Table 4

The bear genes showing rapid evolution in bear lineage (CDS coverage ≥ 80%).

Gene Symbol

P valuea

CDS Coverage d

Biological functionse


PNPLA4

0.001

0.145

0.649

0.984

Lipid catabolic process

CDC42SE1

0.001

0.0001

0.433

0.987

Signal transduction; Regulation of cell shape

CNPY2

0.002

0.027

0.402

1

Unknown

TMED2

0.011

0.006

0.211

1

Vesicle-mediated transport;

CSRP3

0.012

0.014

0.113

0.994

Regulation of the force of heart contraction; Cellular calcium ion homeostasis;

CHCHD1

0.016

0.144

4.156

0.991

Unknown

TNNI3

0.017

0.018

0.145

0.86

Cardiac muscle contraction; Regulation of systemic arterial blood pressure by ischemic conditions; Cellular calcium ion homeostasis;

APOHL

0.018

0.226

0.506

0.962

Negative regulation of endothelial cell proliferation; Triacylglycerol metabolic process; Blood coagulation, intrinsic pathway;

C1orf52

0.019

0.078

0.711

1

Unknown

PLNM

0.02

0.058

Inf*

0.981

Regulation of the force of heart contraction; Cellular calcium ion homeostasis; Blood circulation

C19orf39

0.021

0.301

0.948

0.925

Unknown

BPHL

0.024

0.127

0.314

0.859

Proteolysis; Response to toxin; Cellular amino acid and derivative metabolic process

YIPF3

0.028

0.021

0.08

0.854

Cell differentiation

DR1

0.029

0.001

0.191

0.824

Negative regulation of transcription

RBM8AM

0.033

0.0001

0.068

0.821

RNA processing; mRNA binding

POLR2C

0.039

0.003

0.037

0.876

Transcription initiation

ATP6V1FH

0.042

0.009

Inf*

0.991

Ion transport; ATP synthesis coupled proton transport;

CISD2

0.043

0.011

0.15

1

Regulation of cellular respiration


ap-value calculated from the LRT under chi-squared distribution with df = 1.

b ω1 is the Ka/Ks value of the bear lineage; c ω0 is the average Ka/Ks value in the rest of lineages.

dThe coverage of protein coding region of bear EST using human RefSeq sequence as reference.

eBiological functions obtained from GO annotations.

* In these cases, the rate of synonymous substitution reaches zero (Ks = 0) and Ka/Ks diverges and represented as Inf here.

H, L, MThe gene shows significantly differential expression (P < 0.05, one-way ANOVA) in heart, liver, or skeletal muscle tissue respectively.

Zhao et al. BMC Genomics 2010 11:201   doi:10.1186/1471-2164-11-201

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