Table 3. Pathway annotation by DAVID bioinformatics resource.
The 65 significant genes (133 overlapped probes) which were differentially regulated in H99 compared to environmental strains were analyzed. Shown were representative of each annotation cluster detected. Count represents number of genes which match the pathway database, and % represents the percentage of gene hits among the total genes in the pathway database. Enrichment score (ES) of each group was measured by the geometric mean of the EASE Scores (modified Fisher Exact) associated with the enriched annotation terms that belong to this gene group. Population hit (Pop Hits) represents how many have the function name in your gene list of interest, and population total (Pop Total) represents how many genes in overall population has that function name in the background genome (all genes in the species of interest in DAVID database). False discovery rate (FDR) represents the percentages of test which might be false positive. P values were analyzed using Fisher exact score to identify which sub-populations are over- or under-represented in a sample. Data were considered significant if *P<0.05.
| Category | Term | Genes | ES | Count | % | Pop Hits | Pop Total | FDR | P |
|---|---|---|---|---|---|---|---|---|---|
| GOTERM_MF_FAT | GO:0046872~ Metal ion binding | UGA3, SSM4, PUT3, YPR013C, SAC6, ENO2, AKR1, ARN1, ILV3, ARN2, NFI1 | 1.67 | 11 | 37.9 | 830 | 4190 | 16.7 | 0.0159* |
| GOTERM_MF_FAT | GO:0051119~ Sugar transmembrane transporter activity | MAL31, SNF3, MPH2 | 1.65 | 3 | 10.3 | 26 | 4190 | 10.9 | 0.0101* |
| GOTERM_BP_FAT | GO:0044257~ Cellular protein catabolic process | SIP5, PEP4, SSM4, DCS1, NFI1 | 0.66 | 5 | 17.2 | 351 | 4870 | 82.9 | 0.1255 |
| GOTERM_CC_FAT | GO:0016021~ Integral to membrane | SSM4, MAL31, SNF3, MPH2, AKR1, VBA5, ARN1, ARN2 | 0.44 | 8 | 27.5 | 1488 | 4595 | 99.7 | 0.4214 |
| GOTERM_MF_FAT | GO:0003700~ Transcription factor activity | UGA3, PUT3, HMRA1 | 0.28 | 3 | 10.3 | 135 | 4190 | 91.1 | 0.1917 |
| UP_SEQ_FEATURE | UP_SEQ_FEATURE~ Transit peptide:Mitochondrion | AIM45, MMF1, ILV3 | 0.27 | 3 | 10.3 | 325 | 6448 | 99.7 | 0.415 |
| GOTERM_CC_FAT | GO:0043233~ Organelle lumen | PEP4, AIM45, RNA15, MMF1 | 0.17 | 4 | 13.7 | 783 | 4595 | 99.9 | 0.6522 |