TABLE 4.
Overrepresented functional categories in Cap1p ChIP-chip data
| GO terma | CGD accession no. (ontology classification)b | % Frequencyc (no. of genes) | % Genome frequencyd (no. of genes) | P valuee | Genesf |
|---|---|---|---|---|---|
| Response to chemical stimulusg | GO:0042221 (P) | 27 (24) | 5.4 (342) | 5.0 × 10−09 | PDR16, SSA2, CIP1, CAP1, orf19.2262, CCP1, RTA2, SOD1, RIB1, orf19.3537, SHA3, GLR1, GCS1, CDR4, HXK2, RHR2, MDR1, CAT1, CYS3, YCF1, FLU1, FCR1, ALS6, TRX1 |
| Oxidoreductase activity | GO:0016491 (F) | 21.3 (19) | 4.6 (293) | 1.1 × 10−06 | IFD6, EBP1, RNR22, orf19.2262, CCP1, SOD1, OYE32, GRE2, orf19.3234, OYE23, OYE2, orf19.3537, ADH1, GLR1, GRP2, ERO1, orf19.5517, CAT1, orf19.6757 |
| Response to oxidative stress | GO:0006979 (P) | 12.4 (11) | 1.3 (84) | 4.1 × 10−06 | CIP1, CAP1, orf19.2262, CCP1, SOD1, orf19.3537, GLR1, GCS1, MDR1, CAT1, TRX1 |
| Response to stimulusg | GO:0050896 (P) | 31.5 (28) | 10.2 (647) | 5.9 × 10−06 | PDR16, SSA2, CIP1, CAP1, orf19.2262, CCP1, RTA2, SOD1, RIB1, GRE2, orf19.3537, SHA3, GLR1, GCS1, CDR4, HXK2, RHR2, MDR1, EFG1, CAT1, CYS3, YCF1, FLU1, orf19.6757, FCR1, ALS6, TRX1, YIM1 |
| Response to drug | GO:0042493 (P) | 14.6 (13) | 2.3 (145) | 2.0 × 10−05 | PDR16, CAP1, RTA2, SOD1, RIB1, GCS1, CDR4, RHR2, MDR1, CYS3, YCF1, FLU1, FCR1 |
| Cell fraction | GO:000267 (C) | 15.7 (14) | 3.3 (212) | 6.5 × 10−05 | PDR16, SSA2, EBP1, orf19.251, orf19.2693, PDC11, orf19.3121, PGI1, ADH1, GRP2, RHR2, orf19.5517, CCC1, GST3 |
| Hyphal cell wall | GO:0030446 (C) | 5.6 (5) | 0.6 (35) | 6.2 × 10−03 | SSA2, EBP1, orf19.251, PDC11, ADH1 |
| Response to cadmium ion | GO:0046686 (P) | 3.4 (3) | 0.1 (6) | 1.2 × 10−02 | CIP1, CAP1, GCS1 |
| Phospholipid transport | GO:0015914 (P) | 4.5 (4) | 0.3 (17) | 1.7 × 10−02 | PDR16, GIT1, RTA2, orf19.932 |
| Regulation of nitrogen utilization | GO:0006808 (P) | 3.4 (3) | 0.1 (7) | 2.0 × 10−02 | orf19.2693, orf19.3121, GST3 |
Grouping of the Cap1p (Cap1p-HA3 or Cap1p-CSE-HA3) targets identified in ChIP-chip data according to GO terminology determined by using the online CGD GO Term Finder tool (http://www.candidagenome.org/cgi-bin/GO/goTermFinder). Analysis conducted in September 2008.
Ontology classification: P, biological process; C, cellular component; F, molecular function.
Percentages were calculated based on the number of genes in each GO category divided by the total number (89 genes).
Percentages were calculated based on the number of genes in each category divided by the total number of annotated genes of the C. albicans genome, according to CGD (6,334 genes).
P values for the overrepresented categories were calculated using a hypergeometric distribution with multiple hypothesis correction (i.e., Bonferroni's correction) as described in the GO Term Finder tool website (http://www.candidagenome.org/help/goTermFinder.shtml). The P value cutoff used was ≤0.02.
Gene name or orf19 nomenclature according to CGD. Some genes were attributed to more than one GO term.
The selection criteria for GO term groups with overlapping gene lists (see Materials and Methods for details) was not applied to these two groups, in order to show that “Response to chemical stimulus” was the most significantly overrepresented functional category.