 lncRNA targets the enhancer region and positively regulates the gene expression. |
| Only predicted by TDF | | ZNF30,CEBPZ,RBM19,NCOA2,PUM1,XRN1,ZNF16,ILF3,CPEB2,PBX2,RBM39,ZBTB4,GLYR1,CIRBP,LCORL,JAZF1,MZF1,MYSM1,NRF1,ZNF2,KAT7,ARID2,ZXDC,SUGP2,DMTF1,VEZF1,RBM27,ZNF70,BAZ2A,ZNF77,ZNF24,DDX52,RBM28,ZNF74,TBP,GABPA,IKZF5,ZBED4,DDX55,KMT2B,TET3,ZBTB5,ZFP14,RNPC3,ZFP69,BARD1,SAFB2,KDM5B,ATMIN,THOC1,ZNF25,LARP7,TRNT1,PNPT1,CNOT4,SON,CHTOP,TFAP4,DDX59,CWC22,ZBED5,ZZZ3,SCAF4,CENPT,TTC14,ZBED3,CREB1,MEX3C,RC3H1,PCBP2,MRM1,ZNF44,EEA1,ZNF91,SRSF4,ZFP91,RBMX,AGO2,RBM4B,CSTF3,RBMS3,TIGD6,RBM26,TCFL5,RBM14,PURB,ADNP,GZF1,NCBP1,MYEF2,PPIL4,MBD1,IKZF4,PUS7L,ASH1L,CLOCK,DHX34,NFIA,CASC3,FUBP1,RBM15,ZFP30,SP4,RBM43,MBD2,PRDM4,LIN54,TCF20,AGFG1,UBR5,THAP9,THOC2,DDX6,TSN,ZBTB6,ZNF34,THAP6,DDX17,ZBTB2,E2F5,CSTF1,SRRM2,PUS7,RFX7,E2F6,FOXN3,AQR,ZNF57,ZNF22,FMR1,LCOR,MECP2,PHF1,FOXJ3,PURA,PHAX,ZNF41,ZC3H8,TTF1,RBM41,HSF4,SART3,DZIP3,SRBD1,ZFP62,SGSM2,SMAD3,PAIP1,ZNF28,CPSF2,ZNF45,CELF1,SCMH1,PSPC1,KRR1,TMF1,ELK4,TIGD1,RBM45,NFXL1,BACH1,PRDM2,AGO3,RBM18,NFIB,FOXP1,SRSF2,MBD6,DDX31,TFCP2,ZMAT1,ZNF83,SKIL,QKI,ZFR,ZNF3,RFX3,STAU1,ZFX,ZNF8,NAF1,ZNF18,NKRF,NR2C2,EIF2D,SYNJ1,PCGF2,SIX5,PUS10,GPBP1,ARNT,RBM6,HMGN3,ZNF14,NOP2,G3BP2,RBM48,LSM11,PUM2,XPO1,RBM5,ELF2,SMAD4,RBMS1,NFYB,ZNF43,PTBP3,ZFP28,MTF1,SP3,ZNF17,SRCAP,ZNF84,DDX42,TRA2A,KMT2A,PDCD4,ZNF69,HINFP,XPA,AKAP1,NR2C1,TFDP2,ZFP3,PCGF6,SFPQ,ETV3,TET2,RBM33,NOL8,ATF2,ZNF10 | | Exist in public source | | NA |
| lncRNA targets the promoter region and positively regulates the gene expression. |
| Only predicted by TDF | | E2F5,XPO1,ZNF18,MECP2,BAZ2A,ZMAT1,ZNF57,RBMX,REST,RBM43,ZNF3,PUM2,RBMS1,PPIL4,DDX21,EIF2D,PBX2,ZNF70,SRRM2,TCFL5,CASC3,ZNF30,CDC5L,BPTF,TRA2A,TBP,DDX17,ZFP14,RBM5,PUS7,DDX52,MBNL1,ZFX,ZNF14,TIGD6,FUBP1,LCOR,PSPC1,RBM19,ZNF83,BACH1,THAP9,ADNP,TET2,ETV3,NR2C2,CPSF2,CELF1,ZNF2,STAU1,LCORL,SP3,MZF1,ZBTB4,ZNF22,E2F6,DKC1,ZFP2,ZNF45,SRSF5,TFAP4,ZNF69,DDX46,PUS10,NFX1,ZFP30,JAZF1,AKAP1,SRSF4,PTBP3,THAP6,UBR5,CNOT6,ZNF85,PHF20,RBMS2,FMR1,TFCP2,TERF1,FOXJ3,FOXK1,SRSF1,RBM6,ZFP3,RBMS3,NFIA,RBM39,PCBP2,DDX10,ZBTB6,DDX1,CIRBP | | 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 | | PUF60,RBM42,RNH1 | | 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 | | ENSG00000272335 | ENST00000607056 | exon_skip_55192 | chr11:251819-251936 | -15.91 | -0.2040 | PSMD13 | ENST00000532097 | In-frame | | ENSG00000272335 | ENST00000607056 | exon_skip_150854 | chr17:32366664-32366757 | -11.44 | -0.1634 | ZNF207 | ENST00000321233 | In-frame | | ENSG00000272335 | ENST00000607056 | exon_skip_325891 | chr2:62987930-62988038 | -10.23 | -0.1233 | EHBP1 | ENST00000263991 | In-frame | | ENSG00000272335 | ENST00000607056 | exon_skip_83407 | chr12:53465931-53465973 | -10.35 | -0.2797 | 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 | | ENSG00000272335 | ENST00000607056 | exon_skip_111863 | chr14:23565815-23565892 | -12.93 | -0.1930 | AP1G2 | ENST00000308724,ENST00000397120 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_300663 | chr19:1425877-1425960 | -10.30 | -0.1839 | DAZAP1 | ENST00000233078 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_361485 | chr21:29008239-29008307 | -9.17 | -0.2038 | RWDD2B | ENST00000493196 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_66185 | chr11:124626472-124626609 | -18.44 | -0.1397 | TBRG1 | ENST00000441174 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_382458 | chr3:38131595-38131638 | -10.17 | -0.2365 | ACAA1 | ENST00000333167 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_9446 | chr1:147270931-147271005 | -8.44 | -0.2910 | CHD1L | ENST00000369258 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_66482 | chr11:126274926-126275021 | -12.15 | -0.2132 | FOXRED1 | ENST00000263578 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_380242 | chr3:186784961-186785101 | -15.31 | -0.1331 | EIF4A2 | ENST00000323963 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_470226 | chr7:103307595-103307708 | -12.40 | -0.2385 | PMPCB | ENST00000249269 | Frame-shift | | ENSG00000272335 | ENST00000607056 | exon_skip_377198 | chr3:123130479-123130616 | -15.69 | -0.1453 | PDIA5 | ENST00000316218 | Frame-shift |
| lncRNA targets by miRNA. |
 |
