Genomic location

LINC01943

Gene id: xxx

Name: xxx

Chromosome: xxx, strand xxx, from xxx to xxx (Genome assembly: hg38)

Expression profile

Expression in CD8+ T cells (10x)
Expression pattern of the lncRNA in CD8+ T cells of various tumors from 10x Genomics data.
Expression in CD8+ T cells (smart-seq)
Expression pattern of the lncRNA in CD8+ T cells of various tumors from Smart-seq2 data.
Expression in CD4+ T cells (10x)
Expression pattern of the lncRNA in CD4+ T cells of various tumors from 10x Genomics data.
Expression in CD4+ T cells (smart-seq)
Expression pattern of the lncRNA in CD4+ T cells of various tumors from Smart-seq2 data.
Expression in myeloid cells (10x)
Expression pattern of the lncRNA in myeloid cells of various tumors from 10x Genomics data.
Expression in myeloid cells (smart-seq)
Expression pattern of the lncRNA in myeloid cells of various tumors from 10x Genomics data.

LncRNA cell markers

Specific lncRNAs that can be used to identify and characterize T cells or myeloid cells based on their unique expression patterns (log2FC > 1 for smart-seq; log2FC > 0.1 for 10x , expression ratio > 20%, FDR < 0.05).
Cancer type Cell type Subset cell type Platform Coefficient P value FDR Average log2FC %Cell type %Others

Cell proliferation association

Association between lncRNA expression to T cell proliferation score in tumors (spearman rho > 0.3, expression ratio > 20%, FDR < 0.05).
Cell type Subset cell type Platform Rho P value FDR %Cell type

Differential Expression between normal and tumor tissues

Differential expression pattern of the lncRNA in tumor and normal samples (|log2FC| > 1 for smart-seq; |log2FC| > 0.1 for 10x, expression ratio > 20%, FDR < 0.05).
Cancer type Cell type Subset cell type Normal tumor peripheral Platform Coefficient P value FDR Average log2FC %Cell type

Potentially tumor-reactive T cell-specific lncRNAs

The lncRNA specifically expressed in potentially tumor-reactive T cell-specific lncRNA in tumor samples (log2FC > 1 for smart-seq; log2FC > 0.1 for 10x, expression ratio > 20%, FDR < 0.05).
Cancer type Cell type Platform Coefficient P value FDR Average log2FC %Cell type

Dynamic lncRNAs in CD8+ T cell exhaustion paths

The lncRNA up-regulated or downregulated along the pseudotime of CD8+ T cells from the naive state to the exhausted state (FDR < 0.05, expression ratio in cell type > 20%).
Cancer type Platform Coefficient P value FDR

Dynamic lncRNAs in IL21+ Th1 to Tfh/Th1 cell paths

The lncRNA up-regulated or downregulated along the pseudotime of CD4+ T cells from the naive state to the exhausted state (FDR < 0.05, expression ratio in cell type > 20%).
Cancer type Platform Coefficient P value FDR

Dynamic lncRNAs in Treg cell maturation

The lncRNA up-regulated or downregulated along the pseudotime of CD4+ T cells from the TNFRSF9- Treg to TNFRSF9+ Treg (FDR < 0.05, expression ratio in cell type > 20%).
Cancer type Platform Coefficient P value FDR

Dynamic lncRNAs in LAMP3+ dendritic cell maturation

The lncRNA up-regulated or downregulated throughout the pseudotime of LAMP3+ dendritic cell maturation process (FDR < 0.05, expression ratio in cell type > 20%).
Cancer type Platform Coefficient P value FDR

LncRNAs in cell-type-enriched regulons of T cells and myeloid cells

LncRNAs within the specific regulatory networks (regulons) that are enriched in T cells and myeloid cells (FDR < 0.05, log2FC (10x) > 0 / log2FC (smart-seq) > 0).
Regulons TF Cell type Subset cell type Log2FC (smart-seq) P value (smart-seq) FDR (smart-seq) Log2FC (10x) P value (10x) FDR (10x) Importance

LncRNAs correlated with function of tumor-associated macrophages (TAM)

LncRNAs significantly correlated with angiogenesis or phagocytosis score of TAM (|rho| > 0.5, FDR < 0.05, expression ratio in cell type > 20%).
Cancer type Platform Rho P value FDR %Cell type

LncRNAs associated with survival

LncRNAs significantly associated with patient survival in TCGA (FDR < 0.05, expression level (boxplot Q4) > 1).
Tissue Stage HR P value FDR Logrank P value Logrank FDR n_high_exp n_low_exp Expression

CRISPR-validated tumor-associated lncRNAs regulating immune dynamics

This module presents immune-associated lncRNAs, validated by large-scale CRISPR screens, that function as dual regulators of both tumor fitness and immune dynamics.
Evolutionary conservation CRISPR screening phenotype Validated dataset (PMID) Cell line

LncRNAs overlapped with GWAS SNP

LncRNA gene loci overlapped with GWAS SNPs
SNPs Chr Position Disease/Trait Intergenic P-value PMID

LncRNAs overlapped with immunity quantitative trait loci

LncRNA gene loci overlapped with immunity quantitative trait loci (immunQTLs) affecting tumor microenvironment composition.
SNPs Chr Position Cancer type Cell type log10P Survival association P value survival