## 3 Results and Discussion
To ensure the reliability of our analysis, we had to tackle batch effects that could have resulted in biased or incorrect results when simply consolidating these studies. Without the proper integration of scRNA-seq data, we may have observed a spurious separation between [PERSON] and normal cells, leading to the incorrect identification of dominant genes that may have only been relevant due to the batch effects. However, by performing an accurate deep learning-based integration of the data using the cutting-edge SCALEX tool, we were able to enhance the reliability of our findings and extract valuable biological insights. In addition, our feature selection approach integrated three different machine learning-based strategies to capture the dynamics of gene selection. This integration resulted in a more robust outcome by identifying genes that were dominant from multiple computational perspectives. Moreover, our ranking score, which was based on the Borda count, provided a fair prioritization of the top genes that could distinguish between [PERSON]'s disease and a healthy state. Our in silico pipeline, combined with a thorough biological interpretation, yielded reliable transcriptional biomarkers for AD. However, further in vitro and in vivo validation of these findings is necessary. We conducted an enrichment analysis using Enrichr [24; 25] to explore the high-level functions and utilities of the biological system according to the exported genes. The GO function and Reactome [26] pathway enrichment analyses were performed for most of the provided DEGs (Tables S1-S4). Reactome pathway analysis showed that DEGs were mainly enriched in pathways such as the adaptive and innate immune system, the translocation of the immunological synapse, and PD-1 signaling and neutrophil degranulation were also provided (Figure 3A). The enriched GO terms were divided into the biological process (BP), molecular functions (MF), and cellular component (CC) ontologies. The results of the GO analysis revealed that DEGs were mainly enriched in BP, including the regulation of the immune system, interferone-gamma-mediated signaling, antigen processing, the cellular defense response, and the positive regulation of T cell-mediated immunity (Figure 3B). MF analysis indicated that the DEGs were significantly enriched in MHC class II receptor activity, MHC class II protein complex binding, serine-type peptidase activity, ferric ion binding, superoxide-generating NADPH oxidase activator activity, Tat protein binding and serine-type endopeptidase activity (Figure 3C). For CC, the DEGs were enriched in an MHC and MHC class II protein complex with the luminal side of the endoplasmic reticulum membrane, the integral component of the luminal side of the endoplasmic reticulum membrane and endoplasmatic reticulum for the Golgi transport vesicle membrane (Figure 3D). More precisely, based on our analysis, _EFhd2_ encodes a conserved calcium-binding protein that is highly involved in neurodegeneration. It is widely expressed in the brain and central nervous system with cell-type specific functions, including microtubule transport, and is more abundant in cortical neurons [27]. [PERSON] and [PERSON] found that the down-regulation of the protein could enhance synaptic delivery through kinesin-mediated transport and regulate synaptic plasticity through F-actin binding and Cdc42, Rac and Rho activity [28]. Previous studies identified how EFhd2 interacts with pathologically aggregated tau protein and accomplishes the formation of an amyloid structure [29], while recently, it was reported that EFhd2 in mice interact with several intracellular components such as vesicle trafficking modulators, cellular stress response-regulating proteins, and metabolic proteins [30]. Pathway enrichment analysis showed that a _EFhd2_ was enriched in the RHO GTPase cycle and signaling by Rho GTases and Miro GTPases (Table S5), which are involved in the regulation of cell migration, neuronal development and mitochondrial distribution with neuronal activity [31; 32].