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lncRNA: ENSG00000259969

Summary for RP11-999E24.3

Gene summary

Gene information	Ensembl ID	ENSG00000259969
	Gene symbol	RP11-999E24.3
	Gene name
	HGNC
	Entrez ID
	Gene type	sense_overlapping
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-999E24.3

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
ENSG00000259969	1.112315e+02	-3.489458e+00	1.690605e-01	-2.064029e+01	1.190000e-94	1.480000e-92	DOWN	KIRC
ENSG00000259969	1.763705e+02	-1.960757e+00	1.979838e-01	-9.903625e+00	4.010000e-23	1.340000e-21	DOWN	KIRP
ENSG00000259969	5.107961e+01	-1.824964e+00	2.421178e-01	-7.537501e+00	4.790000e-14	4.590000e-13	DOWN	UCEC

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000259969	-3.425454e-01	3.518835e-18	KIRC	2.184104e-17
ENSG00000259969	-5.235159e-01	5.989890e-22	KIRP	1.829911e-19
ENSG00000259969	-3.480205e-01	3.723978e-18	UCEC	9.759390e-17

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lncRNA-Protein interaction for RP11-999E24.3

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
ENSG00000259969	ENST00000563647	RP11-999E24.3	ENSG00000102038	SMARCA1	88.16	92.4039	P28370	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
ENSG00000259969	ENST00000563647	RP11-999E24.3	ENSG00000134874	DZIP1	77.43	90.8217	Q86YF9	TF	NA
ENSG00000259969	ENST00000563647	RP11-999E24.3	ENSG00000106571	GLI3	55.77	93.3916	P10071	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 RP11-999E24.3

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

Only predicted by TDF

ARHGEF9,CTNNBIP1,ARHGEF17,MORN2,CMTM4,USP27X,ALDH4A1,USP2,SDK1,BPHL,CIRBP,COL6A2,PRX,NICN1,PEBP1,NLGN2,PRICKLE2,FAM168B,ADGRL1,DIP2C,ANO10,FKBP7,NES,P3H3,SPARCL1,GLI3,SEMA5A,OSCP1,SSPN,TUB,C20orf96,ADGRA3,FLT4,NKIRAS1,EFS,TOM1L2,LAYN,B4GAT1,APBB1,GORASP1,SERINC1,ZMYND12,LIMS2,ZER1,GALNT18,CCN2,FAM89A,SLC18B1,USP30,TMEM8B,ARMH4,CCDC8,PTH1R,SPACA9,CNRIP1,PTGFRN,TGFBR3,DACT3,MAGI1,SLC25A42,NAP1L2,NREP,CTSF,BAP1,CRABP1,MTURN,LRP1,ALDH6A1,CYB5D2,APOM,IGIP,BEND5,CD34,BRSK1,SEMA3G,NFIA,EHD3,IGSF3,SNPH,PIP4K2B,SYNE1,SLC22A17,COL9A2,RNF150,CADM1,TMEM242,MRGPRF,ALDH7A1,RAMP2,SCN4B,CYP27B1,SEMA6C,GLT8D1,HSPA12A,CDC42EP3,ACOX2,ANKRD46,TTLL1,KCTD1,HAAO,SUOX,PSKH1,ROBO4,TMEM59L,AGPAT4,PTPN21,ACAA1,DYNLL2,MFAP2,USP46,ST3GAL3,LIN52,KDR,TMEM150C,ZADH2,MAP6,PGBD1,GPX3,TSPAN2,PRCP,NRXN2,FAM228B,SCAP,RAP1GAP,PPM1K,EPM2A,SUFU,C16orf89,MTFR1L,CDKN1C,PDLIM3,GAS1,GINM1,RASSF8,GRAMD1B,POMGNT2,CHST10,MOCS2,RAB11FIP3,FBLN5,DCN,NAP1L3,FRY,EDNRB,DTX3,EMCN,FAM171A1,P3H4,ALDH2,DZIP1,OSR2,SFRP1,ADAMTSL2,ABHD14A,REEP6,CPXM1,LDB2,TMEM25,EPM2AIP1,GNG7,ECI2,DENND2A,GSTA4,GLT8D2,SHF,SEPHS1,BMERB1,PARD6G,OLFM2,MAPK10,SSBP3,NDRG2,DACH1,RCBTB2,MFAP4,NRIP2,BDH2,SMARCA1,PHYHD1,JMY,CYP26B1,TMEM178A

