Table 1. Candidate lncRNAs with differentially methylated promoters and neighboring protein coding genes.
| DMR |
lncRNA |
Protein coding gene |
Expression difference |
Referencea | |||
|---|---|---|---|---|---|---|---|
| Genomic position (mm10) | Gene symbol | ID | Gene symbol | ID | Tumor –Normalb | P-valuec | |
| Hypermethylation | |||||||
| chr1:180332417-180332819 | Gm5069 | NR_003623 | Itpkb | NM_001081175 | |||
| chr2:74762966-74763423 | Haglr | NR_110445 | Hoxd1 | NM_010467 | −0.10 | 0.55 | |
| chr3:37896886-37897206 | Gm20755 | NR_040559 | |||||
| chr3:82876021-82876531 | Rbm46os | NR_040382 | Rbm46 | NM_001277170 | |||
| chr4:114907033-114907726 | Foxd2os | NR_030721 | Foxd2 | NM_008593 | −0.34 | 0.09 | |
| chr4:145463820-145464350 | Smarca5-ps | NR_002888 | |||||
| chr4:152697098-152697448 | Gm833 | NR_033138 | |||||
| chr5:19226691-19226991 | 4921504A21Rik | NR_102341 | Magi2 | NM_001170746 | 0.64 | 0.23 | |
| chr5:57718135-57718436 | 4932441J04Rik | NR_015588 | Pcdh7 | NM_018764 | −1.26 | 0.0007*** | 25 |
| chr6:47943214-47943743 | Zfp783 | NR_027963 | |||||
| chr6:52315701-52316027 | 5730457N03Rik | NR_038163 | Evx1 | NM_007966 | −0.34 | 0.10 | |
| chr6:6864808-6865158 | Dlx6os2 | NR_002839 | |||||
| chr7:14623181-14623487 | Nlrp5-ps | NR_045119 | |||||
| chr7:40899025-40899517 | A230077H06Rik | NR_040329 | Vstm2b | NM_021387 | −0.49 | 0.13 | |
| chr7:51511083-51511470 | Ano5 | NR_073508 | |||||
| chr7:57386794-57387157 | Gm9962 | NR_033504 | Gabrg3 | NM_008074 | −0.45 | 0.04* | 26 |
| chr7:63444419-63444734 | 4930554H23Rik | NR_131089 | Otud7a | NM_130880 | 2.36 | 0.00009**** | 27 |
| chr7:79515301-79515977 | AI854517 | NR_040312 | |||||
| chr8:120230039-120230397 | A330074K22Rik | NR_110496 | |||||
| chr8:121084994-121085403 | Fendrr | NR_045471 | Foxf1 | NM_010426 | 0.30 | 0.11 | |
| chr8:84912426-84912992 | Gm38426 | NR_103491 | |||||
| chr8:99416005-99416420 | A330008L17Rik | NR_132435 | Cdh8 | NM_007667 | 0.01 | 0.97 | |
| chr9:71216962-71217270 | Gm3458 | NR_110518 | Aldh1a2 | NM_009022 | −0.39 | 0.13 | |
| chr10:93336092-93336432 | Gm17745 | NR_038014 | |||||
| chr11:95143377-95143691 | Dlx4os | NR_040279 | Dlx4 | NM_007867 | 0.05 | 0.90 | |
| chr12:20815469-20816034 | 1700030C10Rik | NR_015521 | |||||
| chr13:111868178-111868548 | Gm15326 | NR_130345 | |||||
| chr13:72816340-72816825 | D730050B12Rik | NR_046196 | |||||
| chr14:118234395-118234797 | LOC105245869 | NR_131969 | Sox21 | NM_177753 | −0.27 | 0.37 | |
| chr14:39472112-39472839 | LOC432842 | NR_131973 | Nrg3 | NM_008734 | −0.15 | 0.59 | |
| chr15:83366702-83367300 | 1700001L05Rik | NR_027980 | |||||
| chr16:98081806-98082497 | A630089N07Rik | NR_015491 | |||||
| chr17:34094655-34095214 | BC051537 | NR_046183 | |||||
| chr17:80373020-80373349 | Gm10190 | NR_028385 | |||||
| chr19:30539362-30539867 | Ppp1r2-ps3 | NR_003650 | |||||
