功能途径推理分析 (FPIA)
Irbaz I Badshah1, Pedro R Cutillas2
1Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK.
Methods in molecular biology (Clifton, N.J.)
|August 8, 2025
概括
功能通路推断分析 (FPIA) 通过在干扰后分析类似的表型来识别共同通路中的基因. 本研究详细介绍了"心脏病理"包中的FPIA协议,用于发现新的途径成员,例如与PI3K和TP53相关的成员.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 路径推断对于绘制生物网络和分配基因功能至关重要.
- 现有的方法包括代谢/信号电路的文本挖掘和调控网络的基因表达分析.
- 功能通路推断分析 (FPIA) 通过将具有类似扰乱诱导表型的基因分组为替代方案.
研究的目的:
- 提供一个详细的协议来实现功能途径推理分析 (FPIA) 使用"心脏"R包.
- 展示FPIA的应用,用于识别新途径成员.
- 为了说明FPIA在调查与PI3K和TP53.3等关键信号通路功能相关的基因中的实用性.
主要方法:
- 基于基因依赖数据集的功能途径推理分析 (FPIA).
- 利用从跨细胞线干扰数据中得出的途径成员的概率值.
- 实施和逐步的协议描述在"亲切"R包内.
主要成果:
- 证明了FPIA在映射繁殖途径成员中的有效性.
- 为基因依赖性数据应用FPIA提供了一个实用的协议.
- 成功说明了与PI3K和TP53.3相关的潜在新途径成员的识别.
结论:
- 基于表型相似性,FPIA是一种强大的方法,可以根据表型相似性推断途径成员身份.
- "亲切的"R包有助于实施生物发现的FPIA.
- 这种方法有助于揭示功能关系,并识别关键细胞通路的新组成部分.
相关概念视频
Indirect Motor Pathways
1.7K
The indirect motor or extrapyramidal pathways originate in the brainstem, the lower portion of the brain that connects it to the spinal cord. They consist of several distinct tracts, each with specialized functions. The four main tracts of the indirect motor pathways are the vestibulospinal tract, the reticulospinal tract, the tectospinal tract, and the rubrospinal tract.
The vestibulospinal tract originates in the vestibular nuclei of the brainstem. The vestibular system detects changes in...
The vestibulospinal tract originates in the vestibular nuclei of the brainstem. The vestibular system detects changes in...
1.7K
Amino Acid Biosynthetic Pathways
135
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
135
IP3/DAG Signaling Pathway
12.4K
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
12.4K
Interactions Between Signaling Pathways
6.4K
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
6.4K
Epistasis Analysis
5.2K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.2K
Direct Motor Pathways
2.5K
The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
The corticospinal tract is responsible for the voluntary movement of the limbs and trunk. It originates in the cerebral cortex of the brain and descends through the cerebrum's internal capsule and...
The corticospinal tract is responsible for the voluntary movement of the limbs and trunk. It originates in the cerebral cortex of the brain and descends through the cerebrum's internal capsule and...
2.5K


