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Table 2 Characteristics of significant GO-ontology groups before (all rows) and after REViGO calculation (marked in bold)

From: Analysis of transcriptomic differences between NK603 maize and near-isogenic varieties using RNA sequencing and RT-qPCR

GO:ID Description No. genes AG8025 vs AG8025RR2 No. genes AG9045 AG9045RR2 No. of common genes SEA_FDR mv log10_p-val Frequency (%) Uniquen Dispens
GO:0003006 development process involved in reproduction 350 71 22 0.0310 −1.5086 1.227 0.92 0.00
GO:0042221 Response to chemical 726 150 42 0.0000 −4.4909 4.749 0.34 0.00
GO:0044711 Single-organism biosynthetic process 534 91 24 0.0160 −1.7959 6.613 0.87 0.00
GO:0044763 Single-organism cellular process 1398 238 67 0.0177 −1.7533 19.396 0.87 0.3
GO:0009651 Response to salt stress 178 40 14 0.0024 −2.6289 0.389 0.37 0.41
GO:0009266 Response to temperature stimulus 167 43 10 0.0020 −2.6946 0.601 0.37 0.74
GO:0006970 Response to osmotic stress 186 46 15 0.0016 −2.7945 0.468 0.36 0.71
GO:0044710 Single-organism metabolic process 1112 181 51 0.0210 −1.6778 23.696 0.87 0.42
GO:0051707 Response to other organism 293 63 17 0.0014 −2.8697 0.704 0.33 0.44
GO:0043207 Response to external biotic stimulus 294 64 17 0.0014 −2.8697 0.704 0.33 0.97
GO:0009620 Response to fungus 120 26 9 0.0137 −1.8649 0.285 0.36 0.91
GO:0098542 Defense response to other organism 120 26 9 0.0083 −2.0835 0.601 0.31 0.98
GO:0009607 Response to biotic stimulus 311 66 17 0.0019 −2.7328 0.771 0.42 0.44
GO:0009605 Response to external stimulus 423 82 24 0.0011 −2.9788 1.057 0.41 0.46
GO:1901700 Response to oxygen-containing compound 428 101 29 0.0006 −3.2217 1.196 0.35 0.47
GO:0010033 Response to organic substance 519 121 36 0.0010 −3.0222 2.423 0.31 0.71
GO:0070887 Cellular response to chemical stimulus 349 76 16 0.0186 −1.7317 1.470 0.34 0.73
GO:0006952 Defense response 330 64 15 0.0036 −2.4461 1.312 0.37 0.48
GO:0009628 Response to abiotic stimulus 462 109 25 0.0004 −3.4144 1.925 0.38 0.5
GO:0009719 Response to endogenous stimulus 388 95 27 0.0125 −1.9031 2.168 0.38 0.51
GO:0010035 Response to inorganic substance 261 52 14 0.0108 −1.9666 0.735 0.37 0.62
GO:0006950 Response to stress 821 146 39 0.0077 −2.1135 7.803 0.31 0.62
GO:0001101 Response to acid chemical 290 71 19 0.0075 −2.1240 0.753 0.37 0.62
GO:0009409 Response to cold 125 30 8 0.0031 −2.5157 0.310 0.38 0.68
  1. GO:ID, identity of GO-Ontologies; description, definition of ontologies; nr.genes AG8025 vs AG8025RR2, and nr.genes AG9045 vs AG9045RR2, number of genes in the ontology groups AG8025 vs AG8025RR2, and AG9045 vs AG9045RR2; common genes(nr.), number of genes commonly up- or downregulated genes in both variety pairs; SEA_FDR mv, mean value of AG8025 and AG9045 false discovery rate (p < 0.05); Rev log10, log10 value of REViGO analysis; Frequ, proportion of GO terms in the annotation database; Uniqueness, comparison measure to other ontologies (Parameter for ontology outliers); Dispensability, similarity threshold for elimination of ontologies
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