Table 1

GO enrichment by CCA and PCA

GO term

PCA

CCA

Baseline


Response to biotic stimulus

53, 2.2E-15

61, 2.7E-19

55, 6.2E-17

Defense response

51, 1.1E-14

58, 7.3E-18

53, 3.4E-16

Immune response

47, 3.8E-13

54, 9.5E-17

48, 3.9E-14

Response to pest, pathogen, parasite

29, 7.0E-09

30, 1.4E-08

26, 1.4E-06

Response to other organism

29, 3.0E-08

30, 6.1E-08

26, 4.8E-06

Response to stimulus

61, 6.4E-07

75, 4.1E-12

62, 2.0E-07

Response to stress

35, 9.5E-06

36, 3.6E-05

31, 1.5E-03

Organismal physiological process

54, 5.7E-05

68, 4.8E-10

55, 2.0E-05

Response to external stimulus

22, 1.8E-04

22, 9.4E-04

19, 1.5E-02

Response to wounding

19, 3.3E-04

20, 2.9E-04

16, 3.8E-02


The enriched gene ontology terms from the biological processes category with p-values (Bonferroni corrected) lower than 0.01. Both CCA and PCA result in the same 10 terms, and here they are sorted according to the p-value of the gene list obtained with PCA preprocessing. Each cell lists the count of genes in that term, together with the p-value (Bonferroni corrected). In 9 out of 10 the count is higher for CCA, showing that it is able to capture relevant genes with better accuracy, avoiding outliers. The baseline method shares 8 common GO terms with CCA/PCA, and the two different GO enrichments are Antigen presentation, endogeneous antigen (8, 1.5E-4) and Antigen processing, endogeneous antigen via MHC class I (7, 6.3E-3).

Tripathi et al. BMC Bioinformatics 2008 9:111   doi:10.1186/1471-2105-9-111

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