DEGs in the FOXD1 knockout renal carcinoma cells
To study the functions of FOXD1 on renal carcinoma cells, we analyzed the RNA-seq data from the GEO database (GSE210145). We identified the 693 significantly changed genes (P < 0.01). The top increased and decreased genes were also indicated by the heatmap (Figure 1). We further presented the top ten significant genes in Table 1.
Gene enrichments in the FOXD1 knockout renal carcinoma cells
To clarify the features of significant genes, we introduced the gene enrichment analysis (Figure 2). The top KEGG was identified, including “PI3K−Akt signaling pathway”, “MAPK signaling pathway”, “Transcriptional misregulation in cancer”, “Proteoglycans in cancer”, “Rap1 signaling pathway”, “TNF signaling pathway”, “NF−kappa B signaling pathway”, “AGE−RAGE signaling pathway in diabetic complications”, “Bladder cancer”, and “Malaria”. The top biological processes (BP) were identified, including “neuron projection extension”, “axon extension”, “response to unfolded protein”, “regulation of axon extension”, “positive regulation of axonogenesis”, “isoprenoid biosynthetic process”, “negative regulation of epidermal growth factor receptor signaling pathway”, “terpenoid biosynthetic process”, “pyrimidine deoxyribonucleotide catabolic process”, and “cellular response to follicle−stimulating hormone stimulus”. The top cellular components (CC) were identified, including “collagen−containing extracellular matrix”, “endoplasmic reticulum lumen”, “microtubule associated complex”, “vacuolar lumen”, “basement membrane”, “sarcoplasmic reticulum”, “inclusion body”, “sarcoplasm”, “chaperone complex”, “interstitial matrix”. The top molecular functions (MF) were identified, including “nuclease activity”, “extracellular matrix structural constituent”, “endonuclease activity, active with either ribo− or deoxyribonucleic acids and producing 5'−phosphomonoesters”, “calcium−release channel activity”, “ligand−gated calcium channel activity”, “intracellular ligand−gated ion channel activity”, “proteoglycan binding”, “C4−dicarboxylate transmembrane transporter activity”, “amino acid:cation symporter activity”, and “DNA−(apurinic or apyrimidinic site) endonuclease activity”.
The protein-protein interaction (PPI) network in the FOXD1 knockout renal carcinoma cells
The PPI network was created by using 576 nodes and 2016 edges. The top ten genes with the highest degree scores were presented in Table 2. We further constructed the top two clusters by analyzing the PPI network in Figure 3. Finally, we constructed the Reactome map by using the PPI network and DEGs (Figure 4) and we performed the Reactome analysis to further identify the top ten Reactome biological processes, including “Collagen formation”, “ATF4 activates genes in response to endoplasmic reticulum stress”, “Transcriptional activation of cell cycle inhibitor p21”, “Transcriptional activation of p53 responsive genes”, “TNF receptor superfamily (TNFSF) members mediating non canonical NF-kB pathway”, “Other interleukin signaling”, “PERK regulates gene expression”, “Extracellular matrix organization”, “Activation of Ca-permeable Kainate Receptor”, and “Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA”.