Table 2.
Protein-coding and non-protein coding genes neighboring (within 1000 kb) the 20 lncRNAs whose transcripts were up- or downregulated by 100 µM DEET using GREAT algorithm parameters. The GREAT algorithm defines neighboring genes as those whose transcription start site (TSS) is within 1000 kb of the input lncRNAs. lncRNA = long non-protein coding RNA; kb = kilobases. All gene names are HUGO gene nomenclature committee (HGNC) gene symbols.
| lncRNA | Gene(s) within 1000 kb of lncRNA |
|---|---|
| CYP2B7P | CYP2A7 (−54710), CYP2B6 (−53837), CYP2A6 *, CYP2A13 * |
| HCP5 | MICB (−33621), MICA (+60915) |
| AQP7P1 | ANKRD20A1 (−646908) |
| MALAT1 | SCYL1 (−22962), FRMD8 (+115516), NEAT1 * |
| SCART1 | CYP2E1 (−59218), MTG1 (+67017) |
| PFN1P2 | PPIAL4B (−247525), NBPF9 (−199977) |
| PDXDC2P | PDPR (−92503), CLEC18A (+69943), NQO1 * |
| LINC01000 | CALU (−88173), METTL2B (+174390) |
| LOC100190986 | METTL9 (−166237), NPIPB3 (−13482) |
| PSORS1C3 | POU5F1 (−5124), HLA-C (+96269), HCP5 * |
| LINC01554 | GLRX (−33468), ELL2 (+105889) |
| LOC100272217 | FUBP3 (−1184) |
| LINC00893 | IDS (−28345), CXorf40A (−6965) |
| NEAT1 | SCYL1 (−100412), FRMD8 (+38066), MALAT1 * |
| WASH5P | OR4F17 (−41513) |
| LOC100289230 | CHD1 (−3535) |
| LINC00482 | SLC38A10 (−10731), TMEM105 (+24638) |
| LINC01004 | KMT2E (−27723), LHFPL3 (+657799) |
| ERVK13-1 | KCTD5 (−16561), PDPK1 (+127950), RPS2 * |
| LOC728040 | AFM (+36985), RASSF6 (+101963), CXCL8 * |
* Neighboring differentially expressed protein-coding gene or lncRNA found previously to be within 1000 kb of dysregulated lncRNA (after 100 µM DEET treatment) before the GREAT algorithm parameters were implemented.