Transcript Functional Genomics

Functional Genomics
Branches of Genomics
Structural
Genomics
Metagenomics
Genomics
Comparativ
e Genomics
Functional
Genomics
Why We Need Functional Genomics
Organism
E. coli
yeast
C. elegans
Drosophila
Arabadopsis
mouse
human
# genes
% of genes with
inferred function
Completion date
of genome
4288
6,600
19,000
12-14K
25,000
~30,000?
~30,000?
60
40
40
25
40
10-20
10-20
1997
1996
1998
1999
2000
2002
2000
How to determine functionally related
genes?
• 40% if predicted genes in newly sequenced
genomes cannot be assigned function based
on sequence similarity.
• Genes sharing a common pattern of
expression in many different experiments are
likely to be involved in similar processes.
– Gene A regulates Gene B, or vice versa
– Gene A and Gene B are regulated by Gene C
Orthology, co-orthology and paralogy relationships in the evolution of four genes that arose
from a single common ancestor.
Kristensen D M et al. Brief Bioinform 2011;12:379-391
Published by Oxford University Press 2011.
The reconciliation of the species tree (a) with an instance of a gene tree (b–d) allows for
inference as to when evolutionary events such as speciation (T-branch), gene duplication
(star-branch), or gene loss (X) occurred.
Kristensen D M et al. Brief Bioinform 2011;12:379-391
Published by Oxford University Press 2011.
Grouping of genes in different species that are each others’ BBHs into sets of orthologs and
co-orthologs.
Kristensen D M et al. Brief Bioinform 2011;12:379-391
Published by Oxford University Press 2011.
Clusters of Orthologous Groups (COG)
• Identification of orthologs is critical for
reliable prediction of gene function in newly
sequenced genomes.
• The purpose of COG is to serve as a platform
for functional annotation of newly sequenced
genomes and for study of genome evolution.
Links
• Unicellular clusters (COGs):
– http://www.ncbi.nlm.nih.gov/COG/grace/uni.html
• Eukaryotic orthologous groups (KOGs):
– http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi
• 2003 paper
• 2011 paper