Table 5

Enrichment of GO terms of negatively and positively correlated smRNA-mRNA expression pairs to manually assorted higher order categories
GO process ID Description P
Protein modification
Negative correlation
GO:0006457 Protein folding 0.000
GO:0051082 Unfolded protein binding 0.002
GO:0004252 Serine-type endopeptidase activity 0.013
GO:0018106 Peptidyl-histidine phosphorylation 0.009
GO:0016925 Protein sumoylation 0.005
GO:0003755 Peptidyl-prolyl cis-trans isomerase activity 0.025
GO:0036065 Fucosylation 0.034
GO:0000413 Protein peptidyl-prolyl isomerization 0.021
Positive correlation
GO:0019787 Small conjugating protein ligase activity 0.021
GO:0006487 Protein N-linked glycosylation 0.045
GO:0047485 Protein N-terminus binding 0.013
GO:0070534 Protein K63-linked ubiquitination 0.011
GO:0042787 Protein ubiquitination in ubiquitin-dependent protein catabolic process 0.021
GO:0019773 Proteasome core complex, alpha-subunit complex 0.034
GO:0004180 Carboxypeptidase activity 0.000
Immunity
Negative correlation
GO:0016446 Somatic hypermutation of immunoglobulin genes 0.009
Positive correlation
GO:0002666 Positive regulation of T cell tolerance induction 0.015
GO:0042130 Negative regulation of T cell proliferation 0.024
GO:0002698 Negative regulation of immune effector process 0.036
Signaling
Negative correlation
GO:0023014 Signal transduction by phosphorylation 0.046
GO:0009909 Regulation of flower development 0.034
GO:0010019 Chloroplast-nucleus signaling pathway 0.011
GO:0031930 Mitochondria-nucleus signaling pathway 0.011
Positive correlation
GO:0031930 Mitochondria-nucleus signaling pathway 0.000
DNA damage
Negative correlation
GO:0032404 Mismatch repair complex binding 0.001
GO:0006307 DNA dealkylation involved in DNA repair 0.034
GO:0032300 Mismatch repair complex 0.005
GO:0031072 Heat shock protein binding 0.005
GO:0008630 Intrinsic apoptotic signaling pathway in response to DNA damage 0.038
Positive correlation
GO:0008630 Intrinsic apoptotic signaling pathway in response to DNA damage 0.036
GO:0006289 Nucleotide-excision repair 0.015
Gene expression
Negative correlation
GO:0035552 Oxidative single-stranded DNA demethylation 0.028
GO:0030261 Chromosome condensation 0.004
Positive correlation
GO:0031048 Chromatin silencing by small RNA 0.008
Translation
Negative correlation
GO:0006412 Translation 0.030
GO:0003735 Structural constituent of ribosome 0.006
GO:0022627 Cytosolic small ribosomal subunit 0.009
GO:0042255 Ribosome assembly 0.013
GO:0016071 mRNA metabolic process 0.050
GO:0006364 rRNA processing 0.000
Positive correlation
GO:0008353 RNA polymerase II carboxy-terminal domain kinase activity 0.032
GO:0005689 U12-type spliceosomal complex 0.008
GO:0015935 Small ribosomal subunit 0.000
Metabolism
Negative correlation
GO:0043734 DNA-N1-methyladenine dioxygenase activity 0.030
GO:0051747 Cytosine C-5 DNA demethylase activity 0.030
GO:0043462 Regulation of ATPase activity 0.017
GO:0019213 Deacetylase activity 0.017
GO:0016811 Hydrolase activity 0.045
GO:0019478 D-amino acid catabolic process 0.001
GO:0016308 1-phosphatidylinositol-4-phosphate 5-kinase activity 0.050
GO:0042264 Peptidyl-aspartic acid hydroxylation 0.035
Positive correlation
GO:0006662 Glycerol ether metabolic process 0.008
GO:0042775 mitochondrial ATP synthesis coupled electron transport 0.017
GO:0001522 Pseudouridine synthesis 0.006
GO:0003879 ATP phosphoribosyltransferase activity 0.047
GO:0009982 Pseudouridine synthase activity 0.005
GO:0005388 Calcium-transporting ATPase activity 0.024
GO:0016847 1-aminocyclopropane-1-carboxylate synthase activity 0.018
GO:0042218 1-aminocyclopropane-1-carboxylate biosynthetic process 0.017
GO:0015035 Protein disulfide oxidoreductase activity 0.012
GO:0009062 Fatty acid catabolic process 0.003
GO:0015020 Glucuronosyltransferase activity 0.008
GO:0047661 Amino-acid racemase activity 0.025
GO:0009252 Peptidoglycan biosynthetic process 0.008
GO:0016303 1-phosphatidylinositol-3-kinase activity 0.037
GO:0036092 Phosphatidylinositol-3-phosphate biosynthetic process 0.050
GO:0042823 Pyridoxal phosphate biosynthetic process 0.001
GO:0019213 Deacetylase activity 0.015

Only categories that are negatively and positively correlated are shown.

Baumgarten et al.

Baumgarten et al. BMC Genomics 2013 14:704   doi:10.1186/1471-2164-14-704

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