 lncRNA targets the enhancer region and positively regulates the gene expression. |
| Only predicted by TDF | | TSPYL2,FKBP8,EPOR,ATG13,ARFIP2,THAP4,PRPSAP2,MCRS1,ABHD17A,DNAJC27,CIRBP,PET100,WDR83OS,LYSMD4,KLF2,CACFD1,PPP2R3B,N4BP2L2,BCS1L,ACD,XAB2,MRPL46,ISCU,BCCIP,ACSS1,NDUFA11,SMUG1,MSANTD2,TUBGCP6,FAM200A,LIMS2,OSER1,C6orf136,EIF2B5,SLC2A11,SUGP1,SPG7,NAA80,C19orf44,BAHD1,SIAH1,PPIP5K1,CCNB1IP1,BNIP1,RAB4B,TARBP2,ILKAP,LYRM4,SSU72,CHKB,RIC8B,FANCE,CBY1,WDR83,C3orf18,ANKRD39,PDZD4,BABAM1,ACYP1,CFAP298,TSSC4,DDX49,NAPB,C3orf62,YJU2,CBX7,ZFP62,ALKBH2,ANAPC5,ZBED8,BORCS6,ORMDL1,COQ7,C22orf39,C12orf73,DDX51,AGER,ESS2,FBXW4,TFCP2,TSEN54,LRRC37B,ATG4B,MRPL57,DCUN1D2,PAN2,C2orf76,TEAD2,PFDN5,TIMM10B,FAM193B,SLC25A28,ARFGAP2,CZIB,DMAC2L,HDAC5,N4BP2L1,ELOF1,LNP1,HEXD,SDHAF2,TMEM50B,CCDC24,MRPS25,CCDC12,KAT14,FAM204A,TDRP,ALKBH3,KIF12,RSL24D1,ZNF30,ADO,TRMO,GLI4,SH2B1,FAM98C,NICN1,IP6K2,ZC3H10,IFTAP,MLLT6,PIGH,C9orf78,CAPN10,LARP6,APBB1,CTDSP1,CCDC59,SURF1,TMEM175,PTGES2,C11orf68,TNK2,SEPTIN4,TAMM41,IMP4,ZNF44,TMEM116,MTURN,RIMKLB,ANAPC13,TCTA,CCDC106,MED27,FBXO44,NELFE,GLT8D1,PATZ1,PCED1A,TUSC2,SPRYD3,TARS3,LMF1,UBOX5,DNAJC19,LENG1,DENND6B,ATF4,INPP5E,TOMM22,PPM1K,SGF29,NEK8,ZSWIM1,FIZ1,VPS4A,SERP2,MED19,HEMK1,POMGNT2,TMEM199,PTOV1,PYURF,NDUFA12,C18orf32,NDUFAF5,RBM6,AP5S1,PISD,TMEM134,POP5,CRMP1,NTHL1,GDI1,UBXN6,CUEDC2,MKKS,UBAC1,GGT7,UCKL1,GSTA4,UBXN11,PPCDC,CERS5,RSAD1,PPP1R26,RP9,ARHGEF25,EMC10,ENKD1,ZNF10,NISCH,MORN2,POMT1,YTHDF1,CDPF1,DPY19L2,KATNBL1,MKS1,CDK5RAP1,NME5,IFT88,NPRL2,LARGE2,CLK3,C14orf28,ANKRD10,UQCRB,SGSM3,COQ4,CCDC32,PBXIP1,ARMC5,ST6GALNAC6,SNU13,LRRC23,RBPMS,ZBTB3,BLCAP,BSG,RAMP2,POLI,ELP6,ZNF34,ERMARD,RNF114,PHF1,SAP30L,SNX21,TMEM128,HEXIM2,TGIF2,ARGLU1,NEPRO,UCK1,SMDT1,ANKRD54,RNF25,ZFYVE21,HSPBAP1,YAE1,CENPS,RPS6,PBX4,TMUB2,ZNF3,CIAO2B,TBC1D20,MYL6B,C19orf25,SMARCD1,MYG1,ABHD10,DDX5,DTX3,MTG2,RNF215,GIN1,TLE5,LIPT1,ABHD14A,CRAMP1,LUC7L,COA5,MROH1,C14orf93,LRSAM1,DPH7,MAPKAPK5,FUNDC2,MRPL43,POLR3F,XPA,GPS1,STX2,RWDD2A,ADAL,IMMP1L,C15orf61,RPS29,SLC25A27,TXN2,MRPS26,SERGEF,C7orf31,SNAI3,RRNAD1,CCDC92,ZSWIM7,TRIM39,NEK3,CSAD,KIAA0895L,ZNF77,MYL9,BANF1,TMEM259,FRA10AC1,FBXO10,VPS37B,LIN37,OGA,IFT27,RECQL5,PMF1,NIPSNAP3B,ASB6,LRRC75B,SS18L2,TBC1D17,DCAF16,ARL3,NT5C3B,RNH1,UBE2D4,TM2D3,OSGEPL1,SHC2,SPPL3,DTNB,YAF2,DNAJB2,MRPS31,BEND5,C20orf27,EZH1,TTLL1,TMEM9B,ARVCF,LIAS,IFT46,C12orf76,POLL,FAM228B,WASHC1,WDR61,TIGD1,KLC1,AP3S2,GPS2,TRIM52,NDUFC1,COA8,NOL12,CRYZL1,SUPT3H,CLASRP,TTC32,COMMD6,SS18,RPS24,TAPT1,SETD4,SORBS3,TYSND1,GMEB2,RBM5,BOLA1,RPS19BP1,YPEL3,BCDIN3D,TMEM11,GNG7,ATP5MC2,RXRB,PARP6,DGCR6L,PRPF40B,SIRT6,DXO,USP20,MRFAP1L1 | | Exist in public source | | NA |
