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

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.

Gene Ontology Biological process

Gene Ontology

Gene Ontology

Gene Ontology Evidence codes 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)

Gene Ontology Stats. May 29 th 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)

Gene Ontology Stats. May 29 th Mouse Genome Informatics (The Jackson Laboratory 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]

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)

GOstat Find statistically overrepresented properties within a group of genes as selected by......typically, analysis of a DNA microarray experiment Beissbarth & Speed (2004) Bioinformatics, 20:

gene A gene B gene C gene D gene E XXXX Total set of genes 2,000 of 5,000 are X Not significant YYYY 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 GOstat

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

Web tool

Output

Example We will study the function of a set of genes selected via StemBase (see corresponding Unit for more info on using StemBase)

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

1. Select a set of genes

2. Run in GOstat

Calcium ion binding mannosyl-oligosaccharide mannosidase activity

2. Run in GOstat

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

2. Run in GOstat

3. Examine expression MAN2A _at MAN1A _at Lgals3bp _at

3. Examine expression

To know more Gene Ontology. GOstat Beissbarth & Speed (2004) Bioinformatics, 20: StemBase. See corresponding Unit in this course.