LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues

TL;DR

This paper introduces LncCE, a database that identifies lncRNAs elevated in specific cell types across normal and cancer tissues at the single-cell level.

Contribution

The novel contribution is the systematic identification and visualization of cellularly-elevated lncRNAs across diverse normal and cancer cell types.

Findings

LncCE includes 87,946 entries of CE lncRNAs across 149 cell types from 181 single-cell RNA sequencing datasets.

The database provides co-expression patterns of lncRNAs with protein-coding genes and their biological functions.

LncCE visualizes lncRNA expression changes in cancers and links them to patient survival outcomes.

Abstract

Long non-coding RNAs (lncRNAs) have emerged as significant players in maintaining the morphology and function of tissues and cells. The precise regulatory effectiveness of lncRNAs is closely associated with their spatial expression patterns across tissues and cells. Here, we propose the Cellularly-Elevated LncRNA (LncCE) resource to systematically explore cellularly-elevated (CE) lncRNAs across normal and cancer tissues at single-cell resolution. LncCE encompasses 87,946 entries of CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing datasets, involving 20 fetal normal tissues, 59 adult normal tissues, 32 adult cancer types, and 5 pediatric cancer types. Two main search options are provided via a given lncRNA name or cell type. The results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, their co-expression with protein-coding genes, and their involvement in biological functions. In particular, LncCE provides quantitative visualizations of lncRNA expression changes in cancers compared to control samples, as well as clinical associations with patients’ overall survival. Together, LncCE offers an extensive, quantitative, and user-friendly interface to create a CE expression atlas for lncRNAs across normal and cancer tissues at the single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.

Graphical Abstract

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