Table 1.
Genome-wide hotspots of LXR action
| Region number | Region coordinates | LXR sites | Regulated genes | Regulated gene names | |||
|---|---|---|---|---|---|---|---|
| Chr | Location | T09 | vehicle | Up | Down | ||
| R1 | 1 | 8412456-11763591 | 2 | 1 | 3 | 2 | RP3-477M7.4, KIF1B, EXOSC10, RERE, ENO1 |
| R3 | 1 | 23630263-26071982 | 2 | 2 | 3 | 1 | RPL11, PNRC2, CLIC4, HNRNPR |
| R4 | 1 | 27018838-33511169 | 2 | 0 | 3 | 3 | YTHDF2, SPOCD1, KHDRBS1, SLC9A1, PUM1, SNRNP40 |
| R5 | 1 | 43282794-47844512 | 2 | 2 | 6 | 3 | ERMAP, MED8, POMGNT1, KIAA0494, STIL, CMPK1, GPBP1L1, TMEM69, MKNK1 |
| R6 | 1 | 150237798-154193105 | 1 | 2 | 8 | 2 | MRPS21, MCL1, ENSA, GABPB2, S100A9, S100A8, RPS27, C1orf43, APH1A, PSMD4 |
| R7 | 1 | 154934773-156706753 | 1 | 3 | 4 | 2 | GON4L, KIAA0907, SLC25A44, CCT3, SHC1, C1orf66 |
| R8 | 1 | 201798268-207228338 | 1 | 2 | 5 | 2 | IPO9, UBE2T, KDM5B, TMEM183A, RBBP5, ADIPOR1, SOX13 |
| R10 | 1 | 226626264-229694443 | 4 | 4 | 4 | 0 | RP11-118H4.1, FTHL2, SPHAR, ABCB10 |
| R14 | 2 | 69240275-73460367 | 0 | 2 | 5 | 2 | ANTXR1, GFPT1, SNRNP27, MCEE, C2orf7, TEX261, RAB11FIP5 |
| R20 | 3 | 127317065-129041381 | 1 | 1 | 1 | 2 | CNBP, MCM2, C3orf37 |
| R21 | 3 | 193585240-196669469 | 0 | 2 | 4 | 2 | TM4SF19, AC092933.3, PAK2, NCBP2, TNK2, AC024937.4 |
| R26 | 5 | 137273648-140086267 | 2 | 2 | 6 | 5 | FAM13B, BRD8, ETF1, MATR3, PURA, C5orf53, EGR1, C5orf32, PFDN1, HARS, ZMAT2 |
| R28 | 5 | 175818220-179780388 | 2 | 1 | 2 | 5 | RP11-889L3.1, RNF130, PRELID1, HNRNPAB, RUFY1, CANX, GFPT2 |
| R29 | 5 | 178977558-180671711 | 2 | 0 | 1 | 3 | RNF130, RUFY1, CANX, GFPT2 |
| R34 | 6 | 166778406-170893749 | 1 | 2 | 4 | 0 | BRP44L, CCR6, PSMB1, PDCD2 |
| R39 | 7 | 150069060-151361890 | 1 | 2 | 2 | 2 | GIMAP8, FASTK, GIMAP5, AGAP3 |
| R45 | 8 | 143354160-145736580 | 4 | 5 | 0 | 4 | TOP1MT, PUF60, BOP1, MFSD3 |
| R48 | 9 | 106856540-108403400 | 4 | 4 | 3 | 0 | SMC2, ABCA1, FKTN |
| R51 | 9 | 138541640-140484943 | 7 | 9 | 1 | 2 | EDF1, PMPCA, ZMYND19 |
| R53 | 11 | 308106-911658 | 1 | 2 | 1 | 2 | RPLP2, IFITM2, TMEM80 |
| R56 | 11 | 63448921-66445276 | 5 | 4 | 2 | 8 | TRMT112, PRDX5, RTN3, GPR137, DPF2, SSSCA1, FIBP, DPP3, RBM4, RBM4B |
