Step by step analysis on gene datasets of growth phases in hematopoietic stem cells

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Biochemistry and Biophysics Reports Pub Date : 2024-05-30 DOI:10.1016/j.bbrep.2024.101737

Mohammad Elahimanesh , Nafiseh Shokri , Payam Mohammadi , Najmeh Parvaz , Mohammad Najafi

{"title":"Step by step analysis on gene datasets of growth phases in hematopoietic stem cells","authors":"Mohammad Elahimanesh , Nafiseh Shokri , Payam Mohammadi , Najmeh Parvaz , Mohammad Najafi","doi":"10.1016/j.bbrep.2024.101737","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p>Umbilical cord blood hematopoietic stem cells (UCB–HSCs) have important roles in the treatment of illnesses based on their self-renewal and potency characteristics. Knowing the gene profiles and signaling pathways involved in each step of the cell cycle could improve the therapeutic approaches of HSCs. The aim of this study was to predict the gene profiles and signaling pathways involved in the G0, G1, and differentiation stages of HSCs.</p></div><div><h3>Methods</h3><p>Interventional (n = 8) and non-interventional (n = 3) datasets were obtained from the Gene Expression Omnibus (GEO) database, and were crossed and analyzed to determine the high- and low-express genes related to each of the G0, G1, and differentiation stages of HSCs. Then, the scores of STRING were annotated to the gene data. The gene networks were constructed using Cytoscape software, and enriched with the KEGG and GO databases.</p></div><div><h3>Results</h3><p>The high- and low-express genes were determined due to inter and intra intersections of the interventional and non-interventional data. The non-interventional data were applied to construct the gene networks (n = 6) with the nodes improved using the interventional data. Several important signaling pathways were suggested in each of the G0, G1, and differentiation stages.</p></div><div><h3>Conclusion</h3><p>The data revealed that the different signaling pathways are activated in each of the G0, G1, and differentiation stages so that their genes may be targeted to improve the HSC therapy.</p></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":null,"pages":null},"PeriodicalIF":2.3000,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405580824001018/pdfft?md5=4627663494f5a076a2928c939c99b7b8&pid=1-s2.0-S2405580824001018-main.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemistry and Biophysics Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2405580824001018","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background

Umbilical cord blood hematopoietic stem cells (UCB–HSCs) have important roles in the treatment of illnesses based on their self-renewal and potency characteristics. Knowing the gene profiles and signaling pathways involved in each step of the cell cycle could improve the therapeutic approaches of HSCs. The aim of this study was to predict the gene profiles and signaling pathways involved in the G0, G1, and differentiation stages of HSCs.

Methods

Interventional (n = 8) and non-interventional (n = 3) datasets were obtained from the Gene Expression Omnibus (GEO) database, and were crossed and analyzed to determine the high- and low-express genes related to each of the G0, G1, and differentiation stages of HSCs. Then, the scores of STRING were annotated to the gene data. The gene networks were constructed using Cytoscape software, and enriched with the KEGG and GO databases.

Results

The high- and low-express genes were determined due to inter and intra intersections of the interventional and non-interventional data. The non-interventional data were applied to construct the gene networks (n = 6) with the nodes improved using the interventional data. Several important signaling pathways were suggested in each of the G0, G1, and differentiation stages.

Conclusion

The data revealed that the different signaling pathways are activated in each of the G0, G1, and differentiation stages so that their genes may be targeted to improve the HSC therapy.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

逐步分析造血干细胞生长阶段的基因数据集

背景非脐带血造血干细胞（UCB-HSCs）具有自我更新和效力的特点，在治疗疾病方面发挥着重要作用。了解细胞周期每一步所涉及的基因谱和信号通路可改进造血干细胞的治疗方法。本研究的目的是预测造血干细胞G0、G1和分化阶段所涉及的基因谱和信号通路。方法从基因表达总库（GEO）数据库中获取干预性（n = 8）和非干预性（n = 3）数据集，并对其进行交叉分析，以确定与造血干细胞G0、G1和分化阶段相关的高表达基因和低表达基因。然后，将 STRING 的评分注释到基因数据中。结果高表达基因和低表达基因是根据介入数据和非介入数据的交叉和内交叉确定的。利用非干预数据构建了基因网络（n = 6），并利用干预数据改进了节点。结论这些数据揭示了不同的信号通路在 G0、G1 和分化阶段被激活，因此可以针对这些通路的基因改进造血干细胞的治疗。

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

Biochemistry and Biophysics Reports Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

4.60

自引率

0.00%

发文量

191

审稿时长

59 days

期刊介绍： Open access, online only, peer-reviewed international journal in the Life Sciences, established in 2014 Biochemistry and Biophysics Reports (BB Reports) publishes original research in all aspects of Biochemistry, Biophysics and related areas like Molecular and Cell Biology. BB Reports welcomes solid though more preliminary, descriptive and small scale results if they have the potential to stimulate and/or contribute to future research, leading to new insights or hypothesis. Primary criteria for acceptance is that the work is original, scientifically and technically sound and provides valuable knowledge to life sciences research. We strongly believe all results deserve to be published and documented for the advancement of science. BB Reports specifically appreciates receiving reports on: Negative results, Replication studies, Reanalysis of previous datasets.