UNVEILING THERAPEUTIC TARGETS THROUGH PATHWAY ANALYSIS AND IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN ULCERATIVE COLITIS

Yıl 2024, , 890 - 902, 10.09.2024

Omnia Amir Osman Abdelrazig , Fadilah Fadilah , Linda Erlina , Badriul Hegar

https://doi.org/10.33483/jfpau.1439430

Öz

Objective: This study utilizes integrated bioinformatics to investigate Differentially Expressed Genes (DEGs) and pathways related to ulcerative colitis (UC).
Material and Method: Differentially Expressed Genes were identified from UC patients' colonic mucosal samples and controls using GSE13367 and GSE134025 datasets. Differentially Expressed Genes selection utilized GEO2R and Venn diagrams, followed by functional annotation, pathway analysis, PPI determination via the STRING database, and GO/KEGG enrichment analysis using Metascape.
Result and Discussion: Analysis unveiled 197 DEGs, with 76 up-regulated and 121 down-regulated genes. Up-regulated genes were enriched in humoral immune response, peptidoglycan binding, and NADPH oxidase complex, while down-regulated genes were linked to inorganic anion transport, transmitter-gated ion channel activity, and integral plasma membrane components. In the PPI network, up-regulated DEGs formed a dense network (75 nodes, 190 edges), indicating significant interactions, whereas down-regulated DEGs formed a less dense network (114 nodes, 63 edges). Five hub genes (CXCR4, CXCL13, CXCL1, MMP3) were identified among the 197 DEGs. These findings provide new insights into UC's causes and offer promise for more effective therapeutic approaches.

Anahtar Kelimeler

Bioinformatic analysis, gene expression, inflammatory bowel disease, pathway enrichment analysis, protein interactions

Etik Beyan

None

Destekleyen Kurum

None

ÜLSERATİF KOLİTTE YOLAK ANALİZİ VE FARKLI İFADE EDİLEN GENLERİN BELİRLENMESİ YOLUYLA TERAPÖTİK HEDEFLERİN AÇIĞA ÇIKARILMASI

Öz

vAmaç: Bu çalışma, ülseratif kolit (ÜK) ile ilişkili DEG'leri ve yolları araştırmak için entegre biyoinformatik kullanır.
Gereç ve Yöntem: DEG'ler, GSE13367 ve GSE134025 veri kümelerini kullanarak ÜK hastalarının kolonik mukozal örneklerinden ve kontrollerden belirlendi. DEG seçimi için GEO2R ve Venn diyagramları kullanıldı, ardından fonksiyonel anotasyon ve yol analizi yapıldı. Protein-protein etkileşimleri (PPI'ler) STRING veritabanı kullanılarak belirlendi ve Metascape, Gen Ontolojisi (GO) ve Kyoto Genler ve Genomlar Ansiklopedisi (KEGG) zenginleştirme analizi için kullanıldı.
Sonuç ve Tartışma: Analiz, 197 DEG ortaya koydu, bunların 76'sı yukarı regüle edilmiş ve 121'i aşağı regüle edilmiş genlerdi. Yukarı regüle edilmiş genler, humoral immün yanıt, peptidoglikan bağlanma ve NADPH oksidaz kompleksi gibi süreçlerde zenginleşmişti. Aşağı regüle edilmiş genler, inorganik anyon taşıma, alıcı-gated iyon kanal aktivitesi ve integral plazma membran bileşenleri ile ilişkilendirildi. PPI ağındaki yukarı regüle edilmiş DEG'ler, 75 düğüm ve 190 kenarla yoğun bir ağ oluşturdu, önemli etkileşimleri gösterirken, aşağı regüle edilmiş DEG'ler, 114 düğüm ve 63 kenarla daha az yoğun bir ağ oluşturdu. 197 DEG arasında beş merkezi gen (CXCR4, CXCL13, CXCL1, MMP3) tanımlandı. Bu bulgular, ÜK'nin nedenleri hakkında yeni içgörüler sunmakta ve daha etkili tedavi yaklaşımları için umut vaat etmektedir.

Anahtar Kelimeler

Biyoinformatik analizi, gen ifadesi, inflamatuar bağırsak hastalığı, yol zenginleştirme analizi, protein etkileşimleri

Kaynakça

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