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Table 2 Functional categories of interrupted genes

From: IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes

   

Fisher exact test5

Code

Category

Cumulative

Independent

p-value

p-value

  

Length3

Insertions4

(Over-represented)

(Under-represented)

 

PE/PPE 1

280.083

96

3.97E-16

1.00E + 00

-

Not in COG

670.659

158

1.12E-11

1.00E + 00

M

Cell wall/membrane/envelope biogenesis

144.558

36

4.76E-04

1.00E + 00

T

Signal transduction mechanisms

119.979

24

3.72E-02

9.63E-01

A

RNA processing and modification

648

0

8.75E-02

9.13E-01

N

Cell Motility

657

0

8.87E-02

9.11E-01

L

Replication. recombination and repair2

213.870

37

8,98E-02

9.10E-01

K

Transcription

175.641

24

5,13E-01

4.87E-01

V

Defense mechanisms

46.863

5

6,50E-01

3.50E-01

R

General function prediction only

449.865

57

7.88E-01

2.12E-01

S

Function unknown

199.185

23

8.14E-01

1.86E-01

H

Coenzyme transport and metabolism

171.450

19

8.37E-01

1.63E-01

D

Cell cycle control, cell division. chromosome partitioning

52.116

3

9,37E-01

6.35E-02

F

Nucleotide transport and metabolism

70.152

4

9.70E-01

3.00E-02

U

Intracellular trafficking, secretion. and vesicular transport

24.903

0

9.71E-01

2.93E-02

O

Posttranslational modification, protein turnover. chaperones

114.210

7

9.92E-01

8.51E-03

Q

Secondary metabolites biosynthesis. transport and catabolism

341.379

28

9.99E-01

7.55E-04

I

Lipid transport and metabolism

289.923

19

1.00E + 00

6.52E-05

J

Translation. ribosomal structure and biogenesis

138.906

4

1.00E + 00

1.83E-05

G

Carbohydrate transport and metabolism

168.417

6

1.00E + 00

1.15E-05

P

Inorganic ion transport and metabolism

159.159

4

1.00E + 00

1.61E-06

C

Energy production and conversion

258.336

10

1.00E + 00

1.15E-07

E

Amino acid transport and metabolism

247.980

4

1.00E + 00

1.76E-11

 

Virulence. detoxification and adaptation 6

147.877

7

1.00E + 00

3.55E-04

  1. 1. Proteins belonging to the PE/PPE families were extracted to a separate category, as they constitute an important family of proteins in M. tuberculosis.
  2. 2. The genes for the transposase IS6110 were removed from the category of Replication, recombination and repair.
  3. 3. Cumulative length (bp) of all the genes in a given category. The probability of under or over-representation of a given functional category is dependent on both the number of genes and their length.
  4. 4. Represents the number of independent insertion events identified in genes of a given category.
  5. 5. Probability of over or under-representation of insertion sequences interrupting genes of a given category. In bold, categories with significant over-, under-representation after Bonferroni correction. Bonferroni corrected threshold = 2.2E-3.
  6. 6. This category is not part of COG; it is defined in tuberculist (see Methods).
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BMC Genomics

ISSN: 1471-2164

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