Gene function analysis

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Gene function analysis

• Stem Cell Network
• Microarray Course, Unit 5
• May 2007

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Sections

• Introduction to Gene Ontology
• GOstat
• Example

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Gene Ontology
Michael Ashburner Annotate genes or proteins
Started for Drosophila melanogaster (fly). Now
expanded for all taxa
http//www.geneontology.org
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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.
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http//www.geneontology.org/GO_nature_genetics_200
0.pdf
Gene Ontology
Biological process
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http//www.geneontology.org/GO_nature_genetics_200
0.pdf
Gene Ontology
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http//www.geneontology.org/GO_nature_genetics_200
0.pdf
Gene Ontology
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Gene Ontology
Evidence codes http//www.geneontology.org/GO.evid
ence.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)
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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)
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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

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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)
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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.
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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

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Contigency Table
genes with GO in group
p-value 8e-52
467
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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.
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Web tool
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Web tool
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Output
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Example
We will study the function of a set of genes
selected via StemBase http//www.stembase.ca/ (s
ee corresponding Unit for more info on using
StemBase)
http//gostat.wehi.edu.au/
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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
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1. Select a set of genes
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1. Select a set of genes
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1. Select a set of genes
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1. Select a set of genes
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(No Transcript)
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2. Run in GOstat
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2. Run in GOstat
Calcium ion binding
mannosyl-oligosaccharide mannosidase activity
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2. Run in GOstat
http//www.geneontology.org/amigo
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2. Run in GOstat
Calcium ion binding
mannosyl-oligosaccharide mannosidase activity
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2. Run in GOstat
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3. Examine expression
MAN2A1 1448647_at MAN1A 1417111_at Lgals3bp 14483
80_at
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3. Examine expression
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3. Examine expression
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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.