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. 2015 Nov 19;3:e1429. doi: 10.7717/peerj.1429

Table 3. Enriched GO terms in sets of differentially expressed transcripts in both digestive gland and gill tissues. Data is sorted based on p-value in increasing (p-values are calculated according to the weight algorithm in TopGO).

GO term description GO number Annotated Expected p-value
Digestive gland—upregulated
Vesicle-mediated transport GO:0016192 176 60.79 1.00E–09
Maintenance of protein localization in endoplasmic reticulum GO:0035437 16 5.53 3.80E–08
Cellular response to glucose starvation GO:0042149 19 6.56 5.70E–08
Cellular modified amino acid metabolic process GO:0006575 72 24.87 7.40E–08
ER overload response GO:0006983 15 5.18 1.10E–07
Activation of signaling protein activity involved in unfolded protein response GO:0006987 15 5.18 1.10E–07
Cerebellum structural organization GO:0021589 15 5.18 1.10E–07
Regulation of cell migration GO:0030334 47 16.23 2.40E–06
Negative regulation of cellular response to growth factor stimulus GO:0090288 23 7.94 2.80E–06
Endosomal transport GO:0016197 31 10.71 7.00E–06
Pteridine-containing compound metabolic process GO:0042558 17 5.87 7.00E–06
Secretion by cell GO:0032940 58 20.03 1.50E–05
Coenzyme metabolic process GO:0006732 117 40.41 1.70E–05
Regulation of actin filament polymerization GO:0030833 25 8.63 2.60E–05
Cerebellar Purkinje cell layer development GO:0021680 18 6.22 2.90E–05
Cellular response to interleukin-4 GO:0071353 27 9.33 3.00E–05
Regulation of protein ubiquitination GO:0031396 68 23.49 4.40E–05
Negative regulation of protein polymerization GO:0032272 15 5.18 4.60E–05
Aminoglycan metabolic process GO:0006022 29 10.02 0.00015
Regulation of lipid metabolic process GO:0019216 16 5.53 0.00017
Digestive gland—downregulated
DNA metabolic process GO:0006259 157 102.77 2.60E–09
Ribonucleoprotein complex biogenesis GO:0022613 130 85.1 4.20E–08
mRNA processing GO:0006397 70 45.82 1.80E–06
Cilium morphogenesis GO:0060271 53 34.69 4.10E–06
Transcription from RNA polymerase II promoter GO:0006366 186 121.76 4.90E–06
Mitochondrial ATP synthesis coupled electron transport GO:0042775 81 53.02 1.50E–05
Mitotic nuclear division GO:0007067 82 53.68 2.30E–05
Inorganic cation transmembrane transport GO:0098662 109 71.35 2.80E–05
Chromosome organization GO:0051276 167 109.32 7.20E–05
Microtubule-based movement GO:0007018 97 63.5 8.20E–05
Cilium organization GO:0044782 42 27.49 0.00018
Positive regulation of ubiquitin-protein transferase activity GO:0051443 32 20.95 0.00019
Sodium ion transport GO:0006814 46 30.11 0.00022
Anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process GO:0031145 31 20.29 0.00028
G1/S transition of mitotic cell cycle GO:0000082 44 28.8 0.00029
Mitotic S phase GO:0000084 30 19.64 0.0004
Chromatin remodeling GO:0006338 39 25.53 0.0005
Regulation of multi-organism process GO:0043900 43 28.15 0.00058
Cilium or flagellum-dependent cell motility GO:0001539 17 11.13 0.00073
Histone acetylation GO:0016573 33 21.6 0.00078
Gill—upregulated
Biological process GO:0008150 926 516.95 1.60E–06
Positive regulation of cell growth GO:0030307 12 6.7 0.00087
Carbohydrate metabolic process GO:0005975 39 21.77 0.00149
Cellular catabolic process GO:0044248 30 16.75 0.04401
Protein folding GO:0006457 23 12.84 0.05753
Protein polyubiquitination GO:0000209 17 9.49 0.06629
Lipid metabolic process GO:0006629 24 13.4 0.09686
Intracellular transport GO:0046907 18 10.05 0.11899
Nucleobase-containing compound catabolic process GO:0034655 12 6.7 0.14577
Proteolysis GO:0006508 22 12.28 0.16789
Single-organism developmental process GO:0044767 94 52.48 0.19993
Cellular macromolecular complex assembly GO:0034622 11 6.14 0.20518
Protein complex subunit organization GO:0071822 11 6.14 0.20518
Generation of neurons GO:0048699 16 8.93 0.21463
Vesicle-mediated transport GO:0016192 21 11.72 0.21627
Response to oxygen-containing compound GO:1901700 10 5.58 0.28271
Protein complex assembly GO:0006461 10 5.58 0.31076
Cell cycle GO:0007049 17 9.49 0.31266
Response to external stimulus GO:0009605 17 9.49 0.31266
Positive regulation of transcription, DNA-templated GO:0045893 12 6.7 0.32401
Gill—downregulated
Microtubule-based process GO:0007017 25 7.31 1.40E–07
Energy derivation by oxidation of organic compounds GO:0015980 10 2.92 0.0012
Heterocycle biosynthetic process GO:0018130 35 10.23 0.0041
Aromatic compound biosynthetic process GO:0019438 35 10.23 0.0041
Cellular nitrogen compound biosynthetic process GO:0044271 37 10.82 0.0086
Organic cyclic compound biosynthetic process GO:1901362 38 11.11 0.0121
Biological process GO:0008150 926 270.74 0.0161
Regulation of signal transduction GO:0009966 18 5.26 0.0165
Cellular protein modification process GO:0006464 57 16.67 0.0537
Nucleotide metabolic process GO:0009117 11 3.22 0.0687
Response to organic substance GO:0010033 26 7.6 0.1048
Single-organism transport GO:0044765 66 19.3 0.1202
Cell morphogenesis involved in differentiation GO:0000904 10 2.92 0.1363
Regulation of multicellular organismal process GO:0051239 10 2.92 0.1363
Purine-containing compound metabolic process GO:0072521 10 2.92 0.1363
Single-organism biosynthetic process GO:0044711 19 5.56 0.1603
Cell surface receptor signaling pathway GO:0007166 31 9.06 0.1635
Regulation of biological quality GO:0065008 17 4.97 0.202
Anatomical structure morphogenesis GO:0009653 33 9.65 0.2438
Protein modification by small protein conjugation GO:0032446 28 8.19 0.2836