Table 2. Differentially expressed intergenic lncRNAs.
| Level of Validation | Genecode ID | Alternate ID | Position (GRCh37/hg19) |
|---|---|---|---|
| Known Genes tsl1 | LINC00880 | NR_034007 | chr3: 156799455-156840793 |
| MIR3945HG | TCONS_00008359 | chr4: 185748077-185776905 | |
| LUCAT1 | TCONS_00010402 | chr5: 90597873-90621000 | |
| PVT1 | ENST00000504719 | chr8: 128806778-129113503 | |
| SFTA1P | TCONS_00018434 | chr10: 10825866-10837007 | |
| LINC00460 | ENST00000439790 | chr13: 107028910-107030941 | |
| LINC00197 | TCONS_00023799 | chr15: 95752084-96051089 | |
| MSN | TCONS_00016990 | chrX: 64808260-64845760 | |
| Validated Genes tsl2-tsl3 | MIR4435-2HG | TCONS_l2_00015916 | chr2: 112186885-112268567 |
| CTB-43E15.1 | ENST00000523242 | chr5: 173069521-173085197 | |
| HCG15 | TCONS_l2_00024132 | chr6: 28953517-28959134 | |
| LINC00968 | ENST00000522511 | chr8: 57401656-57472382 | |
| LINC01290 | ENST00000566787 | chr16: 10608698-10622059 | |
| LINC00511 | ENST00000579631 | chr17: 70319263-70599647 | |
| RP11-353N14.2 | TCONS_l2_00011006 | chr17: 77796264-77801616 | |
| LINC00665 | ENST00000586345 | chr19: 36795481-36822667 | |
| LINC00478 | ENST00000428669 | chr21: 17553910-18013444 | |
| Predicted Genes tsl4-tsl5 | RP11-815M8.1 | TCONS_00000738 | chr1: 222054322-222158306 |
| LINC00152 | ENST00000331944 | chr2: 87754947-87821037 | |
| RP11-83M16.6 | ENST00000510621 | chr5: 66995256-67198428 | |
| RP11-359M6.1 | ENST00000548359 | chr12: 79933982-79944315 | |
| RP11-1008C21.2 | TCONS_00023630 | chr15: 38360990-38365188 | |
| Predicted Genes tslNA | TCONS_00007953 | chr4: 1546984-1555291 | |
| TCONS_00025436 | chr17: 53690342-53725799 | ||
| TCONS_00029745 | chr22: 50981205-50983413 |
LncRNAs that were deregulated in three studies (from Figure 3) that also occupy chromosomal regions in between mRNAs. LncRNAs were segregated by their Gencode transcript confidence level (tsl1 = highest quality, full transcript is validated; tsl2-3, one or many spliced ESTs are validated; tsl4-5 = one or none ESTs support the validity of the transcript, and those ESTs are suspect.) Those without a tsl ranking do not have a representative transcript in Gencode. All coordinates span the entire transcript length and are hg19 genome-based. The MSN transcript overlaps in the same orientation the MSN mRNA, therefore there is a high probability that this is not truly a lncRNA (and thus is greyed out in figure).