A computational pipeline for functional gene discovery

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 pip...

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Bibliographic Details
Published in:Scientific reports 2021-12, Vol.11 (1), p.23522-23522, Article 23522
Main Authors: Colon, Aolani, Hirday, Rishabh, Patel, Ami, Poddar, Amrita, Tuberty-Vaughan, Emma, Fu, Tianyue, Ai, Xin, Li, Wei Vivian, Cai, Li
Format: Article
Language:English
Subjects:
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Animals
Cluster Analysis
Computational Biology - methods
Computer applications
Gene Expression Profiling - methods
Gene Ontology
Gene Regulatory Networks - genetics
Genes
Genetic Association Studies - methods
Humanities and Social Sciences
Mice
multidisciplinary
Photoreceptors
Pipelines
Retina
Retina - physiology
RNA-Seq - methods
Science
Science (multidisciplinary)
Sequence Analysis, RNA - methods
Statistical analysis
Synapses
Transcriptome - genetics
Transcriptomes
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-03041-0