Table 1

The coefficient estimates from the GCVAR regression model

Factor

Category

Chromosomes

Average %GC

Average size (mbp)

Coefficient estimate

p-value

Phylum

Acidobacteria

2

60

7.8

-0.23

0.05

Phylum

Actinobacteria

42

66

4.8

-0.11

0.003

Phylum

Bacteroides

16

44

3.6

0.18

<0.001

Phylum

Betaproteobacteria

64

64

3.4

0.1

0.002

Phylum

Chlamydiae

8

43

1.9

-0.28

<0.001

Phylum

Crenarchaeota

16

48

2

0.22

<0.001

Phylum

Cyanobacteria

17

48

4.4

0.3

<0.001

Phylum

Deltaproteobacteria

18

58

4.7

0.15

0.001

Phylum

Epsilonproteobacteria

12

38

1.9

0.1

0.04

Phylum

Euryarcheota

31

46

2.4

0.16

<0.001

Phylum

Firmicutes

89

37

2.6

0.12

<0.001

Phylum

Gammaproteobacteria

92

47

3.7

0.12

<0.001

Phylum

Planctomycetes

1

55

7.2

-0.48

0.002

Phylum

Spirochaetes

11

37

1.7

0.14

0.01

Oxygen

Anaerobic

-

-

-

0.11

<0.001

GC

-

-

-

-

0.37

<0.001


The variable GC is continuous while phylum and oxygen are categorical variables. Note that for the phylum variable we have used the sum-to-zero parameterization, i.e. all estimated effects are deviations from the mean phylum effect. For the oxygen requirement variable however, we used a relative parameterization where the category "aerobic" is the reference, i.e. the estimated effect is the deviation from the aerobic effect. In addition, the number of chromosomes, average %GC, and average genomes size in mbp, are included for each phylogenetic group.

Bohlin et al. BMC Genomics 2010 11:464   doi:10.1186/1471-2164-11-464

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