Gene Ontology (GO)

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Gene Ontology (GO) http//www.geneontology.org/
The Gene Ontology (GO) project is a collaborative
effort to address the need for consistent
descriptions of gene products in different
databases. The GO collaborators are developing
three structured, controlled vocabularies
(ontologies) that describe gene products in terms
of their associated biological processes,
cellular components and molecular functions in a
species-independent manner.
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Molecular Function
Biochemical activity or action of the gene
product. MF describes a capability that the gene
product has and there is no reference to where or
when this activity or usage actually occurs.
Examples enzyme transporter ligand cytochrome
c electron transporter activity
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Biological process
A biological objective to which the gene product
contributes. A biological process is
accomplished via one or more ordered assemblies
of molecular functions. There is generally some
temporal aspect to the process and it will often
involve the transformation of some physical
thing. Examples cell growth and
maintenance cytochrome c oxidative
phosphorylation, induction of cell death
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Cellular Component
A component of a cell that is part of some larger
object or structure. Examples chromosome
nucleus ribosome cytochrome c mitochondrial
matrix, mitochondrial inner membrane
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structure of GO terms
GO0003673 Gene Ontology GO0008150 biological
process GO0016265 death GO0019835cytolysi
s GO0012501 programmed cell
death GO0006915 apoptosis GO0009626
hypersensitive response GO0005575 cellular
component (S.G.Lee, 2004)
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GO parent-child relationship
Child terms are more specific than parent
terms is-a or part-of A mitotic chromosome is
a chromosome A telemere is part-of a chromosome
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Induced Graph Directed Acyclic Graphs (DAG)
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Some remarks
Genes to GO terms many to many GO itself has no
reference to genes GO specifies terminology and
relationship between terms GOs real power comes
from annotation of genes at different GO
terms Each annotation is supported by certain
evidence, e.g. TAS, IEP, ISS
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Are there any GO terms over represented in our
list?
Hypergeometric distribution
N balls, m white, N-m black Draw k balls from N,
X out of k balls are white P(Xi) iCm ?
(k-i)C(N-m) /kCN
(xCm ? (k-x)C(N-m) /kCN)
P-value
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148022 5928 4938 9168 10482 5893 90362
623 5187 5211 7480 9699 4826 64743
656 7320 4430 84679 3141 8310 10218
26009 3676 23072 9607 29927 51491 158
10059 6565 4687 57244 7748 10292 332
4089 7779 2277 5286 6721 6890 10097
5786 1463 26206 6597 3883 10211 2805
11258 9842 5537 221395 10133 5582 4967
4111 8766 5598 9580 317 529 3762
9937 788 4236 6812 3199 10965 23515
9908 10552 1044 3991 4913 6599 79646
7784 9002 3192 596 1559 610 6564
11224 534 398 25939 7270 26 8639
55922 506 6612 4973 6712 11339 26109
7318 55653
library("GOstats") library(hgu95av2) GOHyperG(myLL
, lib"hgu95av2", what"MF)
pvalues GO0015198 GO0015197 GO0015333
GO0015295 GO0005427 GO0008122
1.486752e-06 2.899886e-05 1.320697e-04
1.320697e-04 1.320697e-04 3.932356e-04
goCounts GO0015198 GO0015197 GO0015333
GO0015295 GO0005427 GO0008122 GO0008131
3 6
2 2 2
3 5
numLL 1 6309 numInt 1 73
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Gene zinc finger protein 261 Homo sapiens
Chromosomal location Xq13.1 PubMed, PMID
1048621892058418817323 Gene symbol
ZNF261 GenBank accession X95808 LocusLink,
LocusID 9203 Affymetrix identifier HGU95A
chips 41046_s_at GO "GO0003677" "GO0007275"
"GO0016021"
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Ensembl project www.ensembl.org
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GenMAPP more biology http//www.genmapp.org/
GenMAPP provides users with a tool for
visualizing gene expression data along pathways
(called MAPPs), creating new pathways and
identifying global biological associations within
an expression dataset.
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