| R57 | 11 | 66247879-70053509 | 1 | 2 | 1 | 4 | FADD, DPP3, RBM4, RBM4B, SUV420H1 |
| R59 | 11 | 118230301-126138751 | 1 | 2 | 5 | 6 | UBE4A, AP000926.1, TMEM218, EI24, RPUSD4, ATP5L, ARCN1, HINFP, SLC37A2, FAM118B, SRPR |
| R61 | 12 | 56229243-57628892 | 2 | 1 | 5 | 4 | AC034102.1, CNPY2, PTGES3, NACA, PRIM1, MMP19, RAB5B, RNF41,CS |
| R75 | 16 | 108057-2759032 | 1 | 4 | 4 | 3 | STUB1, FAHD1, NDUFB10, PDPK1, RHBDF1, AC141586.5, KCTD5 |
| R76 | 16 | 2009518-3072385 | 3 | 1 | 3 | 2 | NDUFB10, PDPK1, TNFRSF12A, AC141586.5, KCTD5 |
| R77 | 16 | 28616902-31394319 | 3 | 3 | 2 | 2 | SULT1A1, VKORC1, QPRT, ITGAX |
| R80 | 17 | 3572089-7418491 | 3 | 0 | 5 | 1 | TMEM93, ITGAE, MIS12, TXNDC17, ZBTB4, ACADVL |
| R83 | 17 | 41843489-47502285 | 2 | 1 | 7 | 4 | DUSP3, GJC1, KIAA1267, KPNB1, PNPO, ZNF652, AC004797.1, NMT1, NSF, CDK5RAP3, NFE2L1 |
| R84 | 17 | 55015562-59147703 | 2 | 2 | 3 | 4 | COIL, SRSF1, AC005884.1, SUPT4H1, TRIM37, DHX40, TMEM49 |
| R85 | 17 | 73512608-76377808 | 2 | 1 | 3 | 3 | C17orf95, SRSF2, BIRC5, TSEN54, RHBDF2, SEC14L1 |
| R86 | 17 | 78863340-80685893 | 5 | 4 | 4 | 5 | ARL16, THOC4, SLC16A3, FN3KRP, AC127496.3, ACTG1, HGS, NARF, WDR45L |
| R93 | 19 | 17416476-19617122 | 3 | 0 | 2 | 2 | PDE4C, C19orf50, MRPL34, RFXANK |
| R95 | 19 | 39109721-42789931 | 3 | 1 | 6 | 2 | EIF3K, RPS16, EID2B, PSMC4, HNRNPUL1, RPS19, MRPS12, SERTAD3 |
| R97 | 19 | 49298321-51303301 | 3 | 0 | 0 | 3 | BCAT2, BAX, VRK3 |
| R98 | 19 | 52359054-56499996 | 2 | 1 | 4 | 1 | ZNF577, ZNF83, LILRB3, NLRP8, RPS9 |
| R101 | 20 | 42939823-48809213 | 2 | 2 | 6 | 3 | YWHAB, DNTTIP1, UBE2C, NCOA3, B4GALT5, RNF114, SERINC3, TMEM189-UBE2V1, CEBPB |
| R107 | 22 | 17618400-22901769 | 1 | 1 | 4 | 7 | BID, PI4KA, RANBP1, AC002472.8, CECR5, ATP6V1E1, BCL2L13, COMT, C22orf25, XXbac-B33L19.3, PRAME |
| R108 | 22 | 22890122-25024973 | 2 | 0 | 1 | 2 | MIF, PRAME, GGT1 |
The genomic regions that contain two or more LXR binding sites and three or more T09-regulated genes (red in Figure 2). The locations of each region, the number of LXR peaks and the number and name of the regulated genes are indicated (for a full summary of all regions and additional statistics see additional file 6: Table S3).