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lncRNA: ENSG00000224975

Summary for INE1

Gene summary

Gene information	Ensembl ID	ENSG00000224975
	Gene symbol	INE1
	Gene name	inactivation escape 1
	HGNC	6060
	Entrez ID	8552
	Gene type	sense_intronic
	Synonyms	Xp11.3\|INE1
	UniProtAcc	O15225

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Structure and expression level for INE1

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
ENSG00000224975	7.472137e+01	1.005067e+00	1.193326e-01	8.422403e+00	3.690000e-17	1.880000e-16	UP	KIRC
ENSG00000224975	7.110821e+01	1.092889e+00	1.482702e-01	7.370924e+00	1.690000e-13	1.450000e-12	UP	KICH

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000224975	6.475972e-01	1.522371e-06	CHOL	2.415687e-05
ENSG00000224975	3.245974e-01	1.912792e-03	KICH	2.490647e-03

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lncRNA-Protein interaction for INE1

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
ENSG00000224975	ENST00000456273	INE1	ENSG00000165288	BRWD3	57.21	90.2035	Q6RI45	Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000076108	BAZ2A	50.5	90.2173	Q9UIF9	TF,RBP,Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000164190	NIPBL	45.68	93.067	Q6KC79	Epi	ChIP-seq
ENSG00000224975	ENST00000456273	INE1	ENSG00000118058	KMT2A	68.93	93.0342	Q03164	TF,Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000131149	GSE1	48.18	92.5729	Q14687	Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000167548	KMT2D	39.63	92.241	O14686	Epi	NA

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
ENSG00000224975	ENST00000456273	INE1	ENSG00000118058	KMT2A	68.93	93.0906	Q03164	TF,Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000076108	BAZ2A	50.5	90.5532	Q9UIF9	TF,RBP,Epi	NA
ENSG00000224975	ENST00000456273	INE1	ENSG00000117000	RLF	39.9	91.7545	Q13129	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
ENSG00000224975	ENST00000456273	INE1	ENSG00000076108	BAZ2A	50.5	90.3577	Q9UIF9	TF,RBP,Epi	NA

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lncRNA-DNA interaction for INE1

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 INE1

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

Only predicted by lncTar

GEMIN7,RPS10,TTC1,RNF181,ECH1,GET3,LAMTOR2,PSMB2,MRPL51,STK16,FTL,AURKAIP1,NDUFB2,MRPL40,ATP5PO,SLC25A11,UROD,SURF1,COX6A1,RPS19BP1,NDUFS5,NME1,ARPC4,MFSD5,CLPP,COMMD9,ATP5ME,UBL5,SDHAF2,GPX4,PXMP2,ELOC,CNPY3,TSR3,COX6B1,UQCRC1,MYDGF,PSMC3,CHCHD5,RHOG,CYBA,UBXN1,POLR2L,RPS11,MRPS12,PFN1,NDUFB9,ATP5PD,COPS9,PSENEN,MRPL41,COMMD1,COX14,PARK7,EEF1B2,ATP5MK,FUOM,GPX1,DYNLL1,GALK1,RPS8,AKR7A2,FRG1,RNH1,CUEDC2,MRPL37,RAB5C,EIF6,RPS21,UQCRQ,TXN2,TMEM256,LYPLA2,RPL23A,ATP6V0E1,GSTO1,RPL32,AP2S1,NDUFAF8,NDUFS6,VKORC1,NDUFS3,SPAG7,TWF2,SNRPC,MICOS10,STX8,PGLS,TRMT112,ATP5MC1,ATP5PF,HINT1,PRADC1,HINT2,RHOC,PSMD8,NDUFS8,TMEM258,BRMS1,UBE2F,RPL27,PSMB7,TRAPPC3,PSMB1,POLR2E,NDUFAB1,COX5A,MDH1,UBA52,RACK1,EIF3K,YIF1B,ALKBH7,RPS27A,AGTRAP,SAT2,MRPS15,ARL2,NDUFB7,PRR13,PSMB6,NDUFC2,DUSP23,MRPL34,PSMB3,RPS29,UBB,MTLN,ETFB,NDUFB8,ECHS1,SNX17,SNU13

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
ENSG00000224975	ENST00000456273	exon_skip_1873	chr1:16391374-16391424	-7.71	-0.1928	SZRD1	ENST00000401088	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_83407	chr12:53465931-53465973	-9.13	-0.2536	PCBP2	ENST00000439930	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
ENSG00000224975	ENST00000456273	exon_skip_110959	chr14:20372732-20372857	-16.01	-0.1601	TEP1	ENST00000262715	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_114365	chr14:74290026-74290118	-16.84	-0.2105	ABCD4	ENST00000356924	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_302168	chr19:10680345-10680443	-12.76	-0.1636	ILF3	ENST00000590261	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_370518	chr22:50247691-50247776	-13.46	-0.1683	HDAC10	ENST00000216271	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_382458	chr3:38131595-38131638	-9.60	-0.3429	ACAA1	ENST00000333167	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_340759	chr2:85552415-85552567	-15.74	-0.1405	GGCX	ENST00000233838	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_442657	chr5:74730259-74730398	-15.41	-0.1185	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_509943	chrX:47175018-47175092	-13.68	-0.2206	RBM10	ENST00000377604	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_133217	chr16:8635038-8635079	-14.63	-0.5045	METTL22	ENST00000381920	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_470226	chr7:103307595-103307708	-14.52	-0.2269	PMPCB	ENST00000249269	Frame-shift
ENSG00000224975	ENST00000456273	exon_skip_511212	chrX:71555189-71555385	-20.31	-0.1302	OGT	ENST00000373719	Frame-shift

