Skip to main content

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).