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Table 3 Gene Ontology Analysis

From: Impact of RNA degradation on gene expression profiling

Under-represented Genes
Ontology Rank GO.ID Term Annotated Significant Expected Rank in classic classic elim weight
BP 1 GO:0006099 tricarboxylic acid cycle 41 6 0.23 1 9.7e-08 9.7e-08 9.7e-08
  2 GO:0045900 negative regulation of translational elongation 6 3 0.03 10 3.3e-06 3.3e-06 3.3e-06
  3 GO:0046500 S-adenosylmethionine metabolic process 7 3 0.04 12 5.7e-06 5.7e-06 5.7e-06
  4 GO:0006446 regulation of translational initiation 70 5 0.39 19 4.3e-05 4.3e-05 4.3e-05
  5 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 13 3 0.07 20 4.5e-05 4.5e-05 4.5e-05
  6 GO:0007021 tubulin complex assembly 5 2 0.03 31 0.00030 0.00030 0.00030
  7 GO:0046498 S-adenosylhomocysteine metabolic process 5 2 0.03 32 0.00030 0.00030 0.00030
  8 GO:0030091 protein repair 6 2 0.03 33 0.00045 0.00045 0.00045
  9 GO:0006425 glutaminyl-tRNA aminoacylation 1 1 0.01 51 0.00554 0.00554 0.00554
  10 GO:0006430 lysyl-tRNA aminoacylation 1 1 0.01 52 0.00554 0.00554 0.00554
  11 GO:0043393 regulation of protein binding 25 2 0.14 54 0.00839 0.00839 0.00839
MF 1 GO:0000104 succinate dehydrogenase activity 8 5 0.04 1 2.4e-10 2.4e-10 2.4e-10
  2 GO:0005047 signal recognition particle binding 7 3 0.04 3 5.4e-06 5.4e-06 5.4e-06
  3 GO:0045182 translation regulator activity 211 8 1.15 4 2.1e-05 0.27124 2.1e-05
  4 GO:0008312 7 S RNA binding 14 3 0.08 5 5.5e-05 5.5e-05 5.5e-05
  5 GO:0008119 thiopurine S-methyltransferase activity 3 2 0.02 7 8.8e-05 8.8e-05 8.8e-05
  6 GO:0003924 GTPase activity 328 8 1.79 8 0.00044 0.00044 0.00044
  7 GO:0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity 10 2 0.05 16 0.00129 0.00129 0.00129
  8 GO:0005525 GTP binding 592 10 3.22 19 0.00150 0.00150 0.00150
  9 GO:0009055 electron carrier activity 349 7 1.90 22 0.00304 0.00304 0.00304
  10 GO:0004819 glutamine-tRNA ligase activity 1 1 0.01 26 0.00544 0.00544 0.00544
  11 GO:0004824 lysine-tRNA ligase activity 1 1 0.01 27 0.00544 0.00544 0.00544
  12 GO:0003723 RNA binding 1269 17 6.91 10 0.00052 0.00680 0.00680
CC 1 GO:0005786 signal recognition particle, endoplasmic reticulum targeting 15 4 0.08 3 1.2e-06 1.2e-06 1.2e-06
  2 GO:0005785 signal recognition particle receptor complex 7 3 0.04 5 6.0e-06 6.0e-06 6.0e-06
  3 GO:0005853 eukaryotic translation elongation factor 1 complex 17 3 0.10 11 0.00011 0.00011 0.00011
  4 GO:0002079 inner acrosomal membrane 4 2 0.02 13 0.00019 0.00019 0.00019
  5 GO:0042589 zymogen granule membrane 5 2 0.03 16 0.00031 0.00031 0.00031
  6 GO:0008290 F-actin capping protein complex 7 2 0.04 24 0.00065 0.00065 0.00065
  7 GO:0005743 mitochondrial inner membrane 391 11 2.20 6 1.3e-05 1.3e-05 0.00263
  8 GO:0044444 cytoplasmic part 6340 68 35.62 1 1.5e-09 0.01111 0.00499
  9 GO:0045273 respiratory chain complex II 3 2 0.02 10 9.4e-05 9.4e-05 0.00558
  10 GO:0005759 mitochondrial matrix 295 6 1.66 30 0.00652 0.00652 0.00652
Over-represented Genes
Ontology Rank GO.ID Term Annotated Significant Expected Rank in classic classic elim weight
BP 1 GO:0018279 protein amino acid N-linked glycosylation via asparagine 20 2 0.02 1 0.00013 0.00013 0.00013
  2 GO:0006414 translational elongation 253 3 0.22 3 0.00127 0.00127 0.00127
  3 GO:0000722 telomere maintenance via recombination 2 1 0.00 5 0.00173 0.00173 0.00173
  4 GO:0009446 putrescine biosynthetic process 2 1 0.00 6 0.00173 0.00173 0.00173
  5 GO:0051258 protein polymerization 106 2 0.09 8 0.00374 0.00374 0.00374
  6 GO:0008295 spermidine biosynthetic process 6 1 0.01 9 0.00519 0.00519 0.00519
  7 GO:0007094 mitotic cell cycle spindle assembly checkpoint 8 1 0.01 11 0.00691 0.00691 0.00691
  8 GO:0007018 microtubule-based movement 157 2 0.14 13 0.00802 0.00802 0.00802
  9 GO:0015937 coenzyme A biosynthetic process 10 1 0.01 15 0.00863 0.00863 0.00863
MF 1 GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity 19 2 0.02 1 0.00014 0.00014 0.00014
  2 GO:0008783 agmatinase activity 2 1 0.00 3 0.00187 0.00187 0.00187
  3 GO:0005198 structural molecule activity 1149 5 1.08 4 0.00359 0.13592 0.00359
  4 GO:0004594 pantothenate kinase activity 7 1 0.01 6 0.00654 0.00654 0.00654
  5 GO:0003720 telomerase activity 8 1 0.01 7 0.00747 0.00747 0.00747
CC 1 GO:0008250 oligosaccharyl transferase complex 20 2 0.02 1 0.00013 0.00013 0.00013
  2 GO:0005840 ribosome 407 3 0.35 13 0.00493 0.00493 0.00493
  1. The GO analysis was applied to differentially expressed genes from the comparison TP3 vs. Control. The number of genes belonging to a GO term represented on the microarray (annotated), the number genes in the analyzed gene list (significant) and the expected number of genes by chance are given. The upper part of the table shows GO terms that are highly significant for under-represented genes (p-value < 0.01); the lower part indicates terms that are highly significant for over-represented genes. Calculated p-values for each category from three similar methods (classic, elim, weight) are shown. Each table is separated into three different parts representing the following ontologies: Biological Process (BP), Molecular Function (MF) and Cellular Component (CC).