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.

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

CAIhm

eCAIhm

CAIhm/eCAIhm

CAImt

eCAImt

CAImt/eCAImt


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


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 webcite.

* 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.

Puigbò et al. BMC Bioinformatics 2008 9:65   doi:10.1186/1471-2105-9-65

Open Data