traceable Author Statement (2006) ND: No biological Data available RCA: inferred from Reviewed Computational Analysis TAS: Traceable Author Statement NR: Not Recorded (2006)

  9. Gene Ontology Stats. May 29th 2007. biological_process: 13,553 terms (10,894 in 2006; 9,277 in 2005) cellular_component: 1,966 terms (1,815; 1,512) molecular_function: 7,609 terms (7,927; 6,957), Total: 23,128 terms (20,636; 17,746)

  10. Gene Ontology Stats. May 29th 2007. Mouse Genome Informatics (The Jackson Laboratory http://www.informatics.jax.org/) • biological_process: 14,200 genes, 42,675 annotations (3.0 kw/gene) [13,329 genes, 33,783 annotations (2.5 kw/gene) in 2006] • cellular_component: 14,713 genes, 31,330 annotations (2.1 kw/gene) [13,547 genes, 26,515 annotations (2.0 kw/gene)] • molecular_function: 15,553 genes, 50,343 annotations (3.2 kw/gene) [14,056 genes, 40,806 annotations (2.9 kw/gene)] • 8.3 terms per gene [7.5 in 2006]

  11. Databases using Gene Ontology NetAffx (Affymetrix probe annotations) Flybase (sequences) was the first SGD (yeast) MGI (mouse) InterPro (Protein sequences) ProDom (Protein domains) Entrez Gene (gene information)

  12. GOstat Find statistically overrepresented properties within a group of genes as selected by... ...typically, analysis of a DNA microarray experiment http://gostat.wehi.edu.au/ Beissbarth & Speed (2004) Bioinformatics, 20: 1464-1465.

  13. GOstat Total set of genes 2,000 of 5,000 are X Not significant gene A gene B gene C gene D gene E X X Y Y Total set of genes 4 of 5000 are Y Very significant • Do it for all Gene Ontology terms • Take into account the structure of the ontology • Sort by p-values

  14. Contigency Table genes with GO in group p-value 8e-52 467 51 total genes in group Chi-square Test (Fisher's Exact Test for small values) 9180 176 selected genes (e.g. differentially expressed) reference group (e.g. all genes on array) Probability of obtaining those values from a random distribution.

  15. Web tool

  16. Web tool

  17. Output

  18. Example We will study the function of a set of genes selected via StemBase http://www.stembase.ca/ (see corresponding Unit for more info on using StemBase) http://gostat.wehi.edu.au/

  19. 1. Select a set of genes Objective: Genes correlated to Lgals3bp (lectin, galactoside-binding, soluble, 3 binding protein) A galectin, a beta-galactoside-binding protein implicated in modulating cell-cell and cell-matrix interactions

  20. 1. Select a set of genes

  21. 1. Select a set of genes

  22. 1. Select a set of genes

  23. 1. Select a set of genes

  24. 2. Run in GOstat

  25. 2. Run in GOstat Calcium ion binding mannosyl-oligosaccharide mannosidase activity

  26. 2. Run in GOstat http://www.geneontology.org/amigo

  27. 2. Run in GOstat Calcium ion binding mannosyl-oligosaccharide mannosidase activity

  28. 2. Run in GOstat

  29. 3. Examine expression MAN2A1 1448647_at MAN1A 1417111_at Lgals3bp 1448380_at

  30. 3. Examine expression

  31. 3. Examine expression

  32. To know more • Gene Ontology. http://www.geneontology.org/GO.doc.shtm • GOstat http://gostat.wehi.edu.au Beissbarth & Speed (2004) Bioinformatics, 20: 1464-1465. • StemBase. http://www.stembase.ca See corresponding Unit in this course.

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