| LncRNA Ensembl ID | miRNA ID | LncRNA ENST ID | Binding site in lncRNA | Score | Energy | Align Len | Public source | | ENSG00000272335 | hsa-mir-155 | ENST00000607056 | chr5:44826277-44826344 | 160.00 | -51.16 | 63 | NA | | ENSG00000272335 | hsa-mir-155 | ENST00000607056 | chr5:44828339-44828406 | 156.00 | -50.54 | 65 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827048-44827134 | 204.00 | -58.58 | 88 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827951-44828027 | 178.00 | -60.15 | 78 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827875-44827958 | 176.00 | -57.29 | 83 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44828424-44828512 | 175.00 | -54.50 | 88 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827195-44827289 | 174.00 | -55.80 | 93 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826484-44826576 | 173.00 | -58.32 | 85 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827706-44827799 | 171.00 | -56.50 | 70 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826612-44826717 | 169.00 | -53.29 | 98 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44828293-44828378 | 164.00 | -64.06 | 79 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826094-44826189 | 158.00 | -58.24 | 87 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826329-44826411 | 154.00 | -53.55 | 82 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826712-44826794 | 154.00 | -53.70 | 84 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44826223-44826315 | 153.00 | -55.46 | 88 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44828098-44828182 | 151.00 | -51.68 | 85 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44828187-44828276 | 151.00 | -56.93 | 90 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827284-44827372 | 146.00 | -59.86 | 74 | NA | | ENSG00000272335 | hsa-mir-511 | ENST00000607056 | chr5:44827406-44827509 | 145.00 | -76.63 | 100 | 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 |
| 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 |
| lncRNA regulates mRNA by competing the miRNA binding site with mRNA. |
| LncRNA Ensembl ID | lncRNA-miRNA-mRNA | Cancer Types | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,FBXL2 | THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,USP30 | PCPG,THCA,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,IFT140 | THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,KBTBD7 | PCPG,THCA,ACC,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,ZNF10 | PCPG,THCA,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,KLHDC10 | PCPG,THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,CRTC1 | PCPG,ACC,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,RAB40B | PCPG,THCA,MESO,PAAD,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,OBSL1 | THCA,ACC,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,ZADH2 | PCPG,THCA,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,PREPL | PCPG,THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,EPM2AIP1 | PCPG,THCA,ACC,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,SALL2 | PCPG,THCA,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,GIN1 | THCA,ACC,MESO,PAAD,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,BEX4 | PCPG,THCA,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,B4GAT1 | THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,PLA2G12A | THCA,MESO,PAAD,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-155,SLC25A23 | THCA,ACC,MESO,SARC,THYM | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,KLHDC10 | PCPG,CHOL,MESO,KIRP,LIHC | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,PAK4 | PCPG,CHOL,ACC,KIRP,LIHC | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,PCSK4 | PCPG,CHOL,ACC,MESO,KIRP | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,UBN2 | PCPG,CHOL,ACC,MESO,KIRP | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,DUS4L | PCPG,CHOL,MESO,KIRP,LIHC | | ENSG00000272335 | RP11-53O19.3,hsa-mir-511,SH2B1 | PCPG,CHOL,ACC,MESO,KIRP |
| ORFfinder result for the gencode.v22.lncRNA.transcript.fa. |
| lncRNA Ensembl ID | lncRNA ENST ID | length(AA) | start at transcript | end at transcript | | ENSG00000272335.1 | ENST00000607056.1 | 55 | 410 | 243 |
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