 lncRNA targets the enhancer region and positively regulates the gene expression. |
| Only predicted by TDF | | ZNF30,CEBPZ,PUM1,ILF3,PBX2,RBM39,THAP4,GLYR1,MZF1,MYSM1,NRF1,CSDE1,AKAP8,ZNF2,KAT7,ARID2,ZXDC,SUGP2,TRUB2,DMTF1,VEZF1,RBM27,DDX52,RBM28,ATF6B,TBP,GABPA,DDX55,TET3,ZBTB5,SRP68,ZFP14,RNPC3,KDM5B,ATMIN,LARP7,PNPT1,CNOT4,SON,CHTOP,TFAP4,DDX59,CWC22,ZBED5,ZZZ3,PNO1,MLX,ZBED3,RBM4,CREB1,RC3H1,PCBP2,MRM1,SP100,ZNF44,RBM4B,U2AF2,CSTF3,TIGD6,ZFP1,TCFL5,ERAL1,GZF1,ADNP,NCBP1,TERF2,MBD1,ASH1L,NFYC,DHX34,ASCC1,FUBP1,RBM43,SF3B6,AGFG1,DDX6,TSN,ZBTB6,THAP6,PATZ1,ZBTB2,CSTF1,PUS7,E2F6,BRF2,AQR,ZNF22,SP2,FOXJ3,SRSF9,ZC3H8,TTF1,SART3,THAP1,SRBD1,ILF2,IRF2,NIP7,ZFP62,MEX3D,ZNF48,PARN,PAIP1,ZNF28,CPSF2,ZNF45,CELF1,ELK4,RTCA,RBM45,TIGD1,NFXL1,RBM18,UNC50,MBD6,DDX31,MYNN,TFCP2,ZFR,ZNF3,STAU1,ZNF18,NKRF,EIF2D,SIX5,STAT6,C1D,CPSF3,ZNF14,RFX1,KHDC1,RBM48,PUM2,XPO1,ELF2,SMAD4,NFYB,ZNF43,MTF1,SP3,ZNF84,DDX42,RXRB,TRA2A,CSTF2,NAIF1,AKAP1,HINFP,TFDP2,ZFP3,ADAT1,SFPQ,XPO5,ETV3,TDRKH,NOL8,ATF2 | | Exist in public source | | NA |
| lncRNA targets the promoter region and positively regulates the gene expression. |
| lncRNA targets the promoter region and negatively regulates the gene expression. |
| 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 Ensembl ID | LncRNA ENST ID | Exon ID | Skipped Exon | dG | ndG | Gene name with skipped exon | TransID with skipped exon | ORF mutation | | ENSG00000272913 | ENST00000609975 | exon_skip_84780 | chr12:57720098-57720263 | -23.52 | -0.1452 | OS9 | ENST00000315970 | 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 | | ENSG00000272913 | ENST00000609975 | exon_skip_462160 | chr6:127316449-127316502 | -11.78 | -0.2945 | ECHDC1 | ENST00000531967 | Frame-shift |
| lncRNA targets by miRNA. |
 |
| LncRNA Ensembl ID | miRNA ID | LncRNA ENST ID | Binding site in lncRNA | Score | Energy | Align Len | Public source | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95526361-95526437 | 185.00 | -105.73 | 73 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95526100-95526168 | 177.00 | -92.63 | 72 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525171-95525241 | 170.00 | -107.14 | 73 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525829-95525909 | 164.00 | -95.66 | 76 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525314-95525394 | 161.00 | -96.23 | 78 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525529-95525608 | 157.00 | -92.03 | 77 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525920-95525989 | 155.00 | -87.71 | 71 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525698-95525772 | 152.00 | -90.01 | 76 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95526169-95526233 | 147.00 | -82.84 | 66 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95526253-95526328 | 141.00 | -99.07 | 71 | NA | | ENSG00000272913 | hsa-mir-1258 | ENST00000609975 | chr2:95525110-95525167 | 140.00 | -90.28 | 56 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525293-95525364 | 183.00 | -75.01 | 62 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525841-95525907 | 179.00 | -68.05 | 64 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95526276-95526345 | 167.00 | -67.88 | 69 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525638-95525702 | 165.00 | -56.15 | 62 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525191-95525275 | 162.00 | -81.26 | 82 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95526160-95526231 | 160.00 | -62.37 | 71 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525360-95525423 | 156.00 | -70.85 | 67 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525113-95525191 | 154.00 | -80.59 | 72 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95526436-95526504 | 153.00 | -85.33 | 61 | NA | | ENSG00000272913 | hsa-mir-378a | ENST00000609975 | chr2:95525966-95526027 | 149.00 | -65.57 | 58 | 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 | | ENSG00000272913 | RP11-440D17.3,hsa-mir-1258,NCSTN | KICH,CHOL,GBM,DLBC,LIHC | | ENSG00000272913 | RP11-440D17.3,hsa-mir-1258,VPS54 | KICH,CHOL,GBM,DLBC,LIHC | | ENSG00000272913 | RP11-440D17.3,hsa-mir-378a,TMEM9B | CHOL,BRCA,UVM,GBM,DLBC |
| ORFfinder result for the gencode.v22.lncRNA.transcript.fa. |
| lncRNA Ensembl ID | lncRNA ENST ID | length(AA) | start at transcript | end at transcript | | ENSG00000272913.1 | ENST00000609975.1 | 57 | 299 | 126 |
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