Table I.
GO and KEGG pathway enrichment analysis for genes in the lncRNA-mRNA co-expression network.
| A, GO terms enriched in the lncRNA-mRNA co-expression network | |||
|---|---|---|---|
| Description (ID, name) | Count | FDR | Genes |
| GO:0001501, skeletal system development | 14 | 0.000067700 | RBP4, AEBP1, LGALS3, TUFT1, KLF10, PRELP, MEN1, MEF2D, SBDS, LECT1, TNFSF11, COL1A2, ACAN, PKD1 |
| GO:0009612, response to mechanical stimulus | 5 | 0.003660942 | FOS, BTG2, JUN, PKD1, GFI1 |
| GO:0007179, transforming growth factor beta receptor signaling pathway | 5 | 0.004694322 | FOS, LTBP2, KLF10, JUN, COL1A2 |
| GO:0040008, regulation of growth | 11 | 0.005411270 | MEN1, EPC1, RBP4, HTRA1, LGMN, BCAR1, NOL8, SIPA1, PEX5, GREM1, GAS6 |
| GO:0001503, ossification | 6 | 0.009830659 | MEN1, MEF2D, SBDS, TNFSF11, TUFT1, KLF10 |
| GO:0060348, bone development | 6 | 0.012887071 | MEN1, MEF2D, SBDS, TNFSF11, TUFT1, KLF10 |
| GO:0006357, regulation of transcription from RNA polymerase II promoter | 16 | 0.017700242 | JDP2, EGR2, KLF9, KLF10, FOXO1, NFYC, MEN1, PLAGL1, FOS, EPC1, SMARCD3, JUN, GFI1, LCOR, KLF4, NR1H3 |
| GO:0045893, positive regulation of transcription, DNA-dependent | 12 | 0.019627483 | PLAGL1, MEN1, FOS, EPC1, EGR2, SMARCD3, JUN, FOXF1, NFYC, FOXO1, KLF4, NR1H3 |
| GO:0051254, positive regulation of RNA metabolic process | 12 | 0.020731482 | PLAGL1, MEN1, FOS, EPC1, EGR2, SMARCD3, JUN, FOXF1, NFYC, FOXO1, KLF4, NR1H3 |
| GO:0009628, response to abiotic stimulus | 10 | 0.024048392 | MEN1, FOS, RBP4, TNFSF11, BTG2, HMGCR, JUN, PKD1, GFI1, GRK1 |
| GO:0007178, transmembrane receptor protein serine/threonine kinase signaling pathway | 5 | 0.029381231 | FOS, LTBP2, KLF10, JUN, COL1A2 |
| GO:0030198, extracellular matrix organization | 5 | 0.030296507 | LGALS3, LUM, FOXF1, COL1A2, ACAN |
| GO:0007611, learning or memory | 5 | 0.037173540 | FOS, SBDS, EGR2, HMGCR, JUN |
| GO:0010605, negative regulation of macromolecule metabolic process | 15 | 0.038521124 | JDP2, KLF10, CDC26, SIGIRR, TIMP1, MEN1, EPC1, SET, JUN, SERPINA5, BNIP3L, GFI1, LCOR, KLF4, ADAR |
| GO:0051094, positive regulation of developmental process | 8 | 0.038680685 | MEN1, TNFSF11, KLF10, JUN, CLU, GFI1, OTP, ANGPTL4 |
| GO:0042592, homeostatic process | 15 | 0.045211148 | CLNS1A, RBP4, EGR2, NCDN, MBP, TIMP1, MEN1, TNFSF11, PRDX6, JUN, SERPINA3, TXNRD1, XCR1, QSOX1, CLN5 |
| GO:0045597, positive regulation of cell differentiation | 7 | 0.045820821 | MEN1, TNFSF11, KLF10, JUN, CLU, GFI1, OTP |
| B, KEGG pathways enriched in the lncRNA-mRNA co-expression network | |||
| Description (entry, name) | Count | FDR | Genes |
| hsa04142, Lysosome | 4 | 0.014272775 | CLTA, LGMN, CLN5, CTSF |
| hsa04670, Leukocyte transendothelial migration | 4 | 0.014534463 | BCAR1, SIPA1, CD99, ITGAM |
| hsa03320, PPAR signaling pathway | 3 | 0.018064527 | FADS2, ANGPTL4, NR1H3 |
| hsa04510, Focal adhesion | 5 | 0.018720786 | PARVG, PPP1CA, JUN, BCAR1, COL1A2 |
| hsa04640, Hematopoietic cell lineage | 3 | 0.025076738 | CD1B, CSF3R, ITGAM |
| hsa03020, RNA polymerase | 2 | 0.027129221 | POLR2C, POLR2J2 |
| hsa00240, Pyrimidine metabolism | 3 | 0.028840787 | TXNRD1, POLR2C, POLR2J2 |
| hsa00051, Fructose and mannose metabolism | 2 | 0.031922905 | PFKFB2, AKR1B1 |
| hsa04810, Regulation of actin cytoskeleton | 4 | 0.043576076 | PPP1CA, BCAR1, FGF13, ITGAM |
| hsa04514, Cell adhesion molecules (CAMs) | 3 | 0.043833628 | CD99, SELPLG, ITGAM |
GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; lncRNA, long noncoding RNA; count, number of genes enriched in the GO terms or pathways; FDR, false discovery rate.