Genomics and Applied Biology 2015, Vol. 6, No. 6, 1-7
5
Continuing table 2
GO ACCESSION CHI-SQUARED P-VALUE
GO TERM
GO:0005543
4.5283
9.52E-016
phospholipid binding
GO:0016773
15.8045
7.02E-005
phosphotransferase activity, alcohol group as acceptor
GO:0005886
267.1531
2.20E-016
plasma membrane
GO:0010628
22.9977
1.62E-006
positive regulation of gene expression
GO:0051712
988.1238
2.20E-016
positive regulation of killing of cells of other organism
GO:0006813
22.7576
1.84E-006
potassium ion transport
GO:0046777
25.399
4.66E-007
protein autophosphorylation
GO:0046983
6.5226
4.81E-005
protein dimerization activity
GO:0019904
19.6381
9.36E-006
protein domain specific binding
GO:0006468
144.374
2.20E-016
protein phosphorylation
GO:0004713
95.6153
2.20E-016
protein tyrosine kinase activity
GO:0004725
18.9187
1.36E-005
protein tyrosine phosphatase activity
GO:0042127
20.5976
5.67E-006
regulation of cell proliferation
GO:0009411
4.4694
0.00003451
response to UV
GO:0009615
13.6531
0.0002199
response to virus
GO:0008236
19.3982
1.06E-005
serine-type peptidase activity
GO:0007165
377.3029
2.20E-016
signal transduction
GO:0001501
12.4602
0.0004157
skeletal system development
GO:0043588
5.3875
0.02028
skin development
GO:0046332
4.0154
0.00004509
SMAD binding
GO:0048538
0.02644
0.02644
thymus development
GO:0016055
12.9371
0.0003221
Wnt receptor signaling pathway
the organization of chromatin remodeling complexes,
RNA processing or regulation of DNAase I function
(Olave et al., 2002). In addition, actin plays a direct
role in transcription by RNA polymerases, II and III
(Percipalle and Visa, 2006). Ubiquitination (ubiquitin-
dependent protein catabolic process, ubiquitin-protein
ligase activity) is a reversible post-translational
modification of cellular proteins and is known to play
central roles in the regulation of various cellular
processes, such as protein degradation, protein
trafficking, cell-cycle regulation, DNA repair,
apoptosis and signal transduction (kimura and Tanaka,
2010). Such functions are highly regulated and require
high codon usage bias as witnessed in this study. For
normal cell functioning, protein - protein interaction
and the activities of enzymes are regulated by
phosphorylation of tyrosine. More so, in all genes
activation, phosphorylation plays a central role. It is
not surprising that these molecular functions and
biological processes are enriched in high CUB genes
for cell hemostasis purposes. Taken together, most GO
terms enriched in high CUB genes are important for
day to day physiological functions of the cell and may
be termed as ‘housekeeping’.
Functional enrichment analyses in this study do mimic
Paudel et al. (2013) findings on CNVs. The enrichment
of low CUB involved in the immune related genes is
interesting. Genes involved in virus response such as
interferon (IFN), cytochrome P450 (CYP), are usually
fast evolving due to their importance for the organism
to respond rapid changes in the environment. For
example, members of interferon (IFN) gene families,
involved in defense against viral infections (Table 2),
and CYP genes, which are responsible for detoxification
and drug metabolism, were found to have high CNR
(Paudel et al., 2013) and very plausible in this study.
This could be because these genes are less conserved
and need to evolve fast to adapt to ever changing
antigenic determinants, evolution of pathogen and
immune evasion mechanism explored by pathogens.
The low CUB usage results reported in this study
concur with Paudel et al. (2013) and show that these
types of genes are often found to be CN variable in
pigs. The observed overrepresentation of low codon
