This section presents some key clinical characteristics associated with this dataset. For comprehensive details, please refer to the repository page.
Cell annotation
This section represents some annotation information (patient sources and cell types) for the single-cells. The detailed annotation can be found in the 'metadata' files on repository page.
Mutation Statistics
This section presents some key statistics for sample somatic mutations. For both mutation count distribution and identification of frequently mutated genes, we include all mutations without filtering. A gene is considered mutated if it contains any detectable mutations. For the analysis of top frequent mutations, we have aligned all mutations to the GRCh38 reference genome and excluded those lacking HGVSc identifiers. The table below follows the same criteria, excluding mutations that appear in only a single sample within this dataset.
This section presents some key statistics for gene fusion events. We define fusions as identical when they share the same left and right partner genes. Our analysis includes: (1) calculating sample frequencies for all detected fusions, (2) displaying in the table only those fusions present in at least two samples, and (3) illustrating the most frequently occurring fusions in the accompanying figure.
This section presents some key statistics for copy number alterations (CNAs). At the gene level, we analyze four CNA types (HOMDEL: homozygous deletion, HETLOSS: hemizygous deletion, GAIN: gain, AMP: high-level amplification) and calculate their sample frequencies. The table displays two selected CNA types along with their total sample counts, while the figure illustrates the most frequent CNAs. When copy number segment information is available, we include a heatmap visualization generated using the R package 'copynumber'.
Genomic Event Summary
This section summarizes somatic mutations, fusions, CNAs on an OncoGrid plot. Some important clinical traits are also listed on the plot. Correlations can be made here by selecting a clinical trait and an affected gene. Affected gene is a gene with at least 1 mutation, fusion or CNA (HOMDEL and AMP only) in a sample.
This section presents differentially expressed genes (DEGs) between tumor and normal samples, including all genes expressed in at least one sample. We identify upregulated genes as those with log2FC > 1 and FDR < 0.05, and downregulated genes as those with log2FC < -1 and FDR < 0.05. Functional enrichment analysis was performed using both KEGG and GO databases for all significant DEGs. The results are visualized through: (1) a bubble plot displaying the top 30 enriched KEGG pathways, and (2) a bar plot showing the top 10 enriched GO terms for each category (Biological Process, Cellular Component, and Molecular Function).
"This section presents differentially expressed miRNAs between tumor and normal samples, including all miRNAs detected in at least one sample. miRNAs are classified as upregulated (log2FC > 1 and FDR < 0.05) or downregulated (log2FC < -1 and FDR < 0.05) based on their expression patterns.
This section presents differentially methylated genes (DMGs) between tumor and normal samples. Methylation levels are quantified using mean beta values calculated from CpG sites located within the region spanning 1500bp upstream to 500bp downstream of transcription start sites (TSS). Genes are classified as hypermethylated (log2FC > 1, FDR < 0.05) or hypomethylated (log2FC < -1, FDR < 0.05). Functional enrichment analysis was performed using KEGG and GO databases for all significant DMGs. The results are visualized through: (1) a bubble plot displaying the top 30 enriched KEGG pathways, and (2) a bar plot showing the top 10 enriched GO terms for each category (Biological Process, Cellular Component, and Molecular Function).
This section presents survival analysis across all potential gene strata, including: (1) mutated genes, (2) fusion genes, (3) copy number alteration (CNA) genes (types restricted to HOMDEL, HETLOSS, DIPLOID, GAIN, or AMP), and (4) differentially expressed genes, methylated genes, and miRNAs (categorized as 'high': z-score > 0 or 'low': z-score < 0). All strata are required to include at least 10% of the total samples to ensure statistical reliability.