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Gene & Protein in Disease Bioinformatics to identify gene signatures of CF

cells from control versus treated CF patient samples 2.5. Selection of hub proteins from the PPI network
based on the program of GPL570 (Affymetrix Human Cytoscape (http://www.cytoscape.org/) was used to
Genome U133 Plus 2.0 Array [HG-U133_Plus_ ), which visualize the derived PPI networks. The molecular
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37
was handled by the National Center for Biotechnology complex detection (MCODE) plug-in for Cytoscape was
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Information (NCBI) (https://www.ncbi.nlm.nih.gov/) employed to identify noteworthy modules that possessed
in 2022, was assembled from the GEO database (https:// an established score of higher than three and nodes with a
www.ncbi.nlm.nih.gov/geo/). The GSE70442 dataset
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encompasses eight samples in total. The GSM1754933, larger than four. High-degree nodes were regarded as hub
GSM1754934, GSM1754935, and GSM1754936 were used genes in the PPI network, where nodes’ degree value was
as control bronchial epithelial cells, while the GSM1754937, determined by the number of edges that they included.
GSM1754938, GSM1754939, and GSM1754939 were used The PPI information of the hub genes was measured by
as treated bronchial epithelial cells (treated at 27°C). mapping them. Hub genes from the built PPI network
were assessed using cytoHubba, a Cytoscape plugin. The
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2.2. Identification of DEGs degree score was utilized in this research to discover hub
The statistical program GEO2R (http://www.ncbi.nlm.nih. genes using the cytoHubba program, which calculates hub
gov/geo/geo2r/) was used to verify whether genes showed genes from the PPI network using 11 distinct approaches.
differential expression based on the comparison between 3. Results
control and treated cells of CF. The false discovery rate
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by Benjamini and Hochberg and t-test procedures were 3.1. DEG identification
applied with the GEO2R program to determine the DEGs The GSE70442 dataset comprises eight samples obtained
and compute the FDR and P-values. For the DEGs, we from four CF patients, including four samples maintained
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deemed a P < 0.05 and a logFC >1 (important fold changes) at 37°C as controls and four samples maintained at 27°C as
to be statistically significant. We created a volcano plot treated samples (Table 1). We used GEO2R to determine
based on all the identified DEGs using the R language’s the DEGs from the patients and control groups and to
pheatmap package. To identify the most significant DEGs, obtain the log2FC and P-values. DEGs were defined as
a P < 0.05 was employed as the cutoff value. LogFC ≥1 the resultant genes that satisfied the threshold values,
and logFC ≤−1 were deemed to represent upregulated which were logFC ≥ 1, logFC ≤ −1, and P < 0.05. With
and downregulated DEGs, respectively. 26-28 Afterward, the the help of the GEO2R tool, a total of 4229 genes from the
DEG dataset was gathered and used for further analysis. GEO dataset were found. Using RStudio’s Shiny Volcano
2.3. Functional enrichment of gene sets Plot, we created a volcano plot to compare the patients
and control groups (Figure 2). Subsequently, 211 DEGs
Using DAVID v6.8 (https://david.ncifcrf.gov/), an online
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bioinformatics tool, the first gene ontology (GO) and KEGG Table 1. Essential information of GSE70442 dataset obtained
pathway enhancement assessments of the DEGs were from the GEO database
performed (P < 0.05). The NetworkAnalyst online tool 30
was used to crosscheck the enriched DEGs. The functional Group Accession Organism Disease state Cell Type
experiment is presently a widely utilized technique for Control GSM1754933 Homo sapiens Cystic fibrosis Bronchial
analyzing gene expression function based on the genomic epithelial cells
data collected. 31,32 To comprehend metabolic pathways, the GSM1754934 Homo sapiens Cystic fibrosis Bronchial
Kyoto Encyclopedia of Genes and Genomes (KEGG) was epithelial cells
employed for analyzing functional genomics, 33,34 using Zhang GSM1754935 Homo sapiens Cystic fibrosis Bronchial
et al.’s ontological concepts as the foundation for the analysis. 35 epithelial cells
GSM1754936 Homo sapiens Cystic fibrosis Bronchial
2.4. Network construction through protein–protein epithelial cells
interaction Treated GSM1754937 Homo sapiens Cystic fibrosis Bronchial
With the help of the STRING (v11.0, http://www. epithelial cells
string-db.org/), the protein–protein interaction (PPI) GSM1754938 Homo sapiens Cystic fibrosis Bronchial
network of DEG-encoded proteins was built. STRING is epithelial cells
an extensive online archive containing 24,584,628 proteins GSM1754939 Homo sapiens Cystic fibrosis Bronchial
from 5090 species, specifically designed to predict gene epithelial cells
connections. To be deemed significant, the total score has GSM1754940 Homo sapiens Cystic fibrosis Bronchial
36
to be less than 0.75 (medium confidence level). epithelial cells

Volume 3 Issue 2 (2024) 3 doi: 10.36922/gpd.2937