康塞特预测了空间转录学中的利基感知扰动反应
Xiang Lin1, Zhenglun Kong1, Soumya Ghosh2
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
bioRxiv : the preprint server for biology
|November 26, 2025
概括
一个新的模型CONCERT,通过考虑细胞环境,预测遗传或化学变化如何影响组织中的基因表达. 它改进了空间扰动转录学预测,优于现有的方法.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 系统生物学 系统生物学
背景情况:
- 空间扰乱转录学揭示了组织背景中的基因表达变化.
- 了解细胞微环境如何影响扰动结果至关重要.
研究的目的:
- 开发CONCERT,一个利基意识的生成模型,用于预测扰动后的空间基因表达变化.
- 规范和评估预测任务,包括补丁,边界和利基效应.
主要方法:
- 音乐会使用高斯过程变量自编码器来学习空间内核和嵌入扰动上下文.
- 该模型预测基因表达反应在未被扰乱的区域,组织接口,并基于微环境.
- 对Perturb-map肺部数据集进行的评估与最先进的模型进行对比.
主要成果:
- 康塞特显著优于现有方法,缩短了E距离高达33.77%,并提高了皮尔森相关性高达9.10%.
- 案例研究表明,CONCERT能够重建空间基因表达,进行纵向比较,并在结肠炎和中风模型中解决异质性.
- 该模型准确地预测了在可变条件下和3D配方中的反应.
结论:
- 康塞特推进了空间扰动转录学,使得能够进行特定领域的反事实预测,并重建缺失的空间数据.
- 该模型为了解各种生物组织中复杂的扰动反应提供了一个强大的工具.
相关概念视频
Insensitive Nuclei Enhanced by Polarization Transfer (INEPT)
973
Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) is an advanced Nuclear Magnetic Resonance (NMR) technique specifically designed to detect and enhance the signals of low-abundance nuclei, such as carbon-13 and nitrogen-15, in small molecules. The fundamental principle behind INEPT is the transfer of polarization from a more abundant and highly polarizable nucleus, typically hydrogen-1, to the low-abundance nucleus of interest. This process effectively boosts the NMR signal of the...
973
Transcription Attenuation in Prokaryotes
18.1K
Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure. Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
18.1K
Diversity in Cell Signaling Responses
7.6K
The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity.
Graded and Abrupt Responses
Some signaling systems generate...
Graded and Abrupt Responses
Some signaling systems generate...
7.6K
DNA Microarrays
20.6K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
20.6K


