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lncRNA: ENSG00000274020

Summary for LINC01138

Gene summary

Gene information	Ensembl ID	ENSG00000274020
	Gene symbol	LINC01138
	Gene name	long intergenic non-protein coding RNA 1138
	HGNC	49454
	Entrez ID	388685
	Gene type	lincRNA
	Synonyms	LINC01138\|01q21.2
	UniProtAcc

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Structure and expression level for LINC01138

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
ENSG00000274020	2.522765e+02	1.741226e+00	2.731694e-01	6.374162e+00	1.840000e-10	2.300000e-09	UP	CHOL
ENSG00000274020	2.943325e+02	1.138892e+00	1.057624e-01	1.076840e+01	4.850000e-27	4.280000e-26	UP	KIRC
ENSG00000274020	4.585287e+02	1.051921e+00	1.003112e-01	1.048657e+01	9.960000e-26	5.350000e-24	UP	PRAD
ENSG00000274020	1.902642e+02	1.220686e+00	1.361018e-01	8.968924e+00	2.990000e-19	2.870000e-18	UP	LUAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000274020	5.831899e-01	2.620585e-05	CHOL	1.224396e-04
ENSG00000274020	3.495846e-01	9.457057e-06	ESCA	6.992850e-04
ENSG00000274020	4.102761e-01	4.362287e-26	KIRC	9.347757e-25
ENSG00000274020	3.856459e-01	5.570124e-21	PRAD	1.439437e-19

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lncRNA-Protein interaction for LINC01138

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

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
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000236287	ZBED5	59.66	91.8757	Q49AG3	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000167232	ZNF91	54.8	94.4055	Q05481	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000198521	ZNF43	49.22	93.1011	P17038	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000198040	ZNF84	42.07	92.566	P51523	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000197857	ZNF44	29.73	93.0741	P15621	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000185507	IRF7	23.21	92.0764	Q92985	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000256223	ZNF10	19.78	94.2736	P21506	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000102878	HSF4	17.2	91.931	Q9ULV5	TF	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000144161	ZC3H8	8.87	90.9675	Q8N5P1	TF,RBP	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
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000122965	RBM19	61.63	94.0214	Q9Y4C8	RBP	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000139746	RBM26	56.7	94.7271	Q5T8P6	RBP	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000124193	SRSF6	37.15	93.6818	Q13247	RBP	NA
ENSG00000274020	ENST00000622328	LINC01138	ENSG00000144161	ZC3H8	8.87	90.6735	Q8N5P1	TF,RBP	NA
ENSG00000274020	ENST00000440862	LINC01138	ENSG00000139746	RBM26	49.52	90.3797	Q5T8P6	RBP	NA
ENSG00000274020	ENST00000614292	LINC01138	ENSG00000155363	MOV10	44.98	90.4902	Q9HCE1	RBP,Epi	PAR-CLIP

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lncRNA-DNA interaction for LINC01138

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

Only predicted by TDF

CHTOP,RBM19,TFAP4,PHF1,RBM6,ZBED5,ZC3H8,DDX49,RBM39,CENPT,TTC14,GMEB2,HSF4,RBM5,CIRBP,ELF2,ZFP62,ZNF44,MZF1,ZNF43,NRF1,ZNF91,ZNF84,RBM4B,DMTF1,CSTF3,RXRB,TIGD1,RBM45,RBM26,TRA2A,ZBTB3,MBD4,DHX34,SRSF2,HINFP,MBD6,NR2C1,DDX55,PPIE,STAT2,USF2,ZMAT1,ZNF83,IRF7,ZFP14,RNPC3,ZNF3,SNRPA,NXF1,SAFB2,THOC1,RBM33,MOV10,DDX17,EIF2D,ZNF10

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 LINC01138

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

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

ORF mutation

-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
ENSG00000274020	ENST00000440862	exon_skip_382458	chr3:38131595-38131638	-8.70	-0.6214	ACAA1	ENST00000333167	Frame-shift
ENSG00000274020	ENST00000440862	exon_skip_66482	chr11:126274926-126275021	-13.55	-0.2765	FOXRED1	ENST00000263578	Frame-shift
ENSG00000274020	ENST00000440862	exon_skip_365497	chr22:38067703-38067770	-14.00	-0.2414	PICK1	ENST00000356976,ENST00000404072	Frame-shift
ENSG00000274020	ENST00000440862	exon_skip_380242	chr3:186784961-186785101	-12.27	-0.1379	EIF4A2	ENST00000323963	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 LINC01138

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_18283	ENSG00000274020.1	chr1	148404992	-	lincRNA	LINC01138	ENST00000622328.1	lincRNA	LINC01138-001

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
ENSG00000274020	LncEditing_18283	UCS	chr1_148404992_-	3.018737e+00	1.868678e+00	1.445239e+00	2.316422e+00	2.053522e-02	2.373435e-02	UP
ENSG00000274020	LncEditing_18283	GBM	chr1_148404992_-	3.737299e+00	2.934755e+00	2.867333e+00	2.793813e+00	5.209059e-03	5.852956e-03	UP
ENSG00000274020	LncEditing_18283	LAML	chr1_148404992_-	8.608406e+00	5.765095e+00	1.728903e+00	3.957796e+00	7.564439e-05	1.218003e-04	UP
ENSG00000274020	LncEditing_18283	OV	chr1_148404992_-	4.726622e+00	2.725279e+00	1.258803e+00	6.554459e+00	5.584392e-11	1.040496e-10	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

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
ENSG00000274020.1	ENST00000622328.1	48	171	317
ENSG00000274020.1	ENST00000613452.1	229	16	705
ENSG00000274020.1	ENST00000614292.1	77	5	238
ENSG00000274020.1	ENST00000440862.2	161	795	310

	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