Exist in public source

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

Only predicted by TDF

CYP26B1,GAS1,NAP1L3,JAM2,FLT4,SOCS5,LRP1,ALDH2,ADGRL1,ZER1,AGPAT4,KPNA5,P3H4,PDLIM3,HLF,APOM,CD34,ANKRD46,TBKBP1,CRTC1,GIPC3,ELAC1,CTGF,NFIA,RASSF8,SAT2,OSCP1,CIRBP,TCEAL2

Exist in public source

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

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lncRNA-RNA interaction for RP11-999E24.3

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

Only predicted by lncTar

IKBKE,CASP8,FANCI,PKM,PMM2,NCK1,EDEM2,TPM3,GPN1,ATXN2L,CAD,ATIC,PRDX4,CORO1C,TUBA1C,TICAM1,ORMDL2

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
ENSG00000259969	ENST00000563647	exon_skip_48296	chr10:26755654-26755741	-11.04	-0.1903	ABI1	ENST00000376142	In-frame
ENSG00000259969	ENST00000563647	exon_skip_89597	chr12:6672349-6672532	-20.82	-0.1183	ZNF384	ENST00000361959,ENST00000396801	In-frame
ENSG00000259969	ENST00000563647	exon_skip_353171	chr20:58898940-58898985	-11.52	-0.2743	GNAS	ENST00000371085,ENST00000371100	In-frame
ENSG00000259969	ENST00000563647	exon_skip_353172	chr20:58898940-58898985	-11.52	-0.2743	GNAS	ENST00000371085,ENST00000371100	In-frame
ENSG00000259969	ENST00000563647	exon_skip_48327	chr10:26771074-26771089	-3.82	-0.3820	ABI1	ENST00000376142	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
ENSG00000259969	ENST00000563647	exon_skip_48713	chr10:34336198-34336243	-6.29	-0.5718	PARD3	ENST00000374789	In-frame
ENSG00000259969	ENST00000563647	exon_skip_61919	chr11:67428981-67429022	-8.02	-0.2673	RPS6KB2	ENST00000312629	Frame-shift
ENSG00000259969	ENST00000563647	exon_skip_462144	chr6:125298713-125298816	-8.94	-0.1077	HDDC2	ENST00000398153	Frame-shift
ENSG00000259969	ENST00000563647	exon_skip_289780	chr17:41896619-41896649	-8.45	-0.3521	ACLY	ENST00000352035,ENST00000590151	In-frame
ENSG00000259969	ENST00000563647	exon_skip_303809	chr19:18431352-18431418	-10.39	-0.1889	SSBP4	ENST00000270061	In-frame
ENSG00000259969	ENST00000563647	exon_skip_324294	chr2:27774423-27774530	-10.63	-0.1687	MRPL33	ENST00000296102	Frame-shift
ENSG00000259969	ENST00000563647	exon_skip_148110	chr17:4892401-4892512	-12.19	-0.1311	MINK1	ENST00000355280	In-frame
ENSG00000259969	ENST00000563647	exon_skip_504627	chr9:83973901-83973973	-11.50	-0.1742	HNRNPK	ENST00000351839,ENST00000360384	In-frame

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57994379-57994476	200.00	-75.05	95	NA
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57993752-57993841	182.00	-78.14	84	NA
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57993962-57994054	171.00	-63.10	91	NA
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57994301-57994381	165.00	-69.23	83	NA
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57993549-57993636	164.00	-66.10	87	NA
ENSG00000259969	hsa-mir-142	ENST00000563647	chr14:57994146-57994231	163.00	-70.36	75	NA
ENSG00000259969	hsa-mir-21	ENST00000563647	chr14:57993555-57993631	155.00	-53.00	77	NA
ENSG00000259969	hsa-mir-21	ENST00000563647	chr14:57993678-57993749	153.00	-57.21	71	NA
ENSG00000259969	hsa-mir-21	ENST00000563647	chr14:57994359-57994429	143.00	-54.89	64	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993815-57993895	209.00	-59.21	71	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993648-57993727	189.00	-61.67	78	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57994392-57994477	187.00	-60.46	84	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993975-57994055	184.00	-52.80	83	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993554-57993637	183.00	-53.08	83	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993905-57993982	172.00	-56.90	81	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57994288-57994369	169.00	-58.74	82	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57993751-57993832	168.00	-67.28	80	NA
ENSG00000259969	hsa-mir-29b-1	ENST00000563647	chr14:57994202-57994277	153.00	-50.52	72	NA

