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lncRNA: ENSG00000196167

Summary for COLCA1

Gene summary

Gene information	Ensembl ID	ENSG00000196167
	Gene symbol	COLCA1
	Gene name	colorectal cancer associated 1
	HGNC	33789
	Entrez ID	399948
	Gene type	antisense
	Synonyms	11q23.1\|COLCA1
	UniProtAcc	Q6ZS62

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Structure and expression level for COLCA1

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
ENSG00000196167	6.764223e+02	-1.571515e+00	1.787530e-01	-8.791544e+00	1.480000e-18	8.200000e-18	DOWN	KIRC
ENSG00000196167	3.536906e+03	1.424823e+00	2.322917e-01	6.133766e+00	8.580000e-10	4.810000e-09	UP	KICH
ENSG00000196167	4.922579e+02	-1.692468e+00	2.138090e-01	-7.915793e+00	2.460000e-15	3.560000e-14	DOWN	KIRP

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000196167	3.682459e-01	3.844390e-04	KICH	5.813467e-04
ENSG00000196167	-4.056910e-01	1.718445e-25	KIRC	3.290640e-24
ENSG00000196167	-4.697197e-01	1.975728e-17	KIRP	1.097427e-15
ENSG00000196167	-3.141491e-01	6.889748e-15	LUAD	8.944145e-14

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lncRNA-Protein interaction for COLCA1

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
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000169057	MECP2	70.25	93.9847	P51608	TF,Epi	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000145241	CENPC	124.86	97.2657	Q03188	Epi	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000165288	BRWD3	117.74	93.7666	Q6RI45	Epi	NA
ENSG00000196167	ENST00000355430	COLCA1	ENSG00000145241	CENPC	97.49	95.4228	Q03188	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
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000196670	ZFP62	112.87	95.472	Q8NB50	TF	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000167232	ZNF91	111.48	97.9832	Q05481	TF	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000147124	ZNF41	100.07	96.8531	P51814	TF	NA
ENSG00000196167	ENST00000355430	COLCA1	ENSG00000196670	ZFP62	91.12	92.7109	Q8NB50	TF	NA
ENSG00000196167	ENST00000355430	COLCA1	ENSG00000167232	ZNF91	89.25	96.7799	Q05481	TF	NA
ENSG00000196167	ENST00000355430	COLCA1	ENSG00000147124	ZNF41	80.13	94.7072	P51814	TF	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000169057	MECP2	70.25	93.9249	P51608	TF,Epi	NA
ENSG00000196167	ENST00000532918	COLCA1	ENSG00000167232	ZNF91	110.52	93.2171	Q05481	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
ENSG00000196167	ENST00000532918	COLCA1	ENSG00000122965	RBM19	136.3	92.7549	Q9Y4C8	RBP	NA
ENSG00000196167	ENST00000540738	COLCA1	ENSG00000122965	RBM19	136.81	97.1369	Q9Y4C8	RBP	NA
ENSG00000196167	ENST00000355430	COLCA1	ENSG00000122965	RBM19	110.25	95.4502	Q9Y4C8	RBP	NA

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lncRNA-DNA interaction for COLCA1

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

Only predicted by TDF

MACIR,RBM19,GATA2,MECP2,ITPR2,HEPACAM2,MBOAT1,ZNF41,MTMR10,FECH,SLC29A2,TBC1D24,CENPC,PDP2,TRIP11,EXPH5,CHPT1,ATG2B,MAGI1,ZFP62,TC2N,TMEM116,ILDR1,ITFG2,SEPSECS,ZNF91,BRWD3,RALGAPA2,TMEM161B,ZDHHC23,ABCC5,AMPD3,ATP7A,PPM1L,GOLGA4,PPFIBP2,SVIP,TRIM68,C2CD5,ABHD2,FAN1,MTX3,SLC25A40,TRMT2B,CLDN8,TAPT1,THAP6,IBA57,ABHD18

