Identification of DEGs in endometrial adenocarcinoma cells (Ishikawa cells) after the knockdown of LINC00958
To determine the effects of the knockdown of LINC00958 in Ishikawa cells, we analyzed the RNA-seq data from the GEO database. A total of 981 genes were identified with a threshold of P < 0.001. The top up- and down-regulated genes were shown by the heatmap and volcano plot (Figure 1). The top ten DEGs were listed in Table 1.
Enrichment analyses of DEGs in Ishikawa cells after the knockdown of LINC00958
To further identify the potential signaling pathways after the knockdown of LINC00958 in Ishikawa cells, we performed the KEGG and GO analyses (Figure 2). We identified the top ten KEGG items including “Human T−cell leukemia virus 1 infection”, “Hippo signaling pathway”, “Thyroid hormone signaling pathway”, “Viral life cycle − HIV−1”, “Renal cell carcinoma”, “Glycerophospholipid metabolism”, “PPAR signaling pathway”, “Fatty acid metabolism”, “Mannose type O−glycan biosynthesis”, and “Galactose metabolism”. We identified the top ten biological processes of GO including “positive regulation of cell cycle”, “mitotic nuclear division”, “positive regulation of cell cycle process”, “Golgi organization”, “spindle organization”, “vesicle budding from membrane”, “regulation of ubiquitin−protein transferase activity”, “organelle inheritance”, “Golgi inheritance”, and “Golgi vesicle budding”. We identified the top ten cellular components of GO, including “cell−cell junction”, “spindle”, “ubiquitin ligase complex”, “mitotic spindle”, “trans−Golgi network”, “midbody”, “cullin−RING ubiquitin ligase complex”, “microtubule associated complex”, “cell division site”, and “cleavage furrow”. We identified the top ten molecular functions of GO, including “molecular adaptor activity”, “protein−macromolecule adaptor activity”, “protein serine kinase activity”, “phosphatase regulator activity”, “protein phosphatase regulator activity”, “phosphatase inhibitor activity”, “ubiquitin ligase−substrate adaptor activity”, “core promoter sequence−specific DNA binding”, “steroid hormone receptor activity”, and “cAMP response element binding”.
PPI network and Reactome analyses
To explore the potential associations among the DEGs, we created the PPI network by using 711 nodes and 1669 edges. The combined score > 0.2 was set as a cutoff by using the Cytoscape software. Table 2 indicated the top ten genes with the highest scores. The top two significant modules were presented in Figure 3. We further analyzed the PPI and DEGs with a Reactome map (Figure 4) and figured out the top ten biological processes including "Estrogen-dependent nuclear events downstream of ESR-membrane signaling", "Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1", "Regulation of cholesterol biosynthesis by SREBP (SREBF)", "Defective HDR through Homologous Recombination (HRR) due to PALB2 loss of function", "Defective HDR through Homologous Recombination (HRR) due to BRCA1 loss-of-function", "Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function", "Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function", "Diseases of DNA Double-Strand Break Repair", and "Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)" (Supplemental Table S1).