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Table 1 Analysis of human mitochondrial genes that encode a subunit of complexes I-V of the mitochondrial respiratory chain encoded in the nuclear (a) or mitochondrial (b) genome.

From: E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)

a) Nuclear encoded genes

Complex

Gene name

Length

CAIhm

 

eCAIhm

CAIhm/eCAIhm

CAImt

 

eCAImt

CAImt/eCAImt

     

p = 0.05

p = 0.05

  

p = 0.05

p = 0.05

I

NDUFS1

2184

0.695

*

0.683

1.018

0.434

 

0.519

0.836

 

NDUFS2

1392

0.765

**

0.734

1.042

0.391

 

0.500

0.782

 

NDUFS3

795

0.754

*

0.750

1.005

0.402

 

0.488

0.824

 

NDUFS7

642

0.867

**

0.780

1.112

0.442

 

0.446

0.991

 

NDUFS8

633

0.868

**

0.796

1.090

0.439

 

0.465

0.944

 

NDUFV1

1395

0.825

**

0.774

1.066

0.417

 

0.482

0.865

 

NDUFV2

750

0.695

 

0.703

0.989

0.449

 

0.519

0.865

II

SDHC

510

0.699

*

0.679

1.029

0.377

 

0.457

0.825

 

SDHD

480

0.663

*

0.654

1.014

0.387

 

0.464

0.834

 

SDHA

1995

0.768

*

0.750

1.024

0.423

 

0.496

0.853

 

SDHB

843

0.778

**

0.754

1.032

0.454

 

0.481

0.944

III

UQCRFS1

825

0.711

*

0.711

1.000

0.391

 

0.483

0.810

 

CYC1

978

0.759

*

0.750

1.012

0.379

 

0.449

0.844

IV

COX10

1332

0.744

**

0.713

1.043

0.454

 

0.462

0.983

 

COX11

831

0.738

*

0.725

1.018

0.407

 

0.513

0.793

 

COX15

1140

0.707

*

0.688

1.028

0.411

 

0.472

0.871

V

ATP5B

1590

0.714

*

0.698

1.023

0.412

 

0.507

0.813

 

ATP5A1

1512

0.695

*

0.684

1.016

0.409

 

0.519

0.788

 

ATP5C1

897

0.726

*

0.705

1.030

0.463

 

0.509

0.910

 

ATP5O

642

0.700

**

0.681

1.028

0.429

 

0.486

0.883

 

ATP5D

507

0.807

**

0.748

1.079

0.410

 

0.426

0.962

 

ATP5G1

411

0.776

**

0.707

1.098

0.456

 

0.482

0.946

 

ATP5G2

474

0.752

**

0.686

1.096

0.472

*

0.451

1.047

 

ATP5G3

429

0.720

**

0.678

1.062

0.430

 

0.510

0.843

 

ATP6V1A

1854

0.709

*

0.702

1.010

0.451

 

0.525

0.859

 

ATP6V1B1

1536

0.703

 

0.711

0.989

0.439

 

0.514

0.854

 

ATP6V1D

744

0.676

 

0.697

0.970

0.430

 

0.522

0.824

 

ATP6V1E1

681

0.721

*

0.713

1.011

0.431

 

0.500

0.862

 

ATP6V1E2

681

0.777

**

0.733

1.060

0.410

 

0.466

0.880

 

TCIRG1

2493

0.857

**

0.781

1.097

0.421

 

0.434

0.970

 

ATP6V0D2

1053

0.732

*

0.722

1.014

0.456

 

0.518

0.880

 

ATP6V0C

468

0.838

**

0.748

1.120

0.511

**

0.461

1.108

 

ATP6F

618

0.803

**

0.741

1.084

0.510

 

0.514

0.992

 

ATP6V0D1

1056

0.831

**

0.793

1.048

0.457

 

0.495

0.923

 

ATP6V0A1

2496

0.758

*

0.734

1.033

0.424

 

0.507

0.836

 

ATP6V0A4

2523

0.770

**

0.735

1.048

0.458

 

0.494

0.927

 

ATP6V0A2

2571

0.748

*

0.728

1.027

0.450

 

0.491

0.916

b) Mitochondrial encoded genes

Complex

Gene Name

Length

CAI hm

 

eCAI hm

CAI hm /eCAI hm

CAI mt

 

eCAI mt

CAI mt /eCAI mt

     

p = 0.05

p = 0.05

  

p = 0.05

p = 0.05

I

ND1

957

0.635

 

0.796

0.798

0.760

**

0.456

1.667

 

ND2

1044

0.616

 

0.774

0.796

0.677

**

0.457

1.481

 

ND3

345

0.571

 

0.703

0.812

0.701

**

0.461

1.521

 

ND4L

297

0.550

 

0.679

0.810

0.738

**

0.472

1.564

 

ND4

1377

0.612

 

0.654

0.936

0.722

**

0.455

1.587

 

ND5

1812

0.651

 

0.750

0.868

0.723

**

0.471

1.535

 

ND6

525

0.612

 

0.754

0.812

0.361

 

0.551

0.655

III

CYTB

1134

0.655

 

0.711

0.921

0.758

**

0.481

1.576

IV

COX1

1542

0.644

 

0.750

0.859

0.715

**

0.509

1.405

 

COX2

684

0.641

 

0.713

0.899

0.664

**

0.503

1.320

 

COX3

780

0.656

 

0.725

0.905

0.704

**

0.497

1.416

V

ATP8

207

0.606

 

0.688

0.881

0.633

**

0.452

1.400

 

ATP6

681

0.629

 

0.698

0.901

0.701

**

0.472

1.485

  1. Expected CAIs (eCAIs) at 95% (p = 0.05) and 99% (p = 0.01) confidence and 99% coverage were calculated using the Poisson method of the E-CAI server. For the sake of clarity, only the eCAI values at p = 0.05 are shown. CAIhm and CAImt mean CAI calculated using the mean nuclear and mitochondrial codon usage as a reference set, respectively. CAI values were calculated using the CAIcal tool http://genomes.urv.es/CAIcal.
  2. * and ** mean that the CAI is higher than the eCAI estimated at 95% (*) and 99% (**) confidence and 99% coverage. Normalised CAI values (defined as the quotient between the CAI and its expected value) bigger than one are in bold and must be interpreted as evidence of adaptation to the reference codon usage beyond mere compositional biases.
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BMC Bioinformatics

ISSN: 1471-2105

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