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Table 5 The top 15 significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in MALAT1-ceRNA sub-network

From: Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma

A
 GO-BP Term Enrichment Score Count % P-Value
 positive regulation of transcription from RNA polymerase II promoter 3.579259 20 11.43 <  0.001
 transcription from RNA polymerase II promoter 3.106442 13 7.429 <  0.001
positive regulation of transcription, DNA-templated 3.091753 13 7.429 <  0.001
 neuroepithelial cell differentiation 2.894845 3 1.714 0.001
 positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway 2.772993 4 2.286 0.002
 neural tube formation 2.772164 3 1.714 0.002
 in utero embryonic development 2.425229 7 4 0.004
 kidney development 2.315189 5 2.857 0.005
 camera-type eye morphogenesis 2.158154 3 1.714 0.007
 regulation of protein localization 2.092037 4 2.286 0.008
 inner ear morphogenesis 2.092037 4 2.286 0.008
 positive regulation of branching involved in ureteric bud morphogenesis 2.011071 3 1.714 0.01
 positive regulation of neuroblast proliferation 1.967555 3 1.714 0.011
 negative regulation of transcription from RNA  polymerase II promoter 1.923719 13 7.429 0.012
 cell migration 1.922663 6 3.429 0.012
B
 GO-CC Term Enrichment Score Count % P-Value
 cytosol 3.530641 45 25.71 <  0.001
 nucleus 3.429028 64 36.57 <  0.001
 nucleoplasm 3.288165 39 22.29 <  0.001
 cell-cell adherens junction 2.341584 9 5.143 0.005
 melanosome 2.052614 5 2.857 0.009
 filopodium 1.71293 4 2.286 0.019
 PcG protein complex 1.707154 3 1.714 0.02
 nuclear chromatin 1.705842 6 3.429 0.02
 extracellular exosome 1.429256 32 18.29 0.037
 cis-Golgi network 1.35117 3 1.714 0.045
 spindle microtubule 1.314751 3 1.714 0.048
 cytoplasm 1.239444 52 29.71 0.058
 perinuclear region of cytoplasm 1.205186 10 5.714 0.062
 membrane 1.146558 25 14.29 0.071
 spindle 1.134303 4 2.286 0.073
C
 GO-MF Term Enrichment Score Count % P-Value
 protein binding 3.880727 95 54.29 <  0.001
 sequence-specific DNA binding 3.451663 14 8 <  0.001
 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding 3.120112 9 5.143 <  0.001
 RNA polymerase II core promoter proximal region sequence-specific DNA binding 2.566023 10 5.714 0.003
 poly(A) RNA binding 2.27862 19 10.86 0.005
 transcription factor activity, sequence-specific DNA binding 1.893028 16 9.143 0.013
 zinc ion binding 1.508313 17 9.714 0.031
 cadherin binding involved in cell-cell adhesion 1.481723 7 4 0.033
 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 1.359345 4 2.286 0.044
 vascular endothelial growth factor receptor 2 binding 1.315103 2 1.143 0.048
 N6-methyladenosine-containing RNA binding 1.249923 2 1.143 0.056
 mRNA 5′-UTR binding 1.144306 2 1.143 0.072
 protein heterodimerization activity 1.046398 8 4.571 0.09
 RNA polymerase II regulatory region sequence-specific DNA binding 1.031152 5 2.857 0.093
 DNA binding 1.029587 20 11.43 0.093
D
 GO-MF Term Enrichment Score Count % P-Value
 protein binding 3.880727 95 54.29 <  0.001
 sequence-specific DNA binding 3.451663 14 8 <  0.001
 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding 3.120112 9 5.143 <  0.001
 RNA polymerase II core promoter proximal region sequence-specific DNA binding 2.566023 10 5.714 0.003
 poly(A) RNA binding 2.27862 19 10.86 0.005
 transcription factor activity, sequence-specific DNA binding 1.893028 16 9.143 0.013
 zinc ion binding 1.508313 17 9.714 0.031
 cadherin binding involved in cell-cell adhesion 1.481723 7 4 0.033
 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 1.359345 4 2.286 0.044
 vascular endothelial growth factor receptor 2 binding 1.315103 2 1.143 0.048
 N6-methyladenosine-containing RNA binding 1.249923 2 1.143 0.056
 mRNA 5′-UTR binding 1.144306 2 1.143 0.072
 protein heterodimerization activity 1.046398 8 4.571 0.09
RNA polymerase II regulatory region sequence-specific DNA binding 1.031152 5 2.857 0.093
 DNA binding 1.029587 20 11.43 0.093