Single Cell

Single Cell Web Tools

The single cell web tool provides key interactive and customizable functions including general information, clustering, heatmap and differential expression analysis for lncRNAs based on 49 single cell datasets. 49 lncRNA expression datasets associated with 20 human cancers based on single cell sequencing are obtained from GEO and published literatures. View our Help page for further help.

Cluster

This feature allows the user to perform cluster analysis on single-cell data.

Heatmap Plotting

This function provides heatmap of differential expressed lncRNAs among diverse clusters.

Differential Expression Analysis (DEA)

This function allows users to obtain differential expression information and box plot of lncRNAs.

Information of Single Cell Datasets

ID	Cancer Type	LncRNA Number	Cell Number	Cell Line/Tissue	Library Strategy	Data Sources
Lnc_SingleCell01	Glioblastoma	14789	177	Cell Line: GSC/DGC	RNA-Seq	GSE57872
Lnc_SingleCell02	Glioblastoma	3114	623	Tissue: Brain	RNA-Seq	GSE57872
Lnc_SingleCell03	Lung adenocarcinoma	6834	245	Cell Line: LC-2/ad	RNA-Seq	DRP001358
Lnc_SingleCell04	Lung adenocarcinoma	6530	126	PDX	RNA-Seq	GSE69405
Lnc_SingleCell05	Breast cancer	6196	369	PDX	RNA-Seq	GSE77308
Lnc_SingleCell06	Lung adenocarcinoma	3494	218	Cell Line: A549	RNA-Seq	DRP003337
Lnc_SingleCell07	Breast cancer	6643	317	Tissue: Breast	RNA-Seq	GSE75688
Lnc_SingleCell08	Melanoma	5791	307	Tissue: Skin	RNA-Seq	GSE81383
Lnc_SingleCell09	Non-small cell lung cancer	277	3524	Tissue: Lung	RNA-Seq	E-MTAB-6149
Lnc_SingleCell10	Chronic myelogenous leukemia	6708	267	Cell Line: K562	RNA-Seq	GSE98734
Lnc_SingleCell11	Chronic myelogenous leukemia	4676	1877	Tissue: Bone marrow	RNA-Seq	GSE76312
Lnc_SingleCell12	Colorectal cancer	1169	290	Tissue: Colon	RNA-Seq	GSE81861
Lnc_SingleCell13	Melanoma	2932	575	Cell Line: WM989	RNA-Seq	GSE99330
Lnc_SingleCell14	Esophageal squamous cell carcinoma	6990	314	Cell Line: KYSE-180	RNA-Seq	GSE81812
Lnc_SingleCell15	Glioblastoma	4680	991	Tissue: Brain	RNA-Seq	GSE84465
Lnc_SingleCell16	Non-small cell lung cancer	4117	164	Cell Line: PC-9	RNA-Seq	DRP003981
Lnc_SingleCell17	Alveolar rhabdomyosarcoma	610	6875	Cell Line: Rh41	RNA-Seq	GSE113660
Lnc_SingleCell18	High-grade glioma	603	2772	Tissue: Brain	RNA-Seq	GSE103224
Lnc_SingleCell19	Cervix cancer	10597	126	Cell Line: Hela	RNA-Seq	ERP020478
Lnc_SingleCell20	Colorectal cancer	4561	99	Cell Line: HCT-116	RNA-Seq	GSE51254
Lnc_SingleCell21	Myxoid liposarcoma	1947	96	Cell Line: MLS 1765-92	RNA-Seq	E-MTAB-6142
Lnc_SingleCell22	Lung adenocarcinoma	4748	46	Cell Line: PC-9	RNA-Seq	DRP001358
Lnc_SingleCell23	Lung adenocarcinoma	4510	46	Cell Line: VMRC-LCD	RNA-Seq	DRP001358
Lnc_SingleCell24	Lung adenocarcinoma	4843	50	Cell Line: H358	RNA-Seq	GSE69405
Lnc_SingleCell25	Renal cell carcinoma	3724	35	Tissue: Kidney	RNA-Seq	GSE73121
Lnc_SingleCell26	Renal cell carcinoma	5065	83	PDX	RNA-Seq	GSE73121
