Table 3

List of positively selected genes that intersect DivE's predicted accelerated regions.

Gene symbol

Gene full name

Encode region

Subtree

under

selection

No. of orthologous sequences

P-value


SERPINB7

serpin peptidase inhibitor, clade B (ovalbumin), member 7

ENr122

new world monkeys

13

<.0001


SLC22A4

solute carrier family 22 (organic cation/ergothioneine transporter), member 4

ENm002

orangutan

14

<.0001


UGT1A8

UDP glucuronosyltransferase 1 family, polypeptide A8

ENr131

baboon

7

<.0001


LILRA4

leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4

ENm007

human-orangutan

6

<.0001


APOA4

apolipoprotein A-IV

ENm003

macaque

13

<.0001


HBQ1

hemoglobin, theta 1

ENm008

chimp

14

<.0001


F7

coagulation factor VII (serum prothrombin conversion accelerator)

ENr132

macaque

11

<.0001


C21orf13

(LCA5L)

Leber congenital amaurosis 5-like

ENr133

mouse lemur

13

0.0004


CGN

cingulin

ENr231

dusky titi

13

0.0004


LILRB4

leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4

ENm007

vervet-baboon

6

0.0007


AC006985.5

(HEATR7B1)

HEAT repeat containing 7B1

ENr131

prosimians

9

0.0007


ARHGDIG

Rho GDP dissociation inhibitor (GDI) gamma

ENm008

simians

10

0.0017


F8

coagulation factor VIII, procoagulant component

ENm006

owl monkey

10

0.0026


SYT8

synaptotagmin VIII

ENm011

new world monkeys

8

0.0030


C22orf30 (PRR14L)

proline rich 14-like

ENm004

simians

12

0.0039


HBZ

hemoglobin, zeta

ENm008

macaque

4

0.0043


LILRB5

leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5

ENm007

macaque

3

0.0068


DEPDC5

DEP domain containing 5

ENm004

human-colobus monkey

12

0.007


RPS9

ribosomal protein S9

ENm007

human-colobus monkey

13

0.0227


DDX43

DEAD (Asp-Glu-Ala-Asp) box polypeptide 43

ENr223

new world monkeys

12

0.0246


Positive selection was determined with the codeml program from the PAML package. The first column gives the ENCODE gene symbol followed in parentheses by the corresponding Genbank gene symbol (if different). The fourth column in the table shows the name of the subtree predicted to be accelerated by DivE. If there are multiple species in the selected tree, the clade is specified by the two species whose most common ancestor form the clade's root, or by the clade's name as specified in Figure 1.

Pertea et al. BMC Bioinformatics 2011 12:274   doi:10.1186/1471-2105-12-274

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