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 INE1

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_396901	ENSG00000224975.1	chrX	47205644	+	sense_intronic	INE1	ENST00000456273.1	sense_intronic	INE1-001
LncEditing_396907	ENSG00000224975.1	chrX	47205698	+	sense_intronic	INE1	ENST00000456273.1	sense_intronic	INE1-001
LncEditing_396911	ENSG00000224975.1	chrX	47205704	+	sense_intronic	INE1	ENST00000456273.1	sense_intronic	INE1-001
LncEditing_396913	ENSG00000224975.1	chrX	47205723	+	sense_intronic	INE1	ENST00000456273.1	sense_intronic	INE1-001

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
ENSG00000224975	LncEditing_396901	KIRC	chrX_47205644_+	2.928484e+00	1.285276e+00	8.416971e-01	1.092670e+01	8.591488e-28	3.469280e-27	UP
ENSG00000224975	LncEditing_396901	CHOL	chrX_47205644_+	2.188177e+00	1.438541e+00	1.652557e+00	2.589306e+00	9.616965e-03	1.568592e-02	UP
ENSG00000224975	LncEditing_396907	OV	chrX_47205698_+	2.920266e+00	1.383236e+00	9.275982e-01	8.548526e+00	1.246708e-17	4.458167e-17	UP
ENSG00000224975	LncEditing_396901	TGCT	chrX_47205644_+	2.188877e+00	1.474928e+00	1.755782e+00	3.972151e+00	7.122668e-05	1.008018e-04	UP
ENSG00000224975	LncEditing_396901	CESC	chrX_47205644_+	2.411966e+00	1.192312e+00	9.838184e-01	6.967953e+00	3.215851e-12	9.625874e-12	UP
ENSG00000224975	LncEditing_396901	ESCA	chrX_47205644_+	2.460323e+00	1.369149e+00	1.182637e+00	5.446382e+00	5.140459e-08	1.001339e-07	UP
ENSG00000224975	LncEditing_396907	ESCA	chrX_47205698_+	2.792811e+00	1.417581e+00	1.022195e+00	5.381010e+00	7.406901e-08	1.407513e-07	UP
ENSG00000224975	LncEditing_396911	ESCA	chrX_47205704_+	2.646122e+00	1.352952e+00	1.033304e+00	6.521351e+00	6.967671e-11	2.336678e-10	UP
ENSG00000224975	LncEditing_396913	ESCA	chrX_47205723_+	2.516683e+00	1.376702e+00	1.149020e+00	6.027167e+00	1.668583e-09	4.234079e-09	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
ENSG00000224975	LncEditing_396901	8.086287e-01	1.510289e-02	4.053935e-02
ENSG00000224975	LncEditing_396901	-3.159724e-01	4.300962e-03	6.301634e-03
ENSG00000224975	LncEditing_396907	-5.895244e-01	2.380909e-07	9.393769e-06
ENSG00000224975	LncEditing_396911	-3.573711e-01	5.059950e-04	1.276755e-03
ENSG00000224975	LncEditing_396913	-3.155903e-01	1.639474e-03	2.964673e-03
ENSG00000224975	LncEditing_396901	-7.385907e-01	1.083634e-03	4.334535e-03
ENSG00000224975	LncEditing_396911	-4.890668e-01	1.362943e-03	6.760988e-03

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
ENSG00000224975	ENST00000456273	RHOC	ENSG00000155366	ENST00000369638	-0.1027	161	-	KICH
ENSG00000224975	ENST00000456273	RHOC	ENSG00000155366	ENST00000369637	-0.1218	199	-	KICH
ENSG00000224975	ENST00000456273	RHOC	ENSG00000155366	ENST00000369636	-0.2080	650	-	KICH
ENSG00000224975	ENST00000456273	RHOC	ENSG00000155366	ENST00000369632	-0.5058	259	-	KICH
ENSG00000224975	ENST00000456273	RHOC	ENSG00000155366	ENST00000528831	-0.1550	188	-	KICH
ENSG00000224975	ENST00000456273	SAT2	ENSG00000141504	ENST00000269298	-0.1160	119	-	KIRC,KICH
ENSG00000224975	ENST00000456273	SAT2	ENSG00000141504	ENST00000573566	-0.2242	223	-	KIRC,KICH
ENSG00000224975	ENST00000456273	PXMP2	ENSG00000176894	ENST00000428960	-0.1350	660	-	KICH
ENSG00000224975	ENST00000456273	AKR7A2	ENSG00000053371	ENST00000489286	-0.1842	207	-	KICH
ENSG00000224975	ENST00000456273	AKR7A2	ENSG00000053371	ENST00000481966	-0.1079	641	-	KICH
ENSG00000224975	ENST00000456273	CYBA	ENSG00000051523	ENST00000261623	-0.2857	389	-	KICH
ENSG00000224975	ENST00000456273	CYBA	ENSG00000051523	ENST00000567174	-0.6036	851	-	KICH

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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
ENSG00000224975.1	ENST00000456273.1	79	19	258

	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