single cell gene expression data  (Human Protein Atlas)

Journal: Discover Oncology

Article Title: Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target

doi: 10.1007/s12672-026-04793-9

Figure Lengend Snippet: Flowchart Overview of this MR-based study. LD linkage disequilibrium, ρ-HESS Heritability Estimation from Summary Statistics, GNOVA Genetic covariance analyser, MTAG Multi-Trait Analysis of GWAS, CPASSOC Cross Phenotype Association, GWAS Genome-wide Association Study, MR Mendelian Randomization, GSMR Generalized summary-data-based Mendelian randomization, LDSC-SEG linkage disequilibrium score regression applied to specifically expressed genes, MAGMA Multi-marker Analysis of GenoMic Annotation, SMR Summary-databased Mendelian randomization, Phe-MR phenotypes, MR BMI body mass index, LUSC squamous cell lung cancer; scRNA-seq single-cell RNA sequencing

Article Snippet: The Single-cell RNA sequencing gene expression data were available from https://www.ncbi.nlm.nih.gov/geo/ and [https://singlecell.broadinstitute.org/single_cell](https:/www.singlecell.broadinstitute.org/single_cell) .

Techniques: GWAS, Marker, Single Cell, RNA Sequencing

Journal: Discover Oncology

Article Title: Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target

doi: 10.1007/s12672-026-04793-9

Figure Lengend Snippet: Tissue- and cell type–specific enrichment of SNP heritability for BMI and LUSC. A Tissue-level SNP heritability enrichment for BMI across 53 GTEx tissues estimated using LDSC-SEG. The x-axis shows tissues grouped by organ system, and the y-axis shows the estimated enrichment coefficient (log-scaled or standardized). Tissues surpassing the significance threshold (FDR-adjusted P < 0.05) are highlighted. B Tissue-level SNP heritability enrichment for LUSC using the same LDSC-SEG framework. The x-axis indicates GTEx tissues and the y-axis indicates enrichment coefficients, as in panel ( A ). Tissues with significant enrichment (FDR-adjusted P < 0.05) are labelled, illustrating the overlap and differences in tissue-specific genetic architecture between BMI and LUSC. C – G Cell type–specific SNP heritability enrichment for BMI and LUSC across single-cell RNA sequencing datasets from brain, ileum, heart, and colon, estimated using MAGMA-based cell typing. For each tissue, the left panel shows enrichment for BMI and the right panel shows enrichment for LUSC. The y-axis lists cell types (for example, neurons, epithelial cells, eosinophils, CD8⁺ T cells), and the x-axis shows –log₁₀(P) values for the association between cell type–specific expression and SNP heritability. Cell types with P < 0.05 are indicated in red, highlighting those most strongly enriched for the genetic signal of BMI and/or LUSC. BMI body mass index, LUSC lung squamous cell carcinoma, SNP single nucleotide polymorphism, LDSC-SEG linkage disequilibrium score regression applied to specifically expressed genes, MAGMA Multi-marker Analysis of GenoMic Annotation, scRNA-seq single-cell RNA sequencing, GTEx Genotype-Tissue Expression

Article Snippet: The Single-cell RNA sequencing gene expression data were available from https://www.ncbi.nlm.nih.gov/geo/ and [https://singlecell.broadinstitute.org/single_cell](https:/www.singlecell.broadinstitute.org/single_cell) .

Techniques: Single Cell, RNA Sequencing, Expressing, Marker

Journal: Nucleic Acids Research

Article Title: scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics

doi: 10.1093/nar/gkae821

Figure Lengend Snippet: Presentation of scATAC + RNA data in scMM-atlas. ( A ) Dataset module contains dataset information. The highlighted search box allows users to search for datasets by keyword. Clicking on the blue ‘download’ link allows users to download the relevant data. ( B ) Distribution of the scATAC + RNA dataset in humans and mouse. ( C ) The number of cell lines/tissues/organs for human and mouse. ( D ) The number of cells passed quality control, the average number of detected genes per cell and the average number of detected peaks per cell in each sample. ( E ) Displaying cell heterogeneity and related information for selected datasets. The results were provided in five tabs, namely integration, RNA, ATAC, search and download. In integration tab, the species, sequencing methods, sample condition and cell numbers of the selected data (left); UMAP plot of selected data after WNN integration, colored by cell subset (middle); Cell subset specific markers or correlation between cell subsets (right). ( F ) UMAP plot based on scRNA-seq data in RNA tab. ( G ) UMAP plot based on scATAC-seq data in ATAC tab. ( H ) Displaying the expression level (left) and promoter chromatin accessibility (middle) of interesting gene on UMAP, alternative showing this information by violin plot (right). ( I ) The browser displays the aggregated signal of single cells of each cluster.

Article Snippet: Single Cell Multiome ATAC + Gene Expression data were downloaded directly from the Datasets on 10X Genomics website.

Techniques: Control, Sequencing, Expressing

Journal: Nucleic Acids Research

Article Title: scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics

doi: 10.1093/nar/gkae821

Figure Lengend Snippet: Comprehensive exploration of cell heterogeneity of mouse cerebral cortex by single-cell multimodal omics. ( A ) UMAP projection of cells from mice cerebral cortex after integration of ATAC and RNA-seq data, colored by 39 distinct clusters. ( B ) Astro-Grm3 specific high expressed genes are mainly Wnt signaling associated. ( C ) Enrichment pathways of Astro-Grm3 specific genes. ( D ) UMAP projection of EX-L6-Tle4 subsets using scRNA-seq (left), scATAC-seq (middle) and integrated scATAC + RNA (right). ( E ) The contribution of each mouse cerebral cortex dataset to EX-L6-Tle4 and EX-L6-Tle4-Nrf1. ( F ) Differences of the type of chromatin accessibility between EX-L6-Tle4 and EX-L6-Tle4-Nrf1. ( G ) Reads density around the promoters of EX-L6-Tle4-Nrf1 specific genes, such as Stx6, Denr, Nrf1 and Klf15. ( H ) Enrichment of motifs NRF1 and KLF15 in EX-L6-Tle4-Nrf1 specific chromatin accessible sites. ( I ) EX-L6-Tle4 enriched pathways and EX-L6-Tle4-Nrf1 enriched pathways based on scRNA-seq data. ( J ) Inferred Pseudotime trajectory of EX-L6-Tle4 subsets.

Article Snippet: Single Cell Multiome ATAC + Gene Expression data were downloaded directly from the Datasets on 10X Genomics website.

Techniques: RNA Sequencing