| chrX:12159988-12160665 | 2900008C10Rik | NR_045434 | |||||
| chrX:12761797-12762195 | Gm14634 | NR_045852 | Med14 | NM_012005 | −0.31 | 0.13 | |
| Hypomethylation | |||||||
| chr1:133269974-133270300 | Gm19461 | NR_037984 | |||||
| chr1:136696173-136696502 | Platr22 | NR_037986 | |||||
| chr1:71888158-71888468 | Gm8883 | NR_027658 | |||||
| chr2:118112952-118113258 | Gm13986 | NR_126479 | Thbs1 | NM_011580 | |||
| chr3:116968252-116968565 | 4930455H04Rik | NR_040596 | Palmd | NM_023245 | −0.09 | 0.84 | |
| chr5:112206149-112206560 | 1700028D13Rik | NR_045377 | |||||
| chr5:112206149-112206560 | 1700028D13Rik | NR_045378 | |||||
| chr5:135000770-135001082 | Wbscr25 | NR_026907 | |||||
| chr5:143758048-143758457 | D130017N08Rik | NR_015486 | |||||
| chr6:52165042-52165362 | Hoxaas2 | NR_131182 | Hoxa2 | NM_010451 | −0.39 | 0.28 | |
| chr6:52243386-52243706 | Hoxa11os | NR_015348 | Hoxa11 | NM_010450 | −0.31 | 0.05* | 28, 29 |
| chr7:28496984-28497589 | 1700028B04Rik | NR_033605 | |||||
| chr7:30971903-30972229 | Fam187b | NR_038860 | Lsr | NM_017405 | 3.57 | 0.00004**** | 30 |
| chr8:106133504-106133810 | 1810019D21Rik (Esrp2-as) | NR_040344 | Esrp2 | NM_176838 | 1.55 | 0.0005*** | 12, 14 |
| chr8:11005553-11005971 | 9530052E02Rik | NR_046017 | Irs2 | NM_001081212 | |||
| chr8:70774591-70774966 | 2010320M18Rik | NR_029440 | Pik3r2 | NM_008841 | 0.47 | 0.11 | |
| chr9:40333291-40333624 | 1700110K17Rik | NR_040728 | |||||
| chr9:51875640-51875974 | Arhgap20os | NR_033560 | |||||
| chr11:102377699-102378035 | Bloodlinc | NR_131196 | |||||
| chr11:112711182-112711489 | BC006965 | NR_024085 | |||||
| chr12:11204247-11204597 | 9530020I12Rik | NR_131083 | |||||
| chr12:33149419-33149899 | F730043M19Rik | NR_015602 | Atxn7l1 | NM_028139 | −0.18 | 0.53 | |
| chr13:44216558-44216865 | A330076C08Rik | NR_045088 | |||||
| chr13:63296450-63296765 | Gm16907 | NR_045794 | |||||
| chr14:105589344-105589691 | 9330188P03Rik | NR_102319 | |||||
| chr14:118363552-118363938 | 1700044C05Rik | NR_045624 | |||||
| chr14:118922434-118923043 | Dzip1 | NR_130725 | |||||
| chr14:55071799-55072110 | Zfhx2os | NR_004444 | |||||
| chr15:103147888-103148190 | D930007P13Rik | NR_045743 | |||||
| chr16:95928970-95929274 | 1600002D24Rik | NR_040484 | |||||
| chr17:56554141-56554483 | Gm20219 | NR_130128 | |||||
| chr19:53076038-53076348 | 1700054A03Rik | NR_045320 | |||||
Abbreviation: lncRNA, long noncoding RNA.
Bold indicates Polycomb-associated RNAs.31
a
Ref.: Reference describing the function of significantly differentially expressed genes.
b
Expression data were taken from Herschkowitz et al.24 and include 8 TG tumor samples and 5 FVB/N WT mammary glands. Values are reported as the differences between tumor and normal samples in log2 array intensities relative to a pool of whole mouse embryo RNA.
c
P-values were calculated using two-sided Student’s t-test, *P< 0.05, ***P< 0.001, ****P< 0.0001.