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Variants for RP11-999E24.3

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
ENSG00000259969	ENSG00000110076	NRXN2	ACC,GBM,PAAD,SARC,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000111012	CYP27B1	ACC,KICH,KIRC,KIRP,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000129757	CDKN1C	ACC,KICH,KIRC,KIRP,TGCT,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000131018	SYNE1	ACC,GBM,KIRC,PAAD,THCA		KIRC
ENSG00000259969	ENSG00000134504	KCTD1	ACC,GBM,KIRC,KIRP,TGCT,THYM		KIRC
ENSG00000259969	ENSG00000139971	ARMH4	ACC,GBM,KICH,KIRC,KIRP,PAAD,SARC,TGCT,UCEC,UCS,UVM		KIRC,KIRP
ENSG00000259969	ENSG00000148468	FAM171A1	ACC,GBM,KIRC,KIRP,SARC,TGCT,THCA,UCS		KIRC
ENSG00000259969	ENSG00000149582	TMEM25	ACC,GBM,KIRC,KIRP,TGCT,THYM,UVM		KIRC
ENSG00000259969	ENSG00000175662	TOM1L2	ACC,GBM,KICH,KIRC,KIRP,PAAD,TGCT,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000182118	FAM89A	ACC,KICH,KIRC,KIRP,TGCT,UCEC,UCS		KIRP,UCEC
ENSG00000259969	ENSG00000183723	CMTM4	ACC,GBM,KIRC,KIRP,MESO		KIRC,KIRP
ENSG00000259969	ENSG00000204444	APOM	ACC,KICH,KIRP,THCA,UCS		KIRP
ENSG00000259969	ENSG00000013016	EHD3	GBM,KICH,KIRC,KIRP,PAAD		KIRC,KIRP
ENSG00000259969	ENSG00000023171	GRAMD1B	GBM,KIRC,KIRP,TGCT,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000070778	PTPN21	GBM,KIRC,KIRP,TGCT,THYM,UCEC,UVM		UCEC
ENSG00000259969	ENSG00000073910	FRY	GBM,KICH,KIRC,KIRP,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000076864	RAP1GAP	GBM,KIRC,SARC,TGCT,THCA		KIRC
ENSG00000259969	ENSG00000109339	MAPK10	GBM,KICH,KIRC,KIRP,PAAD,THCA,UCEC		KIRC,UCEC
ENSG00000259969	ENSG00000111897	SERINC1	GBM,PAAD,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000112425	EPM2A	GBM,KIRC,KIRP,THCA,UVM		KIRC,KIRP
ENSG00000259969	ENSG00000119865	CNRIP1	GBM,MESO,PAAD,TGCT,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000151240	DIP2C	GBM,KICH,PAAD,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000152409	JMY	GBM,KIRC,MESO,PAAD,THYM		KIRC
ENSG00000259969	ENSG00000159423	ALDH4A1	GBM,KICH,KIRC,LGG,THCA		KIRC
ENSG00000259969	ENSG00000163644	PPM1K	GBM,KIRC,KIRP,PAAD,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000165795	NDRG2	GBM,KIRC,KIRP,LGG,TGCT,THCA,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000166313	APBB1	GBM,KIRP,PAAD,TGCT,UCEC		UCEC
ENSG00000259969	ENSG00000166402	TUB	GBM,PAAD,TGCT,THCA,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000166780	BMERB1	GBM,KIRC,MESO,TGCT,UCEC		KIRC,UCEC
ENSG00000259969	ENSG00000170153	RNF150	GBM,KIRC,KIRP,PAAD,TGCT,THCA,UCEC,UCS		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000174684	B4GAT1	GBM,KICH,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000180354	MTURN	GBM,KIRC,KIRP,PAAD,SARC,THCA,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000182700	IGIP	GBM,LGG,PAAD,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000186310	NAP1L3	GBM,KIRC,PAAD,SARC,TGCT,THYM,UCEC,UCS		KIRC,UCEC
ENSG00000259969	ENSG00000186462	NAP1L2	GBM,KIRC,PAAD,UCS,UVM		KIRC
ENSG00000259969	ENSG00000197380	DACT3	GBM,PAAD,TGCT,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000264364	DYNLL2	GBM,KIRC,THCA,THYM,UVM		KIRC
ENSG00000259969	ENSG00000273820	USP27X	GBM,MESO,PAAD,TGCT,THYM,UCEC,UVM		UCEC
ENSG00000259969	ENSG00000036672	USP2	KICH,KIRC,KIRP,PAAD,THCA,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000049089	COL9A2	KICH,KIRC,KIRP,TGCT,THYM,UCS		KIRC,KIRP
ENSG00000259969	ENSG00000053702	NRIP2	KICH,KIRP,PAAD,TGCT,THCA,THYM,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000060971	ACAA1	KICH,KIRC,KIRP,UCS,UVM		KIRC,KIRP
ENSG00000259969	ENSG00000069702	TGFBR3	KICH,KIRC,KIRP,THCA,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000072163	LIMS2	KICH,KIRP,PAAD,THCA,UCEC,UVM		KIRP,UCEC
ENSG00000259969	ENSG00000105227	PRX	KICH,KIRC,KIRP,PAAD,THYM,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000109189	USP46	KICH,KIRC,KIRP,SARC,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000112902	SEMA5A	KICH,KIRC,PAAD,TGCT,UCS		KIRC
ENSG00000259969	ENSG00000115255	REEP6	KICH,KIRC,MESO,THYM,UCS		KIRC
ENSG00000259969	ENSG00000118523	CCN2	KICH,KIRC,KIRP,PAAD,TGCT,THYM,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000132688	NES	KICH,KIRC,KIRP,MESO,THCA,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000134198	TSPAN2	KICH,KIRC,PAAD,TGCT,UCEC		UCEC
ENSG00000259969	ENSG00000137274	BPHL	KICH,KIRC,KIRP,SARC,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000152154	TMEM178A	KICH,KIRC,KIRP,TGCT,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000160801	PTH1R	KICH,KIRC,KIRP,PAAD,UCS		KIRC,KIRP
