通过开放集域适应检测单细胞色素可访问性数据中的新型细胞类型
Yuefan Lin1, Zixiang Pan1, Yuansong Zeng1
1School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China.
Briefings in bioinformatics
|July 29, 2024
概括
一种用于单细胞ATAC-seq (scATAC-seq) 数据的新方法OVAAnno准确识别已知和未知的细胞类型. 这种方法使用开放集域调整来改善复杂数据集中的细胞类型注释.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 单细胞技术产生了大量的多组数据,需要强大的细胞类型注释.
- 单细胞数据分析的一个关键挑战是注释在训练数据集中不存在的未知细胞类型.
- 现有的scATAC-seq注释方法往往无法识别这些未知的细胞类型.
研究的目的:
- 开发用于scATAC-seq数据中细胞类型注释的自动化方法,可以检测未知细胞类型.
- 为了解决当前方法的局限性,该方法只将单元分配到已知的类别.
主要方法:
- 开发了OVAAnno,一种自动化的细胞类型注释方法.
- 利用开放式域适应技术来区分已知的和未知的细胞类型.
- 将该方法应用于scATAC-seq和scRNA-seq数据集.
主要成果:
- 在scATAC-seq数据中,OVAAnno成功地识别了已知的和未知的细胞类型.
- 该方法在检测新型细胞群中表现出强大的性能.
- 当应用到单细胞RNA测序 (scRNA-seq) 数据时,OVAAnno也显示出有效性.
结论:
- 通过能够检测未知的细胞类型,OVAAnno在单细胞数据分析方面取得了重大进展.
- 该方法提高了scATAC-seq和scRNA-seq数据的细胞类型注释的准确性和完整性.
- 该代码的可用性有助于在该领域进行进一步的研究和应用.
相关概念视频
Heterochromatin
12.0K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
12.0K
Chromatin Immunoprecipitation- ChIP
11.1K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.1K
Euchromatin
6.9K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
6.9K
Chromatin Modification in iPS Cells
1.6K
Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
1.6K
Spreading of Chromatin Modifications
8.2K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
Writers
The writer...
8.2K


