Institute of Developmental Biology and Neurobiology (iDN), Johannes Gutenberg University Mainz, 55128, Mainz, Germany.
Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, 55131, Mainz, Germany.
BMC Bioinformatics. 2024 Sep 5;25(1):293. doi: 10.1186/s12859-024-05919-y.
Gene expression and alternative splicing are strictly regulated processes that shape brain development and determine the cellular identity of differentiated neural cell populations. Despite the availability of multiple valuable datasets, many functional implications, especially those related to alternative splicing, remain poorly understood. Moreover, neuroscientists working primarily experimentally often lack the bioinformatics expertise required to process alternative splicing data and produce meaningful and interpretable results. Notably, re-analyzing publicly available datasets and integrating them with in-house data can provide substantial novel insights. However, such analyses necessitate developing harmonized data handling and processing pipelines which in turn require considerable computational resources and in-depth bioinformatics expertise.
Here, we present Cortexa-a comprehensive web portal that incorporates RNA-sequencing datasets from the mouse cerebral cortex (longitudinal or cell-specific) and the hippocampus. Cortexa facilitates understandable visualization of the expression and alternative splicing patterns of individual genes. Our platform provides SplicePCA-a tool that allows users to integrate their alternative splicing dataset and compare it to cell-specific or developmental neocortical splicing patterns. All standardized gene expression and alternative splicing datasets can be downloaded for further in-depth downstream analysis without the need for extensive preprocessing.
Cortexa provides a robust and readily available resource for unraveling the complexity of gene expression and alternative splicing regulatory processes in the mouse brain. The data portal is available at https://cortexa-rna.com/.
基因表达和选择性剪接是严格调控的过程，它们塑造了大脑的发育，并决定了分化的神经细胞群体的细胞身份。尽管有多个有价值的数据集可供使用，但许多功能意义，特别是与选择性剪接相关的功能意义，仍未得到很好的理解。此外，主要从事实验工作的神经科学家往往缺乏处理选择性剪接数据并产生有意义和可解释结果所需的生物信息学专业知识。值得注意的是，重新分析公开可用的数据集并将其与内部数据集成可以提供大量新的见解。然而，这种分析需要开发协调的数据处理和处理管道，这反过来又需要大量的计算资源和深入的生物信息学专业知识。
在这里，我们介绍了 Cortexa——一个综合的网页门户，它整合了来自小鼠大脑皮层（纵向或细胞特异性）和海马体的 RNA 测序数据集。Cortexa 便于理解单个基因的表达和选择性剪接模式。我们的平台提供了 SplicePCA——一种工具，允许用户整合他们的选择性剪接数据集，并将其与细胞特异性或发育性新皮层剪接模式进行比较。所有标准化的基因表达和选择性剪接数据集都可以下载，以便进一步进行深入的下游分析，而无需进行大量的预处理。
Cortexa 为揭示小鼠大脑中基因表达和选择性剪接调控过程的复杂性提供了一个强大且易于使用的资源。该数据门户可在 https://cortexa-rna.com/ 访问。