Lnc_SingleCell27	Hepatocellular carcinoma	540	26	Tissue: Liver	RNA-Seq	GSE65364
Lnc_SingleCell28	Acute myeloid leukemia	7000	24	Tissue: Bone marrow	RNA-Seq	E-MTAB-2672
Lnc_SingleCell29	Breast cancer	4869	70	CTC	RNA-Seq	GSE75367
Lnc_SingleCell30	Melanoma	9135	36	Cell Line: WM989	RNA-Seq	GSE97681
Lnc_SingleCell31	Melanoma	10712	86	Cell Line: WM983B	RNA-Seq	GSE97681
Lnc_SingleCell32	Chronic myelogenous leukemia	3338	91	Cell Line: K562	RNA-Seq	GSE76312
Lnc_SingleCell33	Non-small cell lung cancer	819	47	Cell Line: H1437	RNA-Seq	GSE81861
Lnc_SingleCell34	Colorectal cancer	2216	51	Cell Line: HCT-116	RNA-Seq	GSE81861
Lnc_SingleCell35	Chronic myelogenous leukemia	3427	73	Cell Line: K562	RNA-Seq	GSE81861
Lnc_SingleCell36	Lung adenocarcinoma	1895	74	Cell Line: A549	RNA-Seq	GSE81861
Lnc_SingleCell37	Breast cancer	91	33	Cell Line: MDA-MB-231	RNA-Seq	GSE91395
Lnc_SingleCell38	Breast cancer	111	45	Cell Line: MCF-7	RNA-Seq	GSE91395
Lnc_SingleCell39	Neuroblastoma	9394	36	Cell Line: Neuroblastoma cell line	RNA-Seq	GSE90683
Lnc_SingleCell40	Bronchoalveolar carcinoma	2047	96	Cell Line: H1650	RNA-Seq	DRP003981
Lnc_SingleCell41	Lung adenocarcinoma	2340	96	Cell Line: II18	RNA-Seq	DRP003981
Lnc_SingleCell42	Non-small cell lung cancer	2237	96	Cell Line: H1975	RNA-Seq	DRP003981
Lnc_SingleCell43	Non-small cell lung cancer	2007	96	Cell Line: H2228	RNA-Seq	DRP003981
Lnc_SingleCell44	Chronic myelogenous leukemia	733	50	Cell Line: K562	RNA-Seq	GSE94979
Lnc_SingleCell45	Pancreatic ductal adenocarcinoma	4339	96	Cell Line: Pancreatic ductal adenocarcinoma cell lines	RNA-Seq	GSE99305
Lnc_SingleCell46	Acute lymphoblastic leukemia	10048	24	Cell Line: LOUCY/JURKAT	RNA-Seq	GSE100694
Lnc_SingleCell47	Prostate cancer	6059	144	Cell Line: LNCaP	RNA-Seq	GSE99795
Lnc_SingleCell48	Hepatocellular carcinoma	2910	43	Cell Line: HuH-1	RNA-Seq	GSE103866
Lnc_SingleCell49	Hepatocellular carcinoma	3522	55	Cell Line: HuH-7	RNA-Seq	GSE103866

Cluster

This feature allows the user to perform cluster analysis on single-cell data. The function is performed by FindClusters in R package Seurat version 3.1.5 with default parameters besides resolution is 0.5.

Sample: Select a sample for cluster.

Sample Select

Heatmap Plotting

This function provides heatmap of differential expressed lncRNAs among diverse clusters. The function is performed by DoHeatmap in R package Seurat version 3.1.5 with default parameters.

Sample: Select a sample for heatmap.

Sample Select

Differential Expression Analysis (DEA)

This function allows users to obtain differential expression information and box plot of lncRNAs. The function is performed by VlnPlot in R package Seurat version 3.1.5 with default parameters.

Sample: Select a sample for differential analysis.

log2FC: Select a threshold value of fold change for differential analysis.

FDR: Select a threshold value of fdr for differential analysis.

Sample Select

log2FC

FDR