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lncRNA: ENSG00000235531

Summary for MSC-AS1

Gene summary

Gene information	Ensembl ID	ENSG00000235531
	Gene symbol	MSC-AS1
	Gene name	MSC antisense RNA 1
	HGNC	48724
	Entrez ID	100132891
	Gene type	antisense
	Synonyms	08q13.3-q21.11\|MSC-AS1\|RP11-383H13.1
	UniProtAcc

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Structure and expression level for MSC-AS1

AS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.

Differentially expressed gene analysis between cancer and normal samples.

Ensembl ID	Base mean	log2FC(AD/control)	lfcSE	Stat	P-value	Adjc.p-value	DEG direction	Cancer type
ENSG00000235531	1.235760e+03	1.598958e+00	1.173023e-01	1.363109e+01	2.620000e-42	4.610000e-41	UP	KIRC
ENSG00000235531	4.173797e+02	1.585905e+00	2.034554e-01	7.794854e+00	6.450000e-15	8.140000e-14	UP	HNSC
ENSG00000235531	6.268269e+02	1.329058e+00	2.396850e-01	5.545022e+00	2.940000e-08	1.640000e-07	UP	KIRP
ENSG00000235531	5.510700e+02	1.454402e+00	2.024533e-01	7.183886e+00	6.780000e-13	2.900000e-12	UP	LUSC

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000235531	3.547305e-01	4.383511e-10	KIRP	5.251618e-09

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lncRNA-Protein interaction for MSC-AS1

lncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000019549	SNAI2	34.2	92.8597	O43623	TF,Epi	NA
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000115966	ATF2	22.52	93.569	P15336	TF,Epi	ChIP-seq

lncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000169554	ZEB2	57.86	93.2744	O60315	TF	NA
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000081189	MEF2C	42.43	90.2378	Q06413	TF	ChIP-seq
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000019549	SNAI2	34.2	93.0262	O43623	TF,Epi	NA
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000115966	ATF2	22.52	93.9885	P15336	TF,Epi	ChIP-seq
ENSG00000235531	ENST00000512290	RP11-383H13.1	ENSG00000169554	ZEB2	52.62	93.6773	O60315	TF	NA

lncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000235531	ENST00000457356	RP11-383H13.1	ENSG00000172667	ZMAT3	47.75	94.3536	Q9HA38	RBP	NA

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lncRNA-DNA interaction for MSC-AS1

lncRNA targets the enhancer region and positively regulates the gene expression.

Only predicted by TDF

SCARB2,ASPH,POGLUT2,CREB1,WDFY1,AGPS,KLF7,PLOD2,RHOQ,ANXA5,TRAM1,SGTB,GTDC1,DIPK1A,BLOC1S6,CEP170,CCDC88A,DARS1,GXYLT2,RNF217,LNPK,OSTM1,CREG1,GPX8,ASAP1,NSMAF,ARMC1,DEGS1,SSR3,SSPN,SNAI2,IKBIP,MEF2C,ZMAT3,TCEA1,HEYL,DNAJB4,QKI,ARHGAP42,ACVR1,ATF2

Exist in public source

lncRNA targets the promoter region and positively regulates the gene expression.

lncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for MSC-AS1

lncRNA targets the 3'UTR region and negatively regulates the mRNA.

Only predicted by lncTar

SLC25A39

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

lncRNA and exonskipping events positive correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	ORF mutation
ENSG00000235531	ENST00000512290	exon_skip_436488	chr5:96726793-96726859	-8.58	-0.1454	CAST	ENST00000341926,ENST00000395813	In-frame
ENSG00000235531	ENST00000512290	exon_skip_287874	chr17:29085603-29085648	-8.07	-0.5380	MYO18A	ENST00000527372	In-frame
ENSG00000235531	ENST00000512290	exon_skip_382356	chr3:37091466-37091538	-7.89	-0.2321	LRRFIP2	ENST00000336686	In-frame

-lncRNA and exonskipping events are negatively correlated.

lncRNA and exonskipping events negative correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	LOF
ENSG00000235531	ENST00000512290	exon_skip_44853	chr10:104010815-104010908	-12.41	-0.1677	SLK	ENST00000369755	In-frame
ENSG00000235531	ENST00000519751	exon_skip_430601	chr4:82842139-82842481	-30.11	-0.1064	SEC31A	ENST00000355196,ENST00000395310,ENST00000448323	In-frame
ENSG00000235531	ENST00000512290	exon_skip_423795	chr4:55888887-55888932	-8.14	-0.4284	EXOC1	ENST00000346134,ENST00000381295	In-frame
ENSG00000235531	ENST00000512290	exon_skip_461111	chr6:90544551-90544632	-8.04	-0.1462	MAP3K7	ENST00000369329	In-frame
ENSG00000235531	ENST00000512290	exon_skip_499771	chr9:128592982-128593042	-11.26	-0.1908	SPTAN1	ENST00000372731	In-frame
ENSG00000235531	ENST00000512290	exon_skip_456460	chr6:17771113-17771218	-11.23	-0.1497	KIF13A	ENST00000259711	In-frame

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

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Variants for MSC-AS1

RNA A-to-I editing events in lncRNA.

