## 4 Discussion  
### Gene Expression Modules and Pathway Analysis across the Datasets  
ccRCC is the most common type of renal cancer. It progresses rapidly and often metastasizes to other parts of the body. This makes the prognosis difficult to determine [31,32]. Most cases of ccRCC are generally diagnosed in their later stages, so standard treatments are less effective; this is why new diagnostic methods are needed and being developed [32,33]. To address these problems, the present study carried out WGCNA analysis on samples of ccRCC from S1 to S4. This research used the S1 dataset to study the molecular and genetic characteristics of ccRCC and identify the key genes and pathways present from S1 to S4. Following this, the identified targets were analyzed to know if they may serve as potential biomarkers or targets for ccRCC. The KEGG pathway analysis of highly preserved gene modules (Table 11) suggests that these modules are linked to inflammatory pathways that may drive tumor development (Figure 9).  
The analysis of S1 and S4 datasets revealed that specific pathways are present at certain stages of ccRCC (Figure 10). In S1, the HIF-1, TGF-\(\beta\), and PI3K-Akt pathways suggest early tumor adaptation. HIF-1, mediated by the oxygen-sensitive HIF-1\(\alpha\) and HIF-1\(\beta\), helps cancer cells adapt to low oxygen. It is also linked with inflammation since it can regulate inflammatory components [34,35], thus promoting tumor development in ccRCC [36,37]. Enhanced TGF-\(\beta\) signaling can foster a proinflammatory microenvironment [14,38,39,40], reducing the effectiveness of anti-cancer therapies [41]. The PI3 KT-Akt pathway has been known to stimulate inflammation processes and interact with other inflammatory pathways [42], which also accelerates tumor progression [43,44,45,46] and chemotherapy resistance [47]. The Ras and MAPK pathways were found to be present in S2 tumors, which may indicate heightened aggression and immune response in ccRCC [35,36,37,38]. Dysregulated RAS promotes inflammatory cytokine secretion [48,49], influencing ccRCC. The dysregulated MAPK pathway in ccRCC [43,50] leads to the release of cytokines such as IL-6, IL-8, and TNF-\(\alpha\)[44,45,50].  
Hippo signaling was detected in S3. Hippo signaling shows an inverse correlation with the proliferation and invasion of tumors [46,51,52]. Abnormal Hippo can increase cytokine production and activate other cancer pathways like JAK-STAT [47,51,53]. In S4, the NF-\(\kappa\)B pathway and viral carcinogenesis are present. The NF-\(\kappa\)B activated by IL-1 and TNF\(\alpha\) connects inflammation with tumorigenesis [54,55,56]. NF-\(\kappa\)B drives HIF-1\(\alpha\)[57,58]. Hippo, MAPK, PI3K-AKT, and NF-\(\kappa\)B pathways interact with each other, supporting inflammatory signals, cancer cell growth, and therapy resistance [44,47,59,60]. Additionally, viral infections like HPV and CMV associated with inflammation may significantly affect cancer treatment and growth [42,61,62,63]. The findings suggest that these pathways are involved in ccRCC S1-S4, indicating their role as drivers of ccRCC development.  
Figure 9: Signaling pathways associated with inflammation in ccRCC.  
The S1 dataset as a reference set helps track genes and pathways that may be present from S1 to S4. This may facilitate the identification of potential targets associated with ccRCC. The blue, brown, and red co-expression modules were preserved across datasets. Functional annotation linked these modules to inflammation-driven cancer pathways (Tables A3-A5. Studying pathways present at different/certain stages of ccRCC may provide additional knowledge regarding ccRCC, which can help identify potential targets for specific stages of the disease.