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Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma

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资源类型：
Pubmed体系：
作者：
El-Kafrawy Sherif A[1,2] * ; El-Daly Mai M[1,2] ; Bajrai Leena H[1,3] ; Alandijany Thamir A[1,2] ; Faizo Arwa A[1,2] ; Mobashir Mohammad[4,5] ; Ahmed Sunbul S[5] ; Ahmed Sarfraz[6] ; Alam Shoaib[7] ; Jeet Raja[8] ; Kamal Mohammad Amjad[9,10,11,12,13] ; Anwer Syed Tauqeer[5] ; Khan Bushra[5] ; Tashkandi Manal[14] ; Rizvi Moshahid A[5] ; Azhar Esam Ibraheem[1,2] ;
机构： [1]Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia. [2]Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. [3]Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. [4]Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden. [5]Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India. [6]Department of Biosciences, Jamia Millia Islamia, New Delhi, India. [7]Department of Biotechnology, Jamia Millia Islamia, New Delhi, India. [8]Botany Department, Ganesh Dutt College, Begusarai, Bihar, India. [9]Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China. [10]King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia. [11]Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh. [12]Enzymoics, Hebersham, NSW, Australia. [13]Novel Global Community Educational Foundation, Hebersham, NSW, Australia. [14]Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
出处：
DOI： 10.3389/fgene.2022.880440
ISSN：

关键词： HCV and HCC biomarkers gene expression/mutational profiling co-expression network-level understanding

摘要：
Data integration with phenotypes such as gene expression, pathways or function, and protein-protein interactions data has proven to be a highly promising technique for improving human complex diseases, particularly cancer patient outcome prediction. Hepatocellular carcinoma is one of the most prevalent cancers, and the most common cause is chronic HBV and HCV infection, which is linked to the majority of cases, and HBV and HCV play a role in multistep carcinogenesis progression. We examined the list of known hepatocellular carcinoma biomarkers with the publicly available expression profile dataset of hepatocellular carcinoma infected with HCV from day 1 to day 10 in this study. The study covers an overexpression pattern for the selected biomarkers in clinical hepatocellular carcinoma patients, a combined investigation of these biomarkers with the gathered temporal dataset, temporal expression profiling changes, and temporal pathway enrichment following HCV infection. Following a temporal analysis, it was discovered that the early stages of HCV infection tend to be more harmful in terms of expression shifting patterns, and that there is no significant change after that, followed by a set of genes that are consistently altered. PI3K, cAMP, TGF, TNF, Rap1, NF-kB, Apoptosis, Longevity regulating pathway, signaling pathways regulating pluripotency of stem cells, Cytokine-cytokine receptor interaction, p53 signaling, Wnt signaling, Toll-like receptor signaling, and Hippo signaling pathways are just a few of the most commonly enriched pathways. The majority of these pathways are well-known for their roles in the immune system, infection and inflammation, and human illnesses like cancer. We also find that ADCY8, MYC, PTK2, CTNNB1, TP53, RB1, PRKCA, TCF7L2, PAK1, ITPR2, CYP3A4, UGT1A6, GCK, and FGFR2/3 appear to be among the prominent genes based on the networks of genes and pathways based on the copy number alterations, mutations, and structural variants study.Copyright © 2022 El-Kafrawy, El-Daly, Bajrai, Alandijany, Faizo, Mobashir, Ahmed, Ahmed, Alam, Jeet, Kamal, Anwer, Khan, Tashkandi, Rizvi and Azhar.

基金：
Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, Saudi Arabia, grant number FP-5-42 and The APC was funded by FP-5-42
语种：
外文
PubmedID：
中科院(CAS)分区：
出版当年[2022]版：
大类 | 3 区 生物学
小类 | 3 区 遗传学
最新[2023]版：
大类 | 3 区 生物学
小类 | 3 区 遗传学
第一作者：
第一作者机构： [1]Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia. [2]Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
通讯作者：
通讯机构： [1]Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia. [2]Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. [4]Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden. [5]Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India.
推荐引用方式(GB/T 7714)：
El-Kafrawy Sherif A,El-Daly Mai M,Bajrai Leena H,et al.Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma[J].Frontiers in genetics.2022,13:880440.doi:10.3389/fgene.2022.880440.
APA：
El-Kafrawy Sherif A,El-Daly Mai M,Bajrai Leena H,Alandijany Thamir A,Faizo Arwa A...&Azhar Esam Ibraheem.(2022).Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma.Frontiers in genetics,13,
MLA：
El-Kafrawy Sherif A,et al."Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma".Frontiers in genetics 13.(2022):880440

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