管道(软件)
计算生物学
基因
转录组
候选基因
基因表达谱
生物
鉴定(生物学)
基因预测
功能基因组学
计算机科学
生物信息学
基因表达
基因组
遗传学
基因组学
植物
程序设计语言
作者
Aolani Colon,Rishabh Hirday,Ami Patel,Amrita Poddar,Emma Tuberty‐Vaughan,Tianyue Fu,Xin Ai,Wei Vivian Li,Li Cai
标识
DOI:10.1038/s41598-021-03041-0
摘要
Many computational pipelines exist for the detection of differentially expressed genes. However, computational pipelines for functional gene detection rarely exist. We developed a new computational pipeline for functional gene identification from transcriptome profiling data. Key features of the pipeline include batch effect correction, clustering optimization by gap statistics, gene ontology analysis of clustered genes, and literature analysis for functional gene discovery. By leveraging this pipeline on RNA-seq datasets from two mouse retinal development studies, we identified 7 candidate genes involved in the formation of the photoreceptor outer segment. The expression of top three candidate genes (Pde8b, Laptm4b, and Nr1h4) in the outer segment of the developing mouse retina were experimentally validated by immunohistochemical analysis. This computational pipeline can accurately predict novel functional gene for a specific biological process, e.g., development of the outer segment and synapses of the photoreceptor cells in the mouse retina. This pipeline can also be useful to discover functional genes for other biological processes and in other organs and tissues.
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