| lncRNA targets the promoter region and positively regulates the gene expression. |
| Only predicted by TDF | | ANKRD39,SGSM3,DPH7,C22orf39,RP9,APITD1,VPS4A,TTLL1,TEAD2,OSGEPL1,LYSMD4,FAM204A,PISD,ZNF3,EID2B,ZNF30,C3orf18,ATG13,CFAP36,SORBS3,STX16,SNTA1,CUEDC2,HEMK1,ELOF1,MRPS31,RBM5,E4F1,DYNLRB1,DGCR14,NICN1,SS18,UBXN6,C19orf44,FAM73B,THAP7,IL3RA,PRPF40B,KLF2,VPS37D,BEND5,CRYZL1,MCRS1,TUSC2,RIMKLB,SRP14,CLASRP,LUC7L,C14orf79,TMEM134,C3orf62,ZSWIM1,BANF1,TRMO,PTDSS2,ZFP2,SRSF5,MANBAL,SETD4,NEK3,CRTC1,CIRBP,PPCDC,ZSWIM7,ELAC1,PBX4,GGA1,CCDC130,C19orf25,MAGEF1,ARIH2,C21orf59,COMMD3,ING5,ST6GALNAC6,SLC25A35,TFCP2,POMT1,BABAM1,GMPR,SLC25A38,SGF29,ARIH2OS,RBM6,TMEM50B,ALKBH2,FKBP8 | | Exist in public source | | NA |
| lncRNA targets the promoter region and negatively regulates the gene expression. |
| lncRNA targets the 3'UTR region and negatively regulates the mRNA. |
| Only predicted by lncTar | | PNPO,ECT2,LDHA,SPATS2L,FAH,FCGR2A,MYOF,TMOD3,TNFRSF1A,PLIN3,CDCP1,AP2A1,UGGT1,RTCA,IQGAP1,TPM3,RIN3,ERO1A,TUBA1C,SEC23A,GALNT7,DPP3,FNDC3B,ACTR2,ITGB4,BAZ1A,NRDC | | Exist in public source | | NA |
| lncRNA targets the skipped exon region. | | -lncRNA and exonskipping events are positively correlated. |
| LncRNA Ensembl ID | LncRNA ENST ID | Exon ID | Skipped Exon | dG | ndG | Gene name with skipped exon | TransID with skipped exon | ORF mutation | | ENSG00000278126 | ENST00000620274 | exon_skip_150854 | chr17:32366664-32366757 | -12.59 | -0.1517 | ZNF207 | ENST00000321233 | In-frame | | ENSG00000278126 | ENST00000620274 | exon_skip_83395 | chr12:53464759-53464852 | -12.30 | -0.1430 | PCBP2 | ENST00000439930 | In-frame |
| -lncRNA and exonskipping events are negatively correlated. |
| LncRNA Ensembl ID | LncRNA ENST ID | Exon ID | Skipped Exon | dG | ndG | Gene name with skipped exon | TransID with skipped exon | LOF | | ENSG00000278126 | ENST00000620274 | exon_skip_7523 | chr1:78660553-78660654 | -11.12 | -0.1135 | IFI44 | ENST00000370747 | Frame-shift | | ENSG00000278126 | ENST00000620274 | exon_skip_81515 | chr12:42351884-42352049 | -11.78 | -0.1081 | PPHLN1 | ENST00000395568 | In-frame | | ENSG00000278126 | ENST00000620274 | exon_skip_131398 | chr15:101286213-101286293 | -11.30 | -0.2825 | SNRPA1 | ENST00000254193 | Frame-shift | | ENSG00000278126 | ENST00000620274 | exon_skip_324294 | chr2:27774423-27774530 | -11.22 | -0.1476 | MRPL33 | ENST00000296102 | Frame-shift | | ENSG00000278126 | ENST00000620274 | exon_skip_361485 | chr21:29008239-29008307 | -10.51 | -0.2502 | RWDD2B | ENST00000493196 | Frame-shift |
| lncRNA targets by miRNA. |
 |
