Table 2.
Enrichment of GO terms in differentially expressed sequences in Phlebia sp. MG-60
| GO_name | GO_id | Number of sequences | Log Fold Change | Z score | P-value | FDR | |
|---|---|---|---|---|---|---|---|
| MF | ATP binding | GO:0005524 | 799 | 0.2985 | 6.1830 | 6.29E-10 | 1.4E-07 |
| MF | nucleic acid binding | GO:0003676 | 233 | 0.4418 | 4.6111 | 4.01E-06 | 0.0004 |
| MF | phosphogluconate dehydrogenase (decarboxylating) activity | GO:0004616 | 11 | −2.2802 | −4.2490 | 2.15E-05 | 0.0010 |
| BP | pentose-phosphate shunt | GO:0006098 | 11 | −2.2802 | −4.2490 | 2.15E-05 | 0.0010 |
| MF | transferase activity | GO:0016740 | 13 | 1.9417 | 4.2346 | 2.29E-05 | 0.0010 |
| BP | fatty acid biosynthetic process | GO:0006633 | 11 | 2.0965 | 4.1939 | 2.74E-05 | 0.0010 |
| MF | copper ion binding | GO:0005507 | 27 | 1.2629 | 4.0514 | 5.09E-05 | 0.0016 |
| BP | tRNA aminoacylation for protein translation | GO:0006418 | 38 | 0.9948 | 3.8449 | 0.0001 | 0.0032 |
| MF | aminoacyl-tRNA ligase activity | GO:0004812 | 41 | 0.9504 | 3.8284 | 0.0001 | 0.0032 |
| MF | acyl-CoA dehydrogenase activity | GO:0003995 | 16 | −1.7053 | −3.7871 | 0.0002 | 0.0034 |
| MF | oxidoreductase activity, acting on the CH-CH group of donors | GO:0016627 | 25 | −1.3711 | −3.7618 | 0.0002 | 0.0034 |
| CC | integral component of membrane | GO:0016021 | 492 | 0.2125 | 3.7428 | 0.0002 | 0.0034 |
| BP | intracellular protein transport | GO:0006886 | 81 | 0.6338 | 3.7239 | 0.0002 | 0.0034 |
| BP | rRNA processing | GO:0006364 | 17 | 1.4230 | 3.5985 | 0.0003 | 0.0051 |
| MF | nucleotide binding | GO:0000166 | 69 | 0.6564 | 3.5460 | 0.0004 | 0.0058 |
| MF | nitronate monooxygenase activity | GO:0018580 | 16 | −1.5292 | −3.3773 | 0.0007 | 0.0102 |
| MF | coenzyme binding | GO:0050662 | 76 | 0.5828 | 3.3485 | 0.0008 | 0.0106 |
| BP | biosynthetic process | GO:0009058 | 73 | 0.5771 | 3.2533 | 0.0011 | 0.0141 |
| MF | protein binding | GO:0005515 | 816 | 0.1157 | 3.2119 | 0.0013 | 0.0154 |
| MF | DNA-directed RNA polymerase activity | GO:0003899 | 48 | 0.6911 | 3.0976 | 0.0020 | 0.0217 |
| CC | membrane coat | GO:0030117 | 15 | 1.2752 | 3.0474 | 0.0023 | 0.0243 |
| MF | methyltransferase activity | GO:0008168 | 77 | 0.5169 | 3.0342 | 0.0024 | 0.0243 |
| MF | RNA binding | GO:0003723 | 107 | 0.4216 | 3.0033 | 0.0027 | 0.0256 |
| CC | cytoplasm | GO:0005737 | 103 | 0.4287 | 2.9886 | 0.0028 | 0.0256 |
| MF | structural molecule activity | GO:0005198 | 11 | 1.4658 | 2.9773 | 0.0029 | 0.0256 |
| MF | DNA binding | GO:0003677 | 275 | 0.2301 | 2.9679 | 0.0030 | 0.0256 |
| BP | ribosome biogenesis | GO:0042254 | 12 | 1.3692 | 2.9151 | 0.0036 | 0.0282 |
| CC | membrane | GO:0016020 | 319 | 0.2020 | 2.9042 | 0.0037 | 0.0282 |
| MF | magnesium ion binding | GO:0000287 | 27 | 0.8832 | 2.9037 | 0.0037 | 0.0282 |
| MF | catalytic activity | GO:0003824 | 327 | 0.1926 | 2.8416 | 0.0045 | 0.0332 |
| MF | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | GO:0016620 | 10 | 1.4184 | 2.7516 | 0.0059 | 0.0425 |
| CC | small-subunit processome | GO:0032040 | 13 | 1.2130 | 2.7064 | 0.0068 | 0.0472 |
GO gene ontology, PAGE parametric analysis of gene set enrichment, BP biological process, MF molecular function, CC cellular component, FDR False discovery rate, Log Fold Change values between fermenting and non-fermenting conditions were used to calculate Z scores. Log Fold change values of each GO terms upregulated in fermenting condition is represented by positive numbers and downregulated is represented by negative numbers