Genomics and Applied Biology 2015, Vol. 6, No. 6, 1-7
3
the body cells, DNA repair and transmembrane
transport. Ubiquitination, phosphorylation,
protein
kinase binding
and
protein kinase activity are also
highly enriched among high CUB gene
s (Table 1).
3.2 Low codon usage bias and gene ontology
For the lowly biased genes, there was over-repre-
sentation of GO terms related to immune response
(Table 2). For example, biological processes like
defense response, defense to bacteria and virus,
negative regulation of inflammatory cytokines and
apoptotic process
were significant.
Antigen processing
and presentation as well as lysosome which are
acquired and innate immune response respectively
were enriched in low CUB.
Notably were the
over-representations of many GO terms for organs
development (liver, lung, skin, skeletal muscle, and
thymus) and GO terms related to many negative
regulations of some detrimental molecular functions
e.g. low response to ultra violet light and blood
coagulation. Olfactory GO terms like
detection of
chemical stimulus involved in sensory perception of
smell
were also enriched (Table 2).
4 Discussion
GO terms are associated with codon usage bias
GO terms such as phosphorylation involved in gene
regulation mechanisms were found significantly
enriched in highly biased genes. Enriched GO terms
were also found to be associated with major processes
such as transcription of genetic materials for gene
expression, trans-membrane transport of the transcript
from nucleus to cytosol and ribosome manufacture to
facilitate translation. Other major term such as actin
binding play a central role in many eukaryotic cells
basic metabolism. It compliments cytoskeleton to
shape the cells, acts in cell division, motility,
contraction, adhesion, phagocytosis, protein sorting,
DNA repair and signal transduction (Uribe and Jay,
2009). Many studies have established the presence of
actin in the nucleus and cytoplasm and have shown
that its functions are diverse in both cell components.
Possible roles for nuclear actin include contribution to
Table 1 The overrepresented GO terms for the 5% highly codon biased genes of the pig genome
GO ACCESSION
CHI-SQUARED
P-VALUE
GO TERM
GO:0003779
14.8161
0.0001185
actin binding
GO:0009986
21.3826
3.76E-006
cell surface
GO:0006281
12.9777
0.0003152
DNA repair
GO:0020037
23.3437
1.36E-006
Heme binding
GO:0060749
0.019
0.00003
mammary gland alveolus development
GO:0005624
20.806
5.08E-006
membrane fraction
GO:0003676
113.4532
2.20E-016
nucleic acid binding
GO:0005730
41.2299
1.35E-010
nucleolus
GO:0005654
8.1772
0.004242
nucleoplasm
GO:0000166
131.9434
2.20E-016
nucleotide binding
GO:0005634
352.4049
2.20E-016
nucleus
GO:0055114
63.8083
1.37E-015
oxidation-reduction process
GO:0016491
48.2633
3.73E-012
oxidoreductase activity
GO:0008233
26.921
2.12E-007
peptidase activity
GO:0016310
26.921
2.12E-007
phosphorylation
GO:0005886
127.9523
2.20E-016
plasma membrane
GO:0004672
61.0469
5.57E-015
protein kinase activity
GO:0019901
18.1546
2.04E-005
protein kinase binding
GO:0030529
15.2761
9.29E-005
ribonucleoprotein complex
GO:0005840
20.5753
5.73E-006
ribosome
GO:0003735
21.0366
4.51E-006
structural constituent of ribosome
GO:0005198
14.8161
0.0001185
structural molecule activity
GO:0055085
53.909
2.10E-013
transmembrane transport
GO:0006511
12.5187
0.0004029
ubiquitin-dependent protein catabolic process
GO:0004842
14.7011
0.000126
ubiquitin-protein ligase activity
