Identification and characteristic analysis of enhancers across 13 major cancer types.

IF 0.8 Q3 PSYCHOLOGY, MULTIDISCIPLINARY

Pastoral Psychology Pub Date : 2021-08-02 eCollection Date: 2021-09-01 DOI:10.1093/pcmedi/pbab019

Mingming Qian, Wenzhu Wang, Yana Zhang, Yi Zhao, Huige Quan, Yuting Chen, Xinyue Dai, Zhiyun Guo

{"title":"Identification and characteristic analysis of enhancers across 13 major cancer types.","authors":"Mingming Qian, Wenzhu Wang, Yana Zhang, Yi Zhao, Huige Quan, Yuting Chen, Xinyue Dai, Zhiyun Guo","doi":"10.1093/pcmedi/pbab019","DOIUrl":null,"url":null,"abstract":"Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed (DE) enhancers. Furthermore, a total of 1036 DE genes regulated by DE enhancers were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 single nucleotide polymorphisms (SNPs) were located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites of 758 transcription factors, which were shown to be highly correlated with tumorigenesis and development.","PeriodicalId":19961,"journal":{"name":"Pastoral Psychology","volume":"66 1","pages":"204-208"},"PeriodicalIF":0.8000,"publicationDate":"2021-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982554/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Pastoral Psychology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1093/pcmedi/pbab019","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2021/9/1 0:00:00","PubModel":"eCollection","JCR":"Q3","JCRName":"PSYCHOLOGY, MULTIDISCIPLINARY","Score":null,"Total":0}

引用次数: 0

Abstract

Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed (DE) enhancers. Furthermore, a total of 1036 DE genes regulated by DE enhancers were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 single nucleotide polymorphisms (SNPs) were located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites of 758 transcription factors, which were shown to be highly correlated with tumorigenesis and development.

查看原文本刊更多论文

对 13 种主要癌症类型的增强子进行识别和特征分析。

增强子在癌症等各种疾病中经常发生突变和失调。通过整合哺乳动物基因组（FANTOM）增强子表达谱的功能注释和来自癌症基因组图谱（TCGA）的13种癌症及其相应癌旁组织的RNA-seq数据，我们系统地鉴定了4702个显著差异表达（DE）的增强子。此外，我们还发现了1036个受DE增强子调控的DE基因。研究发现，在这13种癌症中，大多数（61.13%）增强子是泛在表达的，而DE增强子更有可能是组织特异性表达的，而且由DE增强子调控的DE基因在癌症相关通路中明显富集。最后，研究表明，有74个单核苷酸多态性（SNPs）位于37个DE增强子中，这些SNPs影响了758个转录因子功能结合位点的获得和丢失，而这些位点与肿瘤的发生和发展高度相关。

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分钟内获得全文求助全文

来源期刊

Pastoral Psychology Multiple-

CiteScore

1.40

自引率

25.00%

发文量

期刊介绍： Pastoral Psychology, founded in 1950, is one of the most well-established and respected journals in the field of psychology and religion/spirituality. Pastoral Psychology is an international forum that publishes scholarly, peer-reviewed original articles that address varied aspects of religion and spirituality from physical, human science, and interfaith perspectives. Historically, the word “pastoral” has referred to the care of individuals, families, and communities. Today, we additionally consider “pastoral” in terms of lived experience as it relates to embodiment, the social-political, economic, spiritual, and environmental dimensions of life. All theoretical perspectives are welcome, as Pastoral Psychology regularly publishes articles from a variety of schools of thought, including, but not limited to, psychoanalytic and other dynamic psychologies, cognitive psychologies, experimental and empirical psychologies, humanistic psychology, transpersonal psychology, and cultural psychology. Insights from existential perspectives, intersectional theories, philosophical and theological theories, gender and queer studies, sociology, anthropology, public mental health, and cultural and empirical studies are welcome. Theoretical contributions that have direct or indirect relevance for practice, broadly construed, are especially desirable, as our intended audience includes not only academics and scholars in religion and science, but also religious and spiritual leaders, as well as caregivers, chaplains, social workers, counselors/therapists, clinical psychologists, psychiatrists, and persons interested in matters of religion/spirituality and psychology. Pastoral Psychology welcomes scholarship and reflection from all religious and spiritual traditions. In addition to scholarly research papers, the journal welcomes thoughtful essays on a wide range of issues and various genres of writing, including book reviews and film reviews. The community of scholars represented in its pages has demonstrated that the life challenges the journal seeks to address are universally shared, yet also reflect individual social, cultural, and religious locations. The journal, therefore, welcomes submissions from scholars from around the world.