LncRNAediting ID

LncRNA Ensembl ID

Chromosome

Editing Position

Strand

Gene Type

Gene Name

Transcript ID

Transcript Type

Transcript Name

Edited-associated DElncRNAs in cancer.

LncRNA Ensembl ID

LncRNA Index

Cancer Type

Chr_Postion_Strand

AVE1

AVE2

log2FC

W-value

P-value

Adjc.p-value

Change

Correlation between RNA A-to-I editing events's frequecy and lncRNA expression.

LncRNA Ensembl ID

LncRNA Index

Correlation

P-value

Adjc.p-value

Cis-expression quantitative trait loci(cis-eQTL) of lncRNA.

LncRNA Ensembl ID

LncRNA Name

SNP info

Number of Positive corelated Cancer

Positive corelated Cancer

Number of Negative corelated Cancer

Negative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncRNA regulates differentially expressed genes by function as enhancer.

LncRNA Ensembl ID	PC Gene ID	PC Gene Name	Positive correlated cancers	Cancer with PC gene up-regulation	Cancer with PC gene down-regulation
ENSG00000235531	ENSG00000165895	ARHGAP42	ACC,KIRC,KIRP,PAAD,SKCM,UVM	KIRC
ENSG00000235531	ENSG00000172986	GXYLT2	ACC,HNSC,KIRC,KIRP,PAAD,UCS	KIRC,KIRP
ENSG00000235531	ENSG00000115866	DARS1	ESCA,KIRC,PAAD,UCS,UVM	KIRC
ENSG00000235531	ENSG00000123096	SSPN	ESCA,HNSC,KIRC,PAAD,UVM	KIRC
ENSG00000235531	ENSG00000143753	DEGS1	ESCA,KIRC,KIRP,PAAD,UVM	KIRC
ENSG00000235531	ENSG00000152952	PLOD2	ESCA,HNSC,KIRC,PAAD,UVM	HNSC,KIRC
ENSG00000235531	ENSG00000153317	ASAP1	ESCA,HNSC,KIRC,KIRP,PAAD,SKCM	KIRC
ENSG00000235531	ENSG00000164294	GPX8	ESCA,HNSC,KIRC,KIRP,PAAD	HNSC,KIRP
ENSG00000235531	ENSG00000166130	IKBIP	ESCA,HNSC,KIRC,KIRP,PAAD	HNSC,KIRC,KIRP
ENSG00000235531	ENSG00000134901	POGLUT2	HNSC,KIRC,KIRP,PAAD,UVM	HNSC,KIRC,KIRP

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lncRNAs regulate the target genes through recruiting transcript factors

LncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

LncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

LncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

LncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.

LncRNA Ensembl ID

LncRNA ENST ID

PC Gene Name

PC Gene ID

PC ENST ID

nDG

Cancer with PC gene up-regulation

Cancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncRNA regulates mRNA by competing the miRNA binding site with mRNA.

LncRNA Ensembl ID

lncRNA-miRNA-mRNA

Cancer Types

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lncRNA coding potential

ORFfinder result for the gencode.v22.lncRNA.transcript.fa.

lncRNA Ensembl ID	lncRNA ENST ID	length(AA)	start at transcript	end at transcript
ENSG00000235531.8	ENST00000521467.4	37	562	675
ENSG00000235531.8	ENST00000522519.4	100	425	123
ENSG00000235531.8	ENST00000524152.4	182	279	827
ENSG00000235531.8	ENST00000457356.7	67	6	209
ENSG00000235531.8	ENST00000519751.4	122	366	1
ENSG00000235531.8	ENST00000518916.4	108	325	2
ENSG00000235531.8	ENST00000518700.3	104	311	0
ENSG00000235531.8	ENST00000519068.2	66	270	467
ENSG00000235531.8	ENST00000523133.1	70	243	455
ENSG00000235531.8	ENST00000512290.2	63	445	254

	lncRNA summary
	lncRNA structure and expression level
	lncRNA-Protein interaction
	lncRNA-DNA interaction
	lncRNA-RNA interaction
	Variants in lncRNA
	lncRNAs regulate the target genes through functioning as enhancers
	lncRNAs regulate the target genes through recruiting transcript factors
	lncRNAs regulate the alternative splicing events through interacting with splicing factor
	lncRNAs regulate mRNA through targeting the 3'-UTR region
	lncRNAs regulate mRNA by competing with miRNA
	lncRNA coding potential