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Center for Computational Systems Medicine
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lncRNA summary

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lncRNA structure and expression level

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lncRNA-Protein interaction

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lncRNA-DNA interaction

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lncRNA-RNA interaction

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Variants in lncRNA

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lncRNAs regulate the target genes through functioning as enhancers

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lncRNAs regulate the target genes through recruiting transcript factors

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lncRNAs regulate the alternative splicing events through interacting with splicing factor

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lncRNAs regulate mRNA through targeting the 3'-UTR region

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lncRNAs regulate mRNA by competing with miRNA

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lncRNA coding potential

lncRNA: ENSG00000235453

Summary for TOPORS-AS1

check button Gene summary

Gene informationEnsembl ID

ENSG00000235453

Gene symbol

TOPORS-AS1

Gene name
HGNC
Entrez ID

100129250

Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for TOPORS-AS1

check buttonDifferentially expressed gene analysis between cancer and normal samples.
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value

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lncRNA-Protein interaction for TOPORS-AS1

lncrna_protein
check buttonlncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).
Epi result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000149929HIRIP314.2193.5142Q9BW71EpiNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000154832CXXC141.6593.0564Q9P0U4TF,EpiNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000078487ZCWPW136.7590.3879Q9H0M4EpiNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000105619TFPT13.2891.1167P0C1Z6EpiNA

check buttonlncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).
TF result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000167967E4F170.0392.0709Q66K89TFNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000154832CXXC141.6593.4812Q9P0U4TF,EpiNA
ENSG00000235453ENST00000425533TOPORS-AS1ENSG00000071655MBD310.5492.8589O95983TF,EpiNA
ENSG00000235453ENST00000425533TOPORS-AS1ENSG00000125817CENPB7.5290.8287P07199TFNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000176946THAP47.4790.7254Q8WY91TFNA
ENSG00000235453ENST00000453396TOPORS-AS1ENSG00000126456IRF33.0191.1316Q14653TFNA

check buttonlncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).
RBP result
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source
ENSG00000235453ENST00000425533TOPORS-AS1ENSG00000105705SUGP117.9690.0007Q8IWZ8RBPNA
ENSG00000235453ENST00000425533TOPORS-AS1ENSG00000125970RALY6.6394.0107Q9UKM9RBPNA

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lncRNA-DNA interaction for TOPORS-AS1

