scCancerExplorer:一个全面的数据库,可以交互探索人类胰腺癌单细胞多组数据
Changzhi Huang1,2, Zekai Liu1, Yunlei Guo1
1State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China.
Nucleic acids research
|November 18, 2024
概括
scCancerExplorer是一个新的数据库,用于探索单细胞多组癌症数据. 它整合了50种癌症类型的基因组,表观基因组和转录基因组数据,帮助癌症研究.
科学领域:
- 癌症生物学 癌症生物学
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 文字转录学 (Transcriptomics) 是一个学科.
- 生物信息学是一种生物信息学.
背景情况:
- 基因组,表观基因组和转录基因组的改变是癌症的关键特征.
- 表观遗传调节对于癌症的发展和进展至关重要.
- 单细胞表观基因组数据为癌症研究提供了新的途径,但缺乏综合数据库.
研究的目的:
- 开发一个全面的,用户友好的数据库,用于对人类胰腺癌中单细胞多组数据的交互探索.
- 解决单细胞表观基因组数据分析现有数据库的缺口.
- 为了促进对50种癌症类型的基因表达,染色质可访问性,DNA甲基化和基因组变异的调查.
主要方法:
- 开发scCancerExplorer,一个数据库集成单细胞基因组,表观基因组 (染色质可访问性,DNA甲基化) 和转录组数据.
- 实施了五个互动模块:综合多组学分析,单细胞转录组,单细胞表观基因组,单细胞基因组和TCGA分析.
- 包括用于分析基因表达,转录因子活性,DNA甲基化,拷贝数变异和TCGA存活数据的功能.
主要成果:
- scCancerExplorer提供了对50种人类癌症类型的单细胞多组数据的交互式探索.
- 该数据库使用户能够调查基因表达,染色质可访问性,DNA甲基化,拷贝数变异和转录因子活性.
- 用户可以在平台内直接执行TCGA生存分析.
结论:
- scCancerExplorer是一个新的数据库,它弥合了复杂的单细胞多omics数据和研究人员之间的差距.
- 其丰富,互动的功能使其与以前的资源区别开来,可以更深入地了解泛癌单细胞数据.
- 预计该数据库将通过更容易访问和分析多主题数据,加速癌症研究的进展.
相关概念视频
02:21Cancers Originate from Somatic Mutations in a Single Cell
12.7K
Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
12.7K
02:43Mouse Models of Cancer Study
4.7K
Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
4.7K
01:05Cancer-Critical Genes II: Tumor Suppressor Genes
8.3K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
8.3K
01:21Cancer Survival Analysis
870
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
870