ENSG00000259969	ENSG00000163171	CDC42EP3	KICH,KIRC,KIRP,PAAD,TGCT,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000164035	EMCN	KICH,KIRC,KIRP,PAAD,TGCT,THCA,THYM,UCEC,UCS,UVM		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000165868	HSPA12A	KICH,KIRP,PAAD,TGCT,THYM		KIRP
ENSG00000259969	ENSG00000168306	ACOX2	KICH,KIRC,KIRP,TGCT,THCA,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000171533	MAP6	KICH,KIRP,PAAD,TGCT,THCA		KIRP
ENSG00000259969	ENSG00000181035	SLC25A42	KICH,KIRP,PAAD,THCA,UCEC		KIRP
ENSG00000259969	ENSG00000198721	ECI2	KICH,KIRC,KIRP,TGCT,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000205659	LIN52	KICH,KIRC,KIRP,PAAD,UCEC,UCS		KIRC,KIRP
ENSG00000259969	ENSG00000211445	GPX3	KICH,KIRC,KIRP,PAAD,THCA		KIRC,KIRP
ENSG00000259969	ENSG00000249242	TMEM150C	KICH,KIRP,MESO,THCA,THYM,UVM		KIRP
ENSG00000259969	ENSG00000003137	CYP26B1	KIRC,TGCT,THCA,UCS,UVM		KIRC
ENSG00000259969	ENSG00000011465	DCN	KIRC,KIRP,PAAD,TGCT,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000066185	ZMYND12	KIRC,KIRP,THCA,THYM,UVM		KIRC
ENSG00000259969	ENSG00000089220	PEBP1	KIRC,KIRP,PAAD,PCPG,THCA,THYM		KIRC
ENSG00000259969	ENSG00000104332	SFRP1	KIRC,KIRP,PAAD,TGCT,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000123094	RASSF8	KIRC,KIRP,PAAD,THYM,UCEC,UCS		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000139531	SUOX	KIRC,PAAD,TGCT,THCA,THYM		KIRC
ENSG00000259969	ENSG00000140092	FBLN5	KIRC,KIRP,PAAD,THCA,UCEC,UCS		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000143061	IGSF3	KIRC,TGCT,THYM,UCS,UVM		KIRC
ENSG00000259969	ENSG00000144647	POMGNT2	KIRC,MESO,PAAD,TGCT,THYM,UCS,UVM		KIRC
ENSG00000259969	ENSG00000145029	NICN1	KIRC,KIRP,TGCT,THCA,UVM		KIRC
ENSG00000259969	ENSG00000153446	C16orf89	KIRC,KIRP,TGCT,THCA,THYM		KIRC,KIRP
ENSG00000259969	ENSG00000165698	SPACA9	KIRC,KIRP,PAAD,TGCT,THCA,UVM		KIRC
ENSG00000259969	ENSG00000172935	MRGPRF	KIRC,KIRP,PAAD,THYM,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000175287	PHYHD1	KIRC,KIRP,TGCT,THYM,UVM		KIRC
ENSG00000259969	ENSG00000176533	GNG7	KIRC,KIRP,TGCT,THCA,THYM,UCEC		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000180447	GAS1	KIRC,KIRP,PAAD,TGCT,UCEC,UVM		KIRC,KIRP,UCEC
ENSG00000259969	ENSG00000186106	ANKRD46	KIRC,KIRP,SARC,THCA,UCEC		KIRP
ENSG00000259969	ENSG00000197859	ADAMTSL2	KIRC,KIRP,PAAD,SARC,UCS		KIRC,KIRP
ENSG00000259969	ENSG00000248487	ABHD14A	KIRC,KIRP,MESO,TGCT,THCA,THYM		KIRC
ENSG00000259969	ENSG00000037280	FLT4	KIRP,PAAD,TGCT,THCA,THYM,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000110328	GALNT18	KIRP,SARC,TGCT,THCA,THYM		KIRP
ENSG00000259969	ENSG00000131477	RAMP2	KIRP,MESO,PAAD,TGCT,THYM,UCEC,UCS		KIRP,UCEC
ENSG00000259969	ENSG00000146966	DENND2A	KIRP,PAAD,TGCT,THYM,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000154133	ROBO4	KIRP,TGCT,THCA,THYM,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000169744	LDB2	KIRP,PAAD,TGCT,THCA,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000174059	CD34	KIRP,MESO,PAAD,TGCT,THCA,UCEC		KIRP,UCEC
ENSG00000259969	ENSG00000079150	FKBP7	MESO,PAAD,SARC,TGCT,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000100842	EFS	MESO,PAAD,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000110811	P3H3	MESO,PAAD,SARC,TGCT,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000120820	GLT8D2	MESO,PAAD,TGCT,THCA,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000123096	SSPN	MESO,PAAD,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000126091	ST3GAL3	MESO,PAAD,TGCT,THYM,UCEC,UVM		UCEC
ENSG00000259969	ENSG00000138606	SHF	MESO,SARC,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000152583	SPARCL1	MESO,PAAD,TGCT,THCA,UCEC		UCEC
ENSG00000259969	ENSG00000154553	PDLIM3	MESO,PAAD,THCA,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000166482	MFAP4	MESO,PAAD,TGCT,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000169992	NLGN2	MESO,PAAD,TGCT,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000088882	CPXM1	PAAD,SARC,TGCT,THCA,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000123384	LRP1	PAAD,TGCT,THYM,UCEC,UCS		UCEC
ENSG00000259969	ENSG00000128052	KDR	PAAD,TGCT,THCA,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000136161	RCBTB2	PAAD,SARC,THCA,UCEC,UVM		UCEC
ENSG00000259969	ENSG00000163637	PRICKLE2	PAAD,TGCT,THCA,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000174080	CTSF	PAAD,THYM,UCEC,UCS,UVM		UCEC
ENSG00000259969	ENSG00000204381	LAYN	PAAD,TGCT,THCA,THYM,UCEC		UCEC
ENSG00000259969	ENSG00000136160	EDNRB	TGCT,THCA,THYM,UCEC,UVM		UCEC

