Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach.

IF 1.3 4区 生物学 Q3 BIOLOGY Theory in Biosciences Pub Date : 2024-09-01 Epub Date: 2024-05-28 DOI:10.1007/s12064-024-00418-3
T Mallikarjuna, N B Thummadi, Vaibhav Vindal, P Manimaran
{"title":"Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach.","authors":"T Mallikarjuna, N B Thummadi, Vaibhav Vindal, P Manimaran","doi":"10.1007/s12064-024-00418-3","DOIUrl":null,"url":null,"abstract":"<p><p>Cervical cancer is one of the most severe threats to women worldwide and holds fourth rank in lethality. It is estimated that 604, 127 cervical cancer cases have been reported in 2020 globally. With advancements in high throughput technologies and bioinformatics, several cervical candidate genes have been proposed for better therapeutic strategies. In this paper, we intend to prioritize the candidate genes that are involved in cervical cancer progression through a fractal time series-based cross-correlations approach. we apply the chaos game representation theory combining a two-dimensional multifractal detrended cross-correlations approach among the known and candidate genes involved in cervical cancer progression to prioritize the candidate genes. We obtained 16 candidate genes that showed cross-correlation with known cancer genes. Functional enrichment analysis of the candidate genes shows that they involve GO terms: biological processes, cell-cell junction assembly, cell-cell junction organization, regulation of cell shape, cortical actin cytoskeleton organization, and actomyosin structure organization. KEGG pathway analysis revealed genes' role in Rap1 signaling pathway, ErbB signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, mTOR signaling pathway, Acute myeloid leukemia, chronic myeloid leukemia, Breast cancer, Thyroid cancer, Bladder cancer, and Gastric cancer. Further, we performed survival analysis and prioritized six genes CDH2, PAIP1, BRAF, EPB41L3, OSMR, and RUNX1 as potential candidate genes for cervical cancer that has a crucial role in tumor progression. We found that our study through this integrative approach an efficient tool and paved a new way to prioritize the candidate genes and these genes could be evaluated experimentally for potential validation. We suggest this may be useful in analyzing the nucleotide sequences and protein sequences for clustering, classification, class affiliation, etc.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.3000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Theory in Biosciences","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s12064-024-00418-3","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/5/28 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Cervical cancer is one of the most severe threats to women worldwide and holds fourth rank in lethality. It is estimated that 604, 127 cervical cancer cases have been reported in 2020 globally. With advancements in high throughput technologies and bioinformatics, several cervical candidate genes have been proposed for better therapeutic strategies. In this paper, we intend to prioritize the candidate genes that are involved in cervical cancer progression through a fractal time series-based cross-correlations approach. we apply the chaos game representation theory combining a two-dimensional multifractal detrended cross-correlations approach among the known and candidate genes involved in cervical cancer progression to prioritize the candidate genes. We obtained 16 candidate genes that showed cross-correlation with known cancer genes. Functional enrichment analysis of the candidate genes shows that they involve GO terms: biological processes, cell-cell junction assembly, cell-cell junction organization, regulation of cell shape, cortical actin cytoskeleton organization, and actomyosin structure organization. KEGG pathway analysis revealed genes' role in Rap1 signaling pathway, ErbB signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, mTOR signaling pathway, Acute myeloid leukemia, chronic myeloid leukemia, Breast cancer, Thyroid cancer, Bladder cancer, and Gastric cancer. Further, we performed survival analysis and prioritized six genes CDH2, PAIP1, BRAF, EPB41L3, OSMR, and RUNX1 as potential candidate genes for cervical cancer that has a crucial role in tumor progression. We found that our study through this integrative approach an efficient tool and paved a new way to prioritize the candidate genes and these genes could be evaluated experimentally for potential validation. We suggest this may be useful in analyzing the nucleotide sequences and protein sequences for clustering, classification, class affiliation, etc.

Abstract Image

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
利用混沌博弈和基于分形的时间序列方法确定宫颈癌候选基因的优先顺序
宫颈癌是全球妇女面临的最严重威胁之一,致死率排名第四。据估计,2020 年全球将报告 604 127 例宫颈癌病例。随着高通量技术和生物信息学的发展,人们提出了一些宫颈癌候选基因,以寻求更好的治疗策略。在本文中,我们打算通过基于分形时间序列的交叉相关方法,对参与宫颈癌进展的候选基因进行优先排序。我们应用混沌博弈表示理论,结合二维多分形去趋势交叉相关方法,对参与宫颈癌进展的已知基因和候选基因进行优先排序。我们获得了 16 个与已知癌基因存在交叉相关性的候选基因。候选基因的功能富集分析表明,它们涉及的GO术语包括:生物过程、细胞-细胞连接组装、细胞-细胞连接组织、细胞形状调控、皮质肌动蛋白细胞骨架组织和肌动蛋白结构组织。KEGG 通路分析显示,基因在 Rap1 信号通路、ErbB 信号通路、MAPK 信号通路、PI3K-Akt 信号通路、mTOR 信号通路、急性髓性白血病、慢性髓性白血病、乳腺癌、甲状腺癌、膀胱癌和胃癌中发挥作用。此外,我们还进行了生存分析,并优先选择了 CDH2、PAIP1、BRAF、EPB41L3、OSMR 和 RUNX1 这六个基因作为宫颈癌的潜在候选基因,这些基因在肿瘤进展中起着至关重要的作用。我们发现,通过这种综合方法,我们的研究成为了一种有效的工具,并为确定候选基因的优先顺序铺平了一条新路。我们认为这可能有助于分析核苷酸序列和蛋白质序列,以进行聚类、分类、隶属类等。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Theory in Biosciences
Theory in Biosciences 生物-生物学
CiteScore
2.70
自引率
9.10%
发文量
21
审稿时长
3 months
期刊介绍: Theory in Biosciences focuses on new concepts in theoretical biology. It also includes analytical and modelling approaches as well as philosophical and historical issues. Central topics are: Artificial Life; Bioinformatics with a focus on novel methods, phenomena, and interpretations; Bioinspired Modeling; Complexity, Robustness, and Resilience; Embodied Cognition; Evolutionary Biology; Evo-Devo; Game Theoretic Modeling; Genetics; History of Biology; Language Evolution; Mathematical Biology; Origin of Life; Philosophy of Biology; Population Biology; Systems Biology; Theoretical Ecology; Theoretical Molecular Biology; Theoretical Neuroscience & Cognition.
期刊最新文献
Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock. Do concepts of individuality account for individuation practices in studies of host–parasite systems? A modeling account of biological individuality Spaces of mathematical chemistry Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach. Application of network pharmacology in synergistic action of Chinese herbal compounds.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1