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for TOPORS-AS1

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
SPICE1,IDH3A,RAB11FIP5,FNIP1,UBR3,MNT,SAV1,SNX33,ARID1A,ANTXR1,MARCHF6,HCFC1,RNF123,PTPRK,TBC1D5,BECN1,MAP4K3,RDX,SBNO2,TCF20,TAF4,USP36,WWC3,TNPO3,KLHL18,QSER1,PPP1R12A,GNL3L,TBC1D4,POLR1B,CAD,KIAA1109,RNF213,EDEM1,ELMO2,EIF4G1,FRG1BP,NEDD1,FCHO2,SMG1,CREBBP,MAT2B,LGALS8,HTT,PBRM1,TRAK1,ZSWIM8,ANKRD28,CAMK2D,HEATR6,ELOA,VPS13B,FAM193A,SRP72,SACM1L,MAN1A2,TRIM5,TDG,SIN3A,YEATS2,UBXN2B,PRRC2C,SYNE2,SNX19,VPS35L,PDPK1,SLC35F5,MLEC,PHF3,CEP120,PAK2,CPEB4,PRRC1,LONP2,ARID1B,TMEM127,CALD1,EPS8,GOLIM4,DENND2B,PTPRE,TTC3,PHF20,KIDINS220,CDC27,ABRAXAS1,GTF2H3,SMARCC1,RNF31,BTBD10,FBXO11,PCDH1,GANAB,SEC23A,MINK1,MKLN1,WDR55,MFSD9,ITSN2,SLTM,MTMR12,PSME3,RB1CC1,KLF13,SAP30L,SMAD1,WIPF2,TANC2,CASP2,AGFG1,FBXL14,SEC22B,LPCAT3,GPD2,CASC3,CLCN7,SGPL1,UBE4B,CDK17,NDST1,POM121,BRPF3,YAP1,SAMD8,GTF3C3,PROSER3,PANX1,MARCHF7,OSBPL8,RNF145,PIEZO1,NCOA4,FBH1,NUP107,MICAL2,OPN3,KAT7,MTRR,KIAA1217,AZI2,UBAP2L,DCP1A,KDM2A,ACTR2,DCAF7,GPATCH8,ABL2,RPAP1,TUT7,MED1,NUP58,NPAT,TGOLN2,HBP1,EIF4G2,IPO9,PPFIBP1,PLEKHA7,CDK13,CDC23,CLASP1,NAA50,CUL2,GID4,GON4L,SMG8,CAB39,HUWE1,PRKAR1A,SLC25A40,SLCO2B1,MIS18BP1,TEP1,CALU,SLC6A6,MBOAT1,ERAP1,BACH1,YME1L1,FARP1,GOLM2,ZZEF1,LPP,DDX42,NSRP1,TRIO,SLC35B4,WDTC1,FAM13B,SH3PXD2B,MED23,ARFGEF1,NOTCH2,ZMYM3,RANBP10,SMARCAD1,ATF1,FNDC3B,NDE1,ARHGAP32,UBFD1,ANKLE2,ADAT1,LATS1,FYCO1,SPOPL,KATNIP,POLG,NOMO2,MYD88,CUL3,RBMS2,TMEM87B,FAM168B,PHF6,PNPO,SLC36A1,SLC30A6,XPO7,VPS4B,ADCY7,UHRF1BP1L,PMM2,LAMA5,POGLUT3,REV1,KHNYN,SIPA1L1,OTUD7B,DOCK4,MICAL3,DNM2,FOXJ3,MAPKBP1,EDC4,UBXN7,LARP1,WIZ,ACTN1,ITGB1,RNF214,HECTD1,DCTN4,NLN,TUT4,SLAIN2,SMG7,PDXDC1,PKN2,SASH1,ARIH1,PUM1,FNDC3A,PRPF40B,KANSL1L,SEC24B,SFT2D2,FLII,KCTD10,FAM91A1,ACAP2,KMT2D,RFX1,CTNNB1,TRAPPC8,PKD2,EXOC7,AP3D1,MON2,USP33,ANKRD27,MAPK14,ZFC3H1,RSBN1,RNF111,TP53BP1,PRRC2A,TUBGCP4,HSPA4,IGF1R,PPIP5K2,ZFR,ZDHHC5,USP32,G3BP1,TTLL5,GIGYF2,DHX38,VPS13D,TFCP2,WBP11,STAT3,FBXL18,PIAS1,DNMT1,TRPM7,POLR1A,UBE3C,TWF1,DDX3X,SOGA1,ASXL2,MAP3K20,PHF8,USP47,POLR2B,ESF1,FRYL,BAZ2A,CEP350,LMBR1,PIKFYVE,MYOF,EGFR,COPG1,HSPG2,EIF3C,BRD1,ASH1L,MAP3K3,ATP2B4,SLC10A7,DNAJC13,GNPTAB,C16orf70,LIG3,VPS50,MED13,RAP1B,TMEM131,DYRK2,EP400,XRN1,SMG6,CEMIP2,ADNP2,KIAA0232,B3GALNT2,SKI,NUP98,KIAA0586,TRIM23,DDX60,ZCCHC14,ATP11A,PLBD2,TRIP12,SRPK2,AKAP10,PRICKLE3,DIAPH1,TM9SF4,GTF2A1,CHD9,CHD2,TFIP11,GGCX,PRKAA1,SOS1,SMAD5,FLNB,SLC12A6,MORC3,CSNK1A1,TUBGCP3,GOSR1,PHF20L1,CTNNA1,ELF1,MOSPD2,KLF6,SUFU,RPE,VRK2,GCC2,TAF2,CHD6,CAST,TEX2,CAMKK2,TRIM33,HEATR5A,FEM1B,AMBRA1,TNFRSF10A,RUSF1,THOC2,CANX,CELF1,SAMD4B,MPRIP,DOCK1,CCNK,CTDSP2,NEMF,SRCAP,HAUS2,TMX3,ZDHHC7,NCOR1,ZFYVE9,FNBP1L,EMC1,SCAF11,PGM2,CNOT1,NF1,DSTYK,SLC35E1,ACIN1,ITSN1,MYH9,ZC3H7A,HERC2,SERINC5,SH3PXD2A,EIF4G3,ATXN1L,DNAJC16,FAM83B,STX17,UBR1,VPS41,SECISBP2L,PCDHGC3,DAG1,CHD8,TAOK3,RAB3GAP1,MED14,TSR1,SLC4A7,HPS3,ILF3,SLC37A3,ADAM10,KIAA0100,XPC,PRDM2,ARHGAP21,TANC1,UBE4A,FAT1,MAP3K2,ERBIN,DNAJC14,INTS3,CAP1,KIF16B,ANKRD11,ITPRIPL2,KATNAL1,WASF2,ATN1,VGLL4,MACF1,SH3GLB1,DHX8,LIMA1,FKTN,NUMB,MARF1,PPRC1,CUL4B,SPRED2,FLNA,C5orf24,ATP2C1,TTLL4,AFDN,ILK,ATXN2L,USP28,RRN3,HEG1,FARP2,TTC17,DYNC1I2,DOCK7,NEK9,SEPTIN11,CLIP1,RFFL,SART3,CORO1C,RAD50,FAM219B,PPIL4,RAI1,NCOA2,UBE3B,RC3H2,SNAP23,NFIC,GTF3C1,TULP3,XPO1,CCSER2,PRR14L,MAPK1,RNF169,UBR5,TRIM35,WDR81,ACACA,USP42,TBC1D2B,RAB11FIP1,ERN1,TRIM56,MIER3,LARP4,USP9X,MAST4,ROCK2,CCDC88A,TNKS1BP1,ZBED6,C1orf109,RHBDD1,NUP62,UEVLD,KDM5C,NOTCH3,TNS1,DCTN1,TGFBRAP1,RREB1,MYO1E,EHF,CPEB2,WNK1,SSH1,RBM41,PFAS,KLHL5,TTF2,CCNYL1,HIP1,DTWD2,SMCHD1,LYSMD3,OSBPL9,KMT2A,NID2,ANKRD26,PAXIP1,HYOU1,USP7,NFAT5,PPIG,KIF2A,DHX15,REST,RAB3D,PLS1,EMSY,SOS2,THRAP3,DYNC1H1,BACE1,PCYT1A,POLK,CPNE8,ACTN4,ELK3,NMT1,DPY19L1,IL6ST,AFF1,CARM1,ABCE1,USP8,PICALM,DHX57,GRHL2,TAOK2,ITFG1,TECPR2,LAMB1,RAD54L2,DOCK6,RBM19,FIGNL1,SPG11,SMC6,INPP4A,GLYR1,ZHX1,IBTK,FER,HGSNAT,BAZ1A,SRGAP2,LMTK2,MARK2,NRDC,RAB6A,PHLPP2,CMIP,LRRC8B,TNS3,KPNB1,GSK3B,STAU1,INAVA,QKI,AEBP2,LRRFIP1,ZFYVE16,OXSR1,GOLGA3,RNF4,NT5C2,RALGAPB,HIPK1,ARHGAP26,RNF40,QTRT2,TACC1,PIK3CB,CDKL5,SNX6,SPIRE1,PSEN1,NSD3,WDR43,CEP104,INTS6,NUP50,PTPN11,NCEH1,SCYL2,MCM3AP,MID2,MTREX,POLR2A,ANKFY1,DDX46,DNAJC11,NR2C2,DIP2A,NSUN2,CLTC,ATRN,GLG1,CREBRF,ARID4B,PARG,CIC,ATP2A2,SON,CCDC47,PTPRG,GART,PTPN12,M6PR,SNX29,PMS2,NRP1,OSBP,APAF1,BBX,TAF1,PCNX1,UBR4,DDI2,NFIX,DMXL2,CRTC3,CDH11,VIRMA,ZNF720,SLF2,IQGAP1,POLR3A,SMPD4,SLMAP,CMTR2,UBR2,KLF7,FBXW11,RFX5,STK24,UTP15,ARHGAP5,BCLAF1,CLCC1,SKIL,MCC,INO80,CSNK2A1,FTO,IKBKG,KDM1B,UBN1,SEC14L1,SETD5,NIPA2,PWWP2A,ARSB,PDLIM5,PCM1,KIF13B,SEPTIN8,DYNC1LI2,VEZT,KBTBD4,CDC40,TNKS,MIDEAS,ZNF106,RASA1,ARHGEF10,PTPN9,PTPRF,SENP6,ABCC1,MBTPS1,SF3A1,MED13L,PHC3,SEPTIN2,ADAM9,COG6,NCKAP5L,MYO10,BCL9L,ABHD5,KSR1,KMT2B,SERINC3,DVL3,TRPS1,DOCK9,SYNJ1,SBF2,ATP9B,GALNT10,ERC1,TNPO1,PGM3,USP31,NEK7,FAM160B1,RO60,CSNK1G3,HEATR5B,SEC31A,DENND5B,TBC1D9B,CYFIP1,ZNF28,ARL2BP,TMEM184C,PPFIA1,ATRX,IPP,BDP1,SYNRG,TTI1,EVC,VPS39,SLC30A7,TPP2,TOP3A,USP10,MORC2,WWC2,AFAP1,PIAS3,AHNAK,LMLN,PHRF1,MCFD2,TRAF7,YTHDC2
Exist in public source
NA

