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lncRNA: ENSG00000229124

Summary for VIM-AS1

Gene summary

Gene information	Ensembl ID	ENSG00000229124
	Gene symbol	VIM-AS1
	Gene name	VIM antisense RNA 1
	HGNC	44879
	Entrez ID	100507347
	Gene type	antisense
	Synonyms	VIM-AS1\|10p13
	UniProtAcc

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Structure and expression level for VIM-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
ENSG00000229124	1.737601e+02	2.725969e+00	4.236156e-01	6.435006e+00	1.230000e-10	1.590000e-09	UP	CHOL
ENSG00000229124	1.250576e+02	-1.311645e+00	1.681503e-01	-7.800431e+00	6.170000e-15	3.000000e-14	DOWN	LUSC

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000229124	4.223392e-01	1.302183e-04	ACC	2.007470e-03
ENSG00000229124	4.578998e-01	1.562375e-03	CHOL	2.446848e-03

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lncRNA-Protein interaction for VIM-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
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000067066	SP100	42.05	92.6007	P23497	TF,Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000107077	KDM4C	38.6	91.3524	Q9H3R0	Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000079263	SP140	29.1	93.1071	Q13342	TF,Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000120616	EPC1	23.73	93.4212	Q9H2F5	Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000112511	PHF1	1.69	90.6663	O43189	TF,Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000120539	MASTL	44.01	93.0082	Q96GX5	Epi	Predict
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000163875	MEAF6	32.22	90.1675	Q9HAF1	Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000108799	EZH1	31.25	94.4074	Q92800	Epi	ChIP-seq
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000168283	BMI1	10.52	92.7708	P35226	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
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000080298	RFX3	43.25	92.8035	P48380	TF	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000067066	SP100	42.05	92.3624	P23497	TF,Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000079263	SP140	29.1	93.2147	Q13342	TF,Epi	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000135899	SP110	27.46	93.5951	Q9HB58	TF	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000126804	ZBTB1	24.23	91.0721	Q9Y2K1	TF	Predict
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000175395	ZNF25	4.57	90.5266	P17030	TF	NA
ENSG00000229124	ENST00000605833	VIM-AS1	ENSG00000112511	PHF1	1.69	91.0088	O43189	TF,Epi	NA
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000144747	TMF1	89.45	91.636	P82094	TF	Predict
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000067066	SP100	74.7	90.2101	P23497	TF,Epi	NA
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000135899	SP110	55.14	90.1206	Q9HB58	TF	NA
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000126804	ZBTB1	46.54	91.5545	Q9Y2K1	TF	Predict
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000197857	ZNF44	13.24	90.0928	P15621	TF	NA
ENSG00000229124	ENST00000437232	VIM-AS1	ENSG00000175395	ZNF25	1.9	90.7885	P17030	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

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lncRNA-DNA interaction for VIM-AS1

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

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 VIM-AS1

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

Only predicted by lncTar

PCCB,GCDH,ERAL1,CLPB,AIFM1

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
ENSG00000229124	ENST00000605833	exon_skip_67074	chr11:406842-406993	-36.78	-0.2554	SIGIRR	ENST00000332725,ENST00000397632,ENST00000431843	Frame-shift

-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
ENSG00000229124	ENST00000605833	exon_skip_41813	chr10:68337857-68337996	-18.15	-0.1592	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000229124	ENST00000605833	exon_skip_53559	chr10:101793912-101793998	-15.24	-0.1772	OGA	ENST00000361464	Frame-shift
ENSG00000229124	ENST00000605833	exon_skip_143275	chr16:24939363-24939597	-35.21	-0.1661	ARHGAP17	ENST00000289968	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 VIM-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
LncEditing_229066	ENSG00000229124.5	chr10	17216937	-	antisense	VIM-AS1	ENST00000605833.1	antisense	VIM-AS1-002
LncEditing_229230	ENSG00000229124.5	chr10	17223058	-	antisense	VIM-AS1	ENST00000605833.1	antisense	VIM-AS1-002
LncEditing_229232	ENSG00000229124.5	chr10	17223060	-	antisense	VIM-AS1	ENST00000605833.1	antisense	VIM-AS1-002

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
ENSG00000229124	LncEditing_229066	LAML	chr10_17216937_-	4.185899e+00	3.161522e+00	2.469635e+00	2.687432e+00	7.200375e-03	8.062070e-03	UP
ENSG00000229124	LncEditing_229230	LAML	chr10_17223058_-	4.524431e+00	3.124184e+00	1.871759e+00	3.620568e+00	2.939568e-04	4.211562e-04	UP
ENSG00000229124	LncEditing_229232	LAML	chr10_17223060_-	4.457977e+00	3.080885e+00	1.876017e+00	3.902903e+00	9.504571e-05	1.508759e-04	UP

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

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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	dG	nDG	Cancer with PC gene up-regulation	Cancer with PC gene Down-regulation
ENSG00000229124	ENST00000437232	GCDH	ENSG00000105607	ENST00000590445	-0.1048	1	-	CHOL
ENSG00000229124	ENST00000437232	GCDH	ENSG00000105607	ENST00000591050	-0.1337	221	-	CHOL
ENSG00000229124	ENST00000437232	CLPB	ENSG00000162129	ENST00000535990	-1.7417	716	-	CHOL
ENSG00000229124	ENST00000437232	CLPB	ENSG00000162129	ENST00000340729	-1.7417	716	-	CHOL
ENSG00000229124	ENST00000437232	CLPB	ENSG00000162129	ENST00000543042	-1.7417	722	-	CHOL
ENSG00000229124	ENST00000605833	GCDH	ENSG00000105607	ENST00000590445	-0.1885	264	-	CHOL
ENSG00000229124	ENST00000605833	GCDH	ENSG00000105607	ENST00000590472	-0.1233	291	-	CHOL
ENSG00000229124	ENST00000605833	GCDH	ENSG00000105607	ENST00000591050	-0.1570	82	-	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000251654	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000490504	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000483687	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000468777	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000462637	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000466072	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000482086	-0.1084	496	LUSC	CHOL
ENSG00000229124	ENST00000605833	PCCB	ENSG00000114054	ENST00000469217	-0.1084	495	LUSC	CHOL
ENSG00000229124	ENST00000605833	AIFM1	ENSG00000156709	ENST00000460436	-0.1081	404	-	CHOL
ENSG00000229124	ENST00000605833	AIFM1	ENSG00000156709	ENST00000346424	-0.1081	404	-	CHOL
ENSG00000229124	ENST00000605833	AIFM1	ENSG00000156709	ENST00000319908	-0.1081	404	-	CHOL
ENSG00000229124	ENST00000605833	AIFM1	ENSG00000156709	ENST00000287295	-0.1314	412	-	CHOL
ENSG00000229124	ENST00000605833	CLPB	ENSG00000162129	ENST00000535990	-0.2617	387	-	CHOL
ENSG00000229124	ENST00000605833	CLPB	ENSG00000162129	ENST00000340729	-0.2617	387	-	CHOL
ENSG00000229124	ENST00000605833	CLPB	ENSG00000162129	ENST00000543042	-0.2921	387	-	CHOL
ENSG00000229124	ENST00000605833	CLPB	ENSG00000162129	ENST00000535477	-0.1013	157	-	CHOL
ENSG00000229124	ENST00000605833	CLPB	ENSG00000162129	ENST00000536297	-0.1069	309	-	CHOL

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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
ENSG00000229124.5	ENST00000437232.4	35	216	109
ENSG00000229124.5	ENST00000605833.1	135	742	335

	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