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 COLCA1

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 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
ENSG00000196167	ENST00000526150	exon_skip_85538	chr12:71894324-71894375	-10.60	-0.2163	TBC1D15	ENST00000550746	In-frame
ENSG00000196167	ENST00000526150	exon_skip_296984	chr18:58335477-58335537	-8.93	-0.1567	NEDD4L	ENST00000400345	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
ENSG00000196167	ENST00000526150	exon_skip_361434	chr21:25997359-25997416	-9.60	-0.2087	APP	ENST00000346798	In-frame
ENSG00000196167	ENST00000526150	exon_skip_470719	chr7:117134123-117134192	-8.03	-0.1255	ST7	ENST00000265437	In-frame
ENSG00000196167	ENST00000526150	exon_skip_376144	chr3:100311832-100311877	-8.58	-0.2451	TBC1D23	ENST00000394144	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 COLCA1

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
ENSG00000196167	ENSG00000066926	FECH	BLCA,ESCA,KIRC,KIRP,LUSC		KIRC,KIRP
ENSG00000196167	ENSG00000140526	ABHD2	BLCA,KICH,KIRC,THYM,UCEC	KICH
ENSG00000196167	ENSG00000166912	MTMR10	BLCA,KIRC,KIRP,LUAD,PAAD		KIRC
ENSG00000196167	ENSG00000198270	TMEM116	BLCA,ESCA,KICH,KIRC,KIRP	KICH	KIRC
ENSG00000196167	ENSG00000110723	EXPH5	CESC,KICH,KIRC,LUAD,PAAD,PRAD	KICH
ENSG00000196167	ENSG00000188175	HEPACAM2	COAD,KICH,KIRC,KIRP,PAAD	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000156284	CLDN8	ESCA,KICH,KIRC,KIRP,LUSC	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000163590	PPM1L	ESCA,HNSC,KICH,KIRC,KIRP	KICH	KIRP
ENSG00000196167	ENSG00000165240	ATP7A	ESCA,KICH,KIRC,KIRP,LUAD,PAAD	KICH
ENSG00000196167	ENSG00000075303	SLC25A40	HNSC,KICH,KIRC,KIRP,PAAD	KICH
ENSG00000196167	ENSG00000133805	AMPD3	HNSC,KICH,KIRC,KIRP,UCEC	KICH
ENSG00000196167	ENSG00000145103	ILDR1	HNSC,KICH,KIRC,PAAD,THYM		KIRC
ENSG00000196167	ENSG00000162065	TBC1D24	HNSC,KICH,KIRC,KIRP,THYM	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000166387	PPFIBP2	HNSC,KICH,KIRC,PAAD,THCA,THYM	KICH
ENSG00000196167	ENSG00000184307	ZDHHC23	HNSC,KICH,KIRC,LUSC,PAAD,PRAD	KICH
ENSG00000196167	ENSG00000198168	SVIP	HNSC,KICH,KIRC,KIRP,PAAD	KICH
ENSG00000196167	ENSG00000123104	ITPR2	KICH,KIRC,KIRP,LUAD,UCEC	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000151276	MAGI1	KICH,KIRC,KIRP,LUAD,PAAD	KICH
ENSG00000196167	ENSG00000164180	TMEM161B	KICH,KIRC,KIRP,LUAD,PAAD,PRAD	KICH
ENSG00000196167	ENSG00000165288	BRWD3	KICH,KIRC,LUAD,PAAD,PRAD	KICH
ENSG00000196167	ENSG00000172197	MBOAT1	KICH,KIRC,KIRP,PAAD,THYM	KICH	KIRP
ENSG00000196167	ENSG00000172840	PDP2	KICH,KIRC,KIRP,LUAD,PAAD	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000174669	SLC29A2	KICH,KIRC,KIRP,PAAD,THYM	KICH	KIRC,KIRP
ENSG00000196167	ENSG00000181751	MACIR	KICH,KIRC,LUSC,PAAD,PRAD	KICH
ENSG00000196167	ENSG00000181873	IBA57	KICH,KIRC,KIRP,LUAD,THYM		KIRP
ENSG00000196167	ENSG00000188559	RALGAPA2	KICH,KIRC,LUAD,PAAD,PRAD	KICH

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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
ENSG00000196167.8	ENST00000620864.1	52	156	1
ENSG00000196167.8	ENST00000540738.3	124	2406	2780
ENSG00000196167.8	ENST00000532918.3	124	2447	2821
ENSG00000196167.8	ENST00000355430.4	124	2276	2650
ENSG00000196167.8	ENST00000526150.1	132	395	0

	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