VITAseer Unveils a Comprehensive Upgrade with Advanced Eukaryotic Single-Cell Analysis
We are excited to announce a significant update to our VITAseer software, now featuring an advanced module designed for in-depth single-cell analysis of eukaryotic samples. This upgrade also introduces comprehensive single-cell lncRNA (long non-coding RNA) analysis capabilities, further enhancing the power and precision of research. The upgraded VITAseer is fully compatible with the extensive single-cell transcriptome data generated by VITA single-cell products, providing a more intuitive and efficient data analysis experience. Key enhancements include improved cell clustering, automated cell type annotation, functional analysis, and cell communication mapping.
In addition, this latest version of VITAseer offers single-cell lncRNA analysis. LncRNAs, non-coding RNA molecules longer than 200 nucleotides, exert major influence on a diverse array of molecular mechanisms, including epigenetics, transcription factor regulation, and post-transcriptional processes. As integral components of complex molecular networks, lncRNAs are increasingly recognized as key players in a wide range of diseases. To deepen the understanding of lncRNA functions, we have introduced a first-of-its-kind analysis module specifically designed for single-cell mRNA and lncRNA analysis of eukaryotic samples.
New Features of Upgraded VITAseer:
1. UMAP Visualization of Cell Clusters Using Both mRNAs and LncRNAs
The upgraded VITAseer introduces a new UMAP visualization feature, allowing users to analyze cell clusters based on both mRNAs and lncRNAs expression data. This analysis capacity leads to more accurate identification of cell subpopulations and enhance the detection of potential disease-related cell subpopulations. The figure below (Figure 1) illustrates that mRNA and lncRNA expression can be used together to cluster cell subpopulations effectively.
Figure 1: UMAP of Cell Clustering by mRNA and LncRNA Expression
2. Automated Cell Type Annotation
In addition to UMAP visualization, VITAseer now offers automated cell type annotation, providing users with pie charts that show cell type proportions and bubble charts that display cell type annotation scores. These visual aids make it easier to identify different cell types intuitively, with the asterisks in the bubble chart marking the best-fit cell type for each cluster (Figure 2).
Figure 2: Bubble Chart Showing Cell Type Annotation Scores
3. Optimized Differential Gene Expression Analysis
Users can now generate detailed heatmaps of differential gene expression, encompassing both mRNA and non-coding RNA, across various cell types (Figure 3). This provides valuable insights into gene regulation and function within specific subpopulations.
Figure 3: Heatmap of Differential Gene Expression
4. Enhanced Pathway Enrichment Analysis
Furthermore, VITAseer now includes enhanced GO and KEGG pathway enrichment analyses. These features allow users to characterize different functions of various cell types/subtypes, providing a clearer understanding of cellular behaviors through comprehensive bubble chart visualizations (Figure 4).
Figure 4: Bubble Charts Showing GO (Upper) and KEGG (Lower) Enrichment Analysis
5. Integrated Cell Communication Analysis
Another major enhancement is the integration of cell communication analysis, enabling users to dive deeper cell-cell interaction networks. The upgraded signaling pathway analysis feature allows for the visualization of interaction counts between different cell types or subtypes (Figure 5) , ligand-receptor pair and signaling pathway analysis between different cell types, offering a clearer understanding of cellular communication.
Figure 5: Pairwise Cell Interaction Count Analysis
6. Identification of Specific LncRNA Markers for Cell Types
VITAseer’s specialized lncRNA analysis module now allows researchers to identify specific lncRNA markers within different cell types or subtypes. This capability helps in mapping lncRNA markers' expression (Figure 6) and exploring their functional roles, shedding light on the complex mechanisms that govern cellular behaviors.
Figure 6. Heatmap of LncRNA Marker Expression in Different Cell Types
Figure 7. Heatmap of Specific LncRNA-mRNA Pair Expression
The upgraded VITAseer is now fully available, offering unparalleled tools for single-cell analysis in eukaryotic samples. For more information or to get the latest version, please contact us at +1 (919)-282-6006 or via email at customerservice@m20genomics.com. We look forward to your feedback and suggestions as we continue to enhance VITAseer, making single-cell transcriptome data processing and analysis more convenient and powerful for our users.