| LncRNA Ensembl ID | miRNA ID | LncRNA ENST ID | Binding site in lncRNA | Score | Energy | Align Len | Public source | | ENSG00000278126 | hsa-mir-3677 | ENST00000620274 | chr12:51202297-51202354 | 194.00 | -59.26 | 52 | NA | | ENSG00000278126 | hsa-mir-3677 | ENST00000620274 | chr12:51201832-51201889 | 165.00 | -53.53 | 55 | NA | | ENSG00000278126 | hsa-mir-3677 | ENST00000620274 | chr12:51202168-51202225 | 144.00 | -60.61 | 58 | NA | | ENSG00000278126 | hsa-mir-378a | ENST00000620274 | chr12:51202117-51202186 | 197.00 | -70.13 | 67 | NA | | ENSG00000278126 | hsa-mir-378a | ENST00000620274 | chr12:51202446-51202510 | 165.00 | -62.35 | 61 | NA | | ENSG00000278126 | hsa-mir-378a | ENST00000620274 | chr12:51201685-51201716 | 155.00 | -52.83 | 32 | NA | | ENSG00000278126 | hsa-mir-378a | ENST00000620274 | chr12:51201753-51201825 | 149.00 | -68.64 | 38 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51202084-51202173 | 181.00 | -77.47 | 97 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51202300-51202389 | 169.00 | -83.82 | 92 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51201767-51201868 | 168.00 | -89.81 | 86 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51202404-51202495 | 166.00 | -68.73 | 85 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51201977-51202063 | 149.00 | -61.45 | 95 | NA | | ENSG00000278126 | hsa-mir-744 | ENST00000620274 | chr12:51202168-51202267 | 142.00 | -78.51 | 104 | NA | | ENSG00000278126 | hsa-mir-940 | ENST00000620274 | chr12:51202300-51202390 | 168.00 | -97.45 | 88 | NA | | ENSG00000278126 | hsa-mir-940 | ENST00000620274 | chr12:51201835-51201925 | 163.00 | -91.02 | 90 | NA | | ENSG00000278126 | hsa-mir-940 | ENST00000620274 | chr12:51202095-51202179 | 150.00 | -90.93 | 89 | NA |
| 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 |
| 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 | | ENSG00000278126 | ENSG00000032742 | IFT88 | ACC,CESC,LUSC,PAAD,THCA | | CESC | | ENSG00000278126 | ENSG00000100307 | CBX7 | ACC,BRCA,CESC,CHOL,DLBC,KICH,KIRC,LUAD,LUSC,PAAD,THYM | | CESC | | ENSG00000278126 | ENSG00000111450 | STX2 | ACC,CESC,KIRP,LUSC,PAAD,TGCT,THCA | | CESC | | ENSG00000278126 | ENSG00000163644 | PPM1K | ACC,CESC,CHOL,LUSC,PAAD | | CESC | | ENSG00000278126 | ENSG00000179476 | C14orf28 | ACC,CESC,CHOL,LGG,THCA,THYM,UVM | | CESC | | ENSG00000278126 | ENSG00000214941 | ZSWIM7 | ACC,CESC,CHOL,LGG,LUSC | | CESC | | ENSG00000278126 | ENSG00000072163 | LIMS2 | BRCA,CESC,CHOL,DLBC,KIRP,LGG,LUAD,LUSC | | CESC | | ENSG00000278126 | ENSG00000101335 | MYL9 | BRCA,CESC,DLBC,SARC,THYM | | CESC | | ENSG00000278126 | ENSG00000120896 | SORBS3 | BRCA,CESC,LGG,PAAD,THCA,THYM,UCEC | | CESC | | ENSG00000278126 | ENSG00000131477 | RAMP2 | BRCA,CESC,CHOL,LGG,LUAD,LUSC,PAAD,THYM | | CESC | | ENSG00000278126 | ENSG00000136003 | ISCU | BRCA,CESC,CHOL,KIRC,LUSC,PAAD,UCEC,UCS | | CESC | | ENSG00000278126 | ENSG00000139597 | N4BP2L1 | BRCA,CESC,KIRP,LUSC,PAAD,UCEC | | CESC | | ENSG00000278126 | ENSG00000160408 | ST6GALNAC6 | BRCA,CESC,DLBC,PAAD,THYM | | CESC | | ENSG00000278126 | ENSG00000162384 | CZIB | BRCA,CESC,CHOL,PAAD,THCA,UCEC,UCS | | CESC | | ENSG00000278126 | ENSG00000166313 | APBB1 | BRCA,CESC,CHOL,KIRP,PAAD,UCEC | | CESC | | ENSG00000278126 | ENSG00000184205 | TSPYL2 | BRCA,CESC,LUAD,LUSC,PAAD,UCEC | | CESC | | ENSG00000278126 | ENSG00000240771 | ARHGEF25 | BRCA,CESC,CHOL,PAAD,UCEC,UCS | | CESC | | ENSG00000278126 | ENSG00000119242 | CCDC92 | CESC,CHOL,KIRP,LUSC,PAAD | | CESC | | ENSG00000278126 | ENSG00000129158 | SERGEF | CESC,CHOL,DLBC,KIRP,PAAD | | CESC | | ENSG00000278126 | ENSG00000144182 | LIPT1 | CESC,CHOL,KIRP,TGCT,THCA,THYM | | CESC | | ENSG00000278126 | ENSG00000169762 | TAPT1 | CESC,KICH,LUAD,LUSC,PAAD,THCA,UCS | | CESC | | ENSG00000278126 | ENSG00000175573 | C11orf68 | CESC,CHOL,DLBC,KICH,KIRP,LGG | | CESC | | ENSG00000278126 | ENSG00000178498 | DTX3 | CESC,CHOL,KICH,KIRC,KIRP,PAAD,THCA,UCEC,UCS | | CESC | | ENSG00000278126 | ENSG00000180354 | MTURN | CESC,CHOL,KICH,KIRC,PAAD,TGCT,THCA | | CESC |
| 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 |
| 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 |
| 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 | | ENSG00000278126 | ENST00000620274 | CDCP1 | ENSG00000163814 | ENST00000296129 | -0.1432 | 1 | CESC | - | | ENSG00000278126 | ENST00000620274 | TUBA1C | ENSG00000167553 | ENST00000549818 | -0.4573 | 52 | CESC | - |
| lncRNA regulates mRNA by competing the miRNA binding site with mRNA. |
| LncRNA Ensembl ID | lncRNA-miRNA-mRNA | Cancer Types | | ENSG00000278126 | RP11-454E5.4,hsa-mir-378a,SCAMP4 | KICH,CHOL,GBM,PAAD,KIRP | | ENSG00000278126 | RP11-454E5.4,hsa-mir-744,SELENOS | KICH,TGCT,LGG,GBM,THYM | | ENSG00000278126 | RP11-454E5.4,hsa-mir-744,PLEKHH1 | KICH,TGCT,ACC,GBM,THYM | | ENSG00000278126 | RP11-454E5.4,hsa-mir-744,FBXO8 | KICH,TGCT,LGG,ACC,GBM | | ENSG00000278126 | RP11-454E5.4,hsa-mir-744,TMEM259 | KICH,TGCT,LGG,ACC,GBM | | ENSG00000278126 | RP11-454E5.4,hsa-mir-744,TMEM9B | KICH,TGCT,LGG,GBM,THYM |
| ORFfinder result for the gencode.v22.lncRNA.transcript.fa. |
| lncRNA Ensembl ID | lncRNA ENST ID | length(AA) | start at transcript | end at transcript | | ENSG00000278126.1 | ENST00000620274.1 | 52 | 405 | 247 |
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