check buttonlncRNA targets the skipped exon region.
-lncRNA and exonskipping events are positively correlated.
lncRNA and exonskipping events positive correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonORF mutation
ENSG00000235453ENST00000425533exon_skip_99856chr13:39042104-39042305-17.18-0.1311NHLRC3ENST00000379600In-frame

-lncRNA and exonskipping events are negatively correlated.
lncRNA and exonskipping events negative correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF
ENSG00000235453ENST00000425533exon_skip_360302chr21:42896926-42897047-13.33-0.1270NDUFV3ENST00000340344Frame-shift
ENSG00000235453ENST00000425533exon_skip_324294chr2:27774423-27774530-18.95-0.1974MRPL33ENST00000296102Frame-shift
ENSG00000235453ENST00000425533exon_skip_90104chr12:10709907-10710114-26.51-0.1366YBX3ENST00000228251In-frame
ENSG00000235453ENST00000425533exon_skip_511212chrX:71555189-71555385-18.55-0.1131OGTENST00000373719Frame-shift
ENSG00000235453ENST00000425533exon_skip_370518chr22:50247691-50247776-15.20-0.2027HDAC10ENST00000216271Frame-shift
ENSG00000235453ENST00000425533exon_skip_29583chr1:114780109-114780215-13.15-0.1686SIKE1ENST00000060969Frame-shift
ENSG00000235453ENST00000425533exon_skip_374375chr3:49675182-49675309-21.81-0.2077APEHENST00000296456Frame-shift

check buttonlncRNA targets by miRNA.
lncRNA targets by miRNA
LncRNA Ensembl IDmiRNA IDLncRNA ENST IDBinding site in lncRNAScoreEnergyAlign LenPublic source
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551737-32551857220.00-125.37117NA
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551303-32551402192.00-89.06110NA
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551898-32552016178.00-98.17110NA
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551159-32551254172.00-93.87107NA
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551600-32551699161.00-93.67109NA
ENSG00000235453hsa-mir-222ENST00000453396chr9:32551426-32551534160.00-96.84104NA
ENSG00000235453hsa-mir-222ENST00000450093chr9:32551851-32551971220.00-125.37117NA
ENSG00000235453hsa-mir-222ENST00000450093chr9:32552012-32552130178.00-98.17110NA
ENSG00000235453hsa-mir-222ENST00000450093chr9:32551774-32551857140.00-91.9295NA
ENSG00000235453hsa-mir-222ENST00000458036chr9:32552826-32552937224.00-117.69112NA
ENSG00000235453hsa-mir-222ENST00000458036chr9:32552380-32552497217.00-108.39121NA
ENSG00000235453hsa-mir-222ENST00000458036chr9:32552548-32552673200.00-114.19118NA
ENSG00000235453hsa-mir-222ENST00000458036chr9:32552928-32553056191.00-114.34126NA
ENSG00000235453hsa-mir-222ENST00000458036chr9:32552687-32552797159.00-99.64109NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552430-32552535225.00-96.95108NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32553058-32553169224.00-117.69112NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552675-32552783220.00-95.05103NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552780-32552905200.00-114.19118NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552562-32552672163.00-93.03108NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552919-32553029159.00-99.64109NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32553160-32553251154.00-91.62105NA
ENSG00000235453hsa-mir-222ENST00000425533chr9:32552349-32552397146.00-83.0549NA

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Variants for TOPORS-AS1

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name

check buttonEdited-associated DElncRNAs in cancer.
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value

check buttonCis-expression quantitative trait loci(cis-eQTL) of lncRNA.
LncRNA Ensembl IDLncRNA NameSNP infoNumber of Positive corelated CancerPositive corelated CancerNumber of Negative corelated CancerNegative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncrna_enhancer
check buttonlncRNA regulates differentially expressed genes by function as enhancer.
LncRNA Ensembl IDPC Gene IDPC Gene NamePositive correlated cancersCancer with PC gene up-regulationCancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

lncrna_TF
check buttonLncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

check buttonLncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

lncrna_AS
check buttonLncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

check buttonLncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncrna_mRNA
check buttonlncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.
LncRNA Ensembl IDLncRNA ENST IDPC Gene NamePC Gene IDPC ENST IDdGnDGCancer with PC gene up-regulationCancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncrna_miRNA
check buttonlncRNA regulates mRNA by competing the miRNA binding site with mRNA.
LncRNA Ensembl IDlncRNA-miRNA-mRNACancer Types

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lncRNA coding potential

check buttonORFfinder result for the gencode.v22.lncRNA.transcript.fa.
lncRNA Ensembl IDlncRNA ENST IDlength(AA)start at transcriptend at transcript
ENSG00000235453.6ENST00000453396.473410631
ENSG00000235453.6ENST00000450093.178672908
ENSG00000235453.6ENST00000458036.112128393
ENSG00000235453.6ENST00000425533.1151596141