1. Overview of LncCE

1.1 The home page of LncCE

LncRNAs are well known as important players in maintaining morphology and function of tissues, and determining their cell specificity is fundamental to better comprehension of their function. LncCE is a database for Cellular-Elevated lncRNAs in human single cells. LncCE provides detailed expression atlas by analyzing single cell RNA sequencing from 2,893,787 single cell samples covering 149 cell types across 79 normal and 37 cancer tissues, enabling the exploration of the expression pattern for lncRNAs across different tissues. Currently, 14,941 CE lncRNAs were comprehensively discovered at the single-cell level.

1.1.1

1.The main function modules of the database are provided in the navigation bar.
2.Input lncRNA to obtain CE lncRNA information.

1.1.2

1.It can be quickly queried by adult and pediatric body maps.
2.Click on the tissues or cancers of interest to view CE lncRNA information.

1.2 Definition of lncNRA classification

2. Four ways to search in LncCE.

2.1.Search normal tissues of LncCE

1.Select one of the 79 normal tissues, including adipose tissue, adrenal gland and so on.
2.Select one of the three resources, including Human Cell Landscape, The Tabula Sapiens and TICA.
3.Select one of CE classification, including CS, CER and CEH.
4.Select a cell type in the corresponding resources and tissues.

2.2 Search cancer type of LncCE

1.Select one of 16 cancer types, including bladder cancer, brain cancer and so on.
2.Select a dataset associated with selected cancers.
3.Select one of CE classification, including CS, CER and CEH.
4.Select a cell type in the corresponding dataset and cancers.

2.3 Search lncRNA of LncCE

Users can obtain the spatial expression pattern of the lncRNA by entering Gene Symbol or Ensembl Id.

2.4.Search single cell of LncCE

1.Select one of 6 compartments, including cancer, endothelial and so on.
2.Select one or all cell types in the corresponding compartment.
3.Select one of 80 normal and 37 cancer tissues from different resources corresponding compartment and cells.

3. Search result in LncCE.

3.1.Search lncRNA of LncCE

1.Resources or datasets for search results.
2.The basic information of CE lncRNA.
3.Click to view the detail information.

4.Spatial expression pattern in cancers.

4.1.1.The selected dataset or resource.
4.1.2.The selected cancer.
4.1.3.Detected increased expression in cells.
4.1.4.The mean expression level of lncRNA in cells.
4.1.5.The distribution of expression level of lncRNA in cells.
4.1.6.Cell clustering based on highly variable genes.
4.1.7.The expression level of lncRNA in cell types.

4.2.1.Other resources besides selecting resources.
4.2.2.The mean expression level of lncRNA in cells of the selected cancer in other resources.
4.2.3.The distribution of expression level of lncRNA in cells of the selected cancer in other resources.
4.2.4.Cell clustering based on highly variable genes in other resources.
4.2.5. The expression level of lncRNA in cell types in other resources.

5.Spatial expression pattern in normal tissues.

5.1.1.Select tissues and resources. 5.1.2.The mean expression level of lncRNA in cells of the selected tissue and resource.
5.1.3.The distribution of expression level of lncRNA in cells of the selected cancer in other resources.
5.1.4.Cell clustering based on highly variable genes in the selected tissue and resource.
5.1.5.The expression level of lncRNA in cell clustering in the selected tissue and resource.

6.LncRNA-mRNA co-expressed network and Prediction of function.

6.1.1.Select a classification.
6.1.2.Select a relative r value.
6.1.3.Predicted function.

7.External links.

8.Differential expression analysis.

9.Survival analysis.

10.Browse and statistics in LncCE.

10.1 LncRNA-Centric

1.Click on the lncRNA based on the tree structure of chromosomes to view its basic information.
2.We provide the top 20 CE lncRNAs with highest entries for all resources.

10.2 Normal-Centric

1.Click on the lncRNA based on the tree structure of normal tissues to view its basic information.
2.We provide the distribution of adult and fetal normal tissues CE lncRNAs for each resource.

10.3 Cancer-Centric

1.Click on the lncRNA based on the tree structure of cancers to view its basic information.
2.We provide the distribution of adult and pediatric cancer CE lncRNAs.