Abstract
Long noncoding RNAs (lncRNA) play important roles in maintaining morphology and function of tissues, and their regulatory effectiveness is closely associated with spatial expression. To provide a comprehensive spatial atlas of expression for lncRNA, we propose LncSpA (http://bio-bigdata.hrbmu.edu.cn/LncSpA) to explore tissue-elevated (TE) lncRNA across human normal and adult and pediatric cancer tissues. In total, 71,131 and 12,007 TE lncRNAs and 634 clinical-related TE lncRNAs were identified across 38 normal and 33 adult cancer tissues. Moreover, 4,688 TE and 413 clinical-related lncRNAs were identified in pediatric cancer. By quick searching or query options, users can obtain eight major types of detailed information for lncRNA via various visualization techniques, including qualitative and quantitative spatial expression in different resources, coexpressed mRNAs, predicted function, known disease association, and the potential to serve as diagnostic or prognostic markers. LncSpA will be a valuable resource to understand lncRNA functions across tissues and cancers, leading to enhanced therapeutic strategies in precision oncology. SIGNIFICANCE: LncSpA is a new interactive resource that provides the spatial expression pattern of lncRNA across thousands of normal and cancer samples representing major tissue types.
Highlights
Long noncoding RNAs control various crucial biological functions to maintain morphology and function of tissues [1]
8,875, 9,837, 13,337, 10,718, and 74,767 TE Long noncoding RNAs (lncRNA) were identified from Integration, Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA), HBM2.0, and FANTOM, respectively (Supplementary Table S2)
12,007 cancer TE lncRNAs were identified across 33 cancer types from TCGA, ranging 64 in CESC to 3,356 in LAML, with a median of 226 TE lncRNAs per cancer type (Fig. 1D)
Summary
Long noncoding RNAs (lncRNA) control various crucial biological functions to maintain morphology and function of tissues [1]. Their precise regulatory effectiveness is closely associated with spatial expression patterns across tissues, whose dysfunction often influences disease development and progression [2]. The first step for exploring the spatial expression patterns is to identify genes with tissue-elevated (TE) expression in a certain tissue or groups. TE genes usually serve as biomarkers of specific biological processes or tissues in which they are expressed [3]. 5), and regulate cell proliferation, survival, and migration/invasion.
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