Table 1 List of 40 lncRNAs differentially expressed in RCC from the present work: 29 intronic lncRNAs and 11 lincRNAs (FDR <5%; >1.5-fold change)
GenBank accession of probe§ | lncRNA type | RefSeq of host gene | Host gene symbol | Genomic coordinates | FDR (%) | Fold change of lncRNA | Average fold change of host gene†|
|---|---|---|---|---|---|---|---|
AW835362 | Intronic | NM_001553 | IGFBP7 | chr4:57928550-57929060 | 0.00 | 4.88 | -1.15 (2/4) |
AW881130 | Intronic | NM_006868 | RAB31 | chr18:9711672-9712160 | 0.00 | 3.72 | 2.56 (5/5) |
BF881464 | Intronic | NM_004930 | CAPZB | chr1:19724054-19724494 | 0.00 | 2.03 | 1.34 (3/5)* |
AW846722 | Intronic | NM_024113 | C11orf49 | chr11:47169567-47169799 | 0.00 | 2.02 | -0.34 (2/4) |
AW815357 | Intronic | NM_153326 | AKR1A1 | chr1:46029945-46030338 | 0.00 | 1.77 | -2.20 (3/3) |
AW937741 | Intronic | NM_003137 | SRPK1 | chr6:35819568-35820194 | 2.46 | 1.7 | -1.37 (3/4) |
BF350736 | Intronic | NM_025228 | TRAF3IP3 | chr1:209954933-209955401 | 1.93 | 1.65 | 1.39 (4/4) |
CK327196 | Intronic | NM_002581 | PAPPA | chr9:119104917-119105402 | 1.86 | 1.63 | -3.49 (5/5) |
BF743551 | Intronic | NM_005720 | ARPC1B | chr7:98991157-98991537 | 1.37 | 1.6 | 2.90 (5/5) |
AW748493 | Intronic | NM_001098634 | RBM47 | chr4:40563872-40564416 | 3.16 | -1.52 | -1.82 (4/4) |
CK327206 | Intronic | NM_015995 | KLF13 | chr15:31628837-31629268 | 2.46 | -1.53 | 1.19 (1/4) |
CK327137 | Intronic | NM_173355 | UPP2 | chr2:158886308-158886559 | 1.37 | -1.55 | -6.05 (1/2) |
BE168993 | Intronic | NM_005882 | MAEA | chr4:1318234-1318651 | 1.68 | -1.56 | -1.63 (2/4) |
BE181783 | Intronic | NM_001893 | CSNK1D | chr17:80226176-80226555 | 0.75 | -1.63 | -1.28 (3/3)* |
AW836810 | Intronic | NM_000314 | PTEN | chr10:89630175-89630699 | 0.00 | -1.63 | 1.74 (4/4) |
BG010306 | Intronic | NM_005474 | HDAC5 | chr17:42175003-42175469 | 0.75 | -1.66 | 0.00 (0/3) |
BF327015 | Intronic | NM_003298 | NR2C2 | chr3:15052840-15053222 | 0.00 | -1.7 | -0.34 (0/5) |
BF882783 | Intronic | NM_004924 | ACTN4 | chr19:39203995-39204367 | 0.75 | -1.74 | -0.29 (1/5) |
BF357721 | Intronic | NM_002755 | MAP2K1 | chr15:66764897-66765436 | 0.00 | -1.78 | 1.52 (3/4) |
BF360792 | Intronic | NM_020387 | RAB25 | chr1:156032114-156032418 | 0.75 | -1.79 | -5.17 (4/4) |
CK327077 | Intronic | NM_001170704 | MBNL3 | chrX:131621693-131622042 | 0.00 | -1.9 | -0.79 (0/5) |
CK327106 | Intronic | NM_005781 | TNK2 | chr3:195591793-195592189 | 0.00 | -1.95 | -1.16 (4/4)* |
BF768459 | Intronic | NM_004924 | ACTN4 | chr19:39200205-39200785 | 0.00 | -2.01 | -0.29 (1/5)* |
BF368747 | Intronic | NM_006516 | SLC2A1 | chr1:43409776-43410148 | 0.00 | -2.01 | 4.43 (5/5) |
BE080597 | Intronic | NM_002829 | PTPN3 | chr9:112237298-112237614 | 0.00 | -2.13 | -2.15 (5/5) |
BF332192 | Intronic | NM_017890 | VPS13B | chr8:100419550-100419768 | 0.00 | -2.13 | 1.37 (3/5) |
BE168995 | Intronic | NM_018253 | YY1AP1 | chr1:155656314-155656660 | 0.00 | -2.23 | n.d. |
CK327034 | Intronic | NM_015575 | GIGYF2 | chr2:233592945-233593379 | 0.00 | -2.45 | 1.16 (2/4) |
BF368584 | Intronic | NM_006260 | DNAJC3 | chr13:96432041-96432369 | 0.00 | -2.81 | 1.74 (1/1) |
BF368636 | lincRNA1 RefSeq ncRNA | NR_028288 | TCL6 | chr14:96131134-96131552 | 0.00 | 1.92 | - |
AW880409 | lincRNA2 RefSeq ncRNA | NR_003255 and NR_001564 | TSIX and XIST | chrX:73042786-73043127 | 1.95 | 1.74 | - |
AW880864 | lincRNA3 | n.a. | n.a. | chr9:18430899-18431447 | 0.41 | 1.68 | - |
BF987841 | lincRNA4 | n.a. | n.a. | chr14:53107162-53107542 | 1.12 | 1.64 | - |
AW880828 | lincRNA5 | n.a. | n.a. | chr2:26955660-26956225 | 0.78 | 1.63 | - |
BF333219 | lincRNA6 | n.a. | n.a. | chr12:49324983-49325465 | 0.75 | -1.63 | - |
BG009895 | lincRNA7 | n.a. | n.a. | chr21:19119867-19120311 | 0.00 | -1.74 | - |
BE710971 | lincRNA8 | n.a. | n.a. | chr17:18176339-18176682 | 0.00 | -1.93 | - |
BE718437 | lincRNA9 | n.a. | n.a. | chr17:56595754-56596085 | 0.00 | -1.94 | - |
BF333731 | lincRNA10 | n.a. | n.a. | chr17:62118605-62119046 | 0.00 | -2.19 | - |
AW996872 | lincRNA11 | n.a. | n.a. | chr15:58887770-58888280 | 0.00 | -2.45 | - |