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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
ENSG00000259969	ENST00000563647	PRDX4	ENSG00000123131	ENST00000379341	-0.2662	349	KIRC	-
ENSG00000259969	ENST00000563647	PRDX4	ENSG00000123131	ENST00000439422	-0.1775	353	KIRC	-
ENSG00000259969	ENST00000563647	PKM	ENSG00000067225	ENST00000565154	-0.1304	291	UCEC	-
ENSG00000259969	ENST00000563647	PKM	ENSG00000067225	ENST00000568459	-0.4377	329	UCEC	-
ENSG00000259969	ENST00000563647	ORMDL2	ENSG00000123353	ENST00000552672	-0.1180	846	UCEC	-
ENSG00000259969	ENST00000563647	ORMDL2	ENSG00000123353	ENST00000550836	-0.1178	274	UCEC	-
ENSG00000259969	ENST00000563647	ORMDL2	ENSG00000123353	ENST00000548974	-0.1265	846	UCEC	-
ENSG00000259969	ENST00000563647	CORO1C	ENSG00000110880	ENST00000546705	-0.4530	104	KIRC,KIRP	-
ENSG00000259969	ENST00000563647	CORO1C	ENSG00000110880	ENST00000421578	-0.6110	599	KIRC,KIRP	-
ENSG00000259969	ENST00000563647	FANCI	ENSG00000140525	ENST00000570225	-0.1178	713	KIRC,KIRP,UCEC	-
ENSG00000259969	ENST00000563647	IKBKE	ENSG00000263528	ENST00000579827	-0.1421	309	KIRP,UCEC	-

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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
ENSG00000259969	RP11-999E24.3,hsa-mir-21,WASF3	UCEC,TGCT,THCA,ACC,KIRP
ENSG00000259969	RP11-999E24.3,hsa-mir-142,WASF3	UCEC,TGCT,ACC,THYM,KIRP

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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
ENSG00000259969.1	ENST00000563647.1	81	699	454

	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