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Table 3 The top 15 significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in ceRNA 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 9.446887 56 13.18 < 0.001
 positive regulation of transcription, DNA-templated 4.759462 29 6.824 < 0.001
 transcription from RNA polymerase II promoter 3.957811 27 6.353 < 0.001
 negative regulation of transcription from RNA polymerase II promoter 3.674737 33 7.765 < 0.001
 protein stabilization 3.580807 12 2.824 < 0.001
 spinal cord development 3.291952 6 1.412 < 0.001
 heart morphogenesis 3.157839 6 1.412 < 0.001
 kidney development 3.144958 9 2.118 < 0.001
 positive regulation of peptidyl-serine phosphorylation 3.001168 8 1.882 < 0.001
 response to cytokine 2.967806 7 1.647 0.001
 regulation of protein localization 2.967806 7 1.647 0.001
 regulation of cell-matrix adhesion 2.914902 4 0.941 0.001
 negative regulation of cell proliferation 2.759652 20 4.706 0.002
 cell migration 2.732195 12 2.824 0.002
 insulin receptor signaling pathway 2.724648 8 1.882 0.002
B
 GO-CC Term Enrichment Score Count % P-Value
 cytosol 5.793638 111 26.12 < 0.001
 cytoplasm 4.942099 154 36.24 < 0.001
 nucleoplasm 4.725908 93 21.88 < 0.001
 nucleus 4.05725 154 36.24 < 0.001
 membrane 3.599508 73 17.18 < 0.001
 cytoskeleton 2.478053 18 4.235 0.003
 cell-cell adherens junction 2.302618 16 3.765 0.005
 cis-Golgi network 1.888299 5 1.176 0.013
 cell-cell junction 1.877361 10 2.353 0.013
 Golgi apparatus 1.852153 30 7.059 0.014
 PcG protein complex 1.690927 4 0.941 0.02
 receptor complex 1.672147 8 1.882 0.021
 lamellipodium 1.616858 9 2.118 0.024
 focal adhesion 1.603246 16 3.765 0.025
 perinuclear region of cytoplasm 1.496331 22 5.176 0.032
C     
 GO-MF Term Enrichment Score Count % P-Value
 protein binding 8.364509 260 61.18 < 0.001
 sequence-specific DNA binding 4.118515 28 6.588 < 0.001
 beta-catenin binding 3.946374 10 2.353 < 0.001
 transcription factor activity, sequence-specific DNA binding 3.635935 41 9.647 < 0.001
 platelet-derived growth factor receptor binding 3.50464 5 1.176 < 0.001
 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding 2.912949 15 3.529 0.001
 transcription regulatory region sequence-specific DNA binding 2.667561 7 1.647 0.002
 protein channel activity 2.637341 4 0.941 0.002
 insulin-like growth factor receptor binding 2.344093 4 0.941 0.005
 insulin binding 2.293839 3 0.706 0.005
 neurotrophin TRKA receptor binding 2.124416 3 0.706 0.008
 microtubule binding 2.037592 12 2.824 0.009
 N6-methyladenosine-containing RNA binding 1.984943 3 0.706 0.01
small GTPase binding 1.982255 4 0.941 0.01
 RNA polymerase II core promoter proximal region sequence-specific DNA binding 1.726919 16 3.765 0.019
D
 KEGG pathway Enrichment Score Count % P-Value
 PI3K-Akt signaling pathway 6.144606 25 5.882 < 0.001
 Prostate cancer 5.389517 12 2.824 < 0.001
 Focal adhesion 4.815445 17 4 < 0.001
 Proteoglycans in cancer 4.365137 16 3.765 < 0.001
 Insulin signaling pathway 4.202316 13 3.059 < 0.001
 Signaling pathways regulating pluripotency of stem cells 4.141148 13 3.059 < 0.001
 Adherens junction 3.732503 9 2.118 < 0.001
 Pathways in cancer 3.709619 22 5.176 < 0.001
 FoxO signaling pathway 3.670169 12 2.824 < 0.001
 Acute myeloid leukemia 3.609095 8 1.882 < 0.001
 Thyroid hormone signaling pathway 3.584028 11 2.588 < 0.001
 Choline metabolism in cancer 3.353402 10 2.353 < 0.001
 Glioma 3.20572 8 1.882 < 0.001
 Melanoma 2.973883 8 1.882 0.001
 HIF-1 signaling pathway 2.844366 9 2.118 0.001