Table 2.
lncRNAs enriched according to breast cancer molecular subtype
| TNBC | HER2-HR+ | HER2+HR+ | HER2+HR− | Normal | |||||
|---|---|---|---|---|---|---|---|---|---|
| Ensembl gene ID | LNCipedia gene ID | Ensembl gene ID | LNCipedia gene ID | Ensembl Gene ID | LNCipedia gene ID | Ensembl gene ID | LNCipedia gene ID | Ensembl gene ID | LNCipedia gene ID |
| ENSG00000263680.2 | lnc-SOX9–4 | ENSG00000248008.2 | NRAV | ENSG00000266469.1 | lnc-CDK12–2 | ENSG00000232044.4 | LINC01105 | ENSG00000264016.2 | lnc-TMEM220–1 |
| ENSG00000227036.2 | lnc-SLC39A11–1 | ENSG00000249042.1 | lnc-ANKRD34B-2 | ENSG00000270145.1 | lnc-CDC6–1 | ENSG00000256940.1 | lnc-FKBP2–1 | ENSG00000234456.3 | MAGI2-AS3 |
| ENSG00000225177.1 | lnc-CCDC28A-1 | ENSG00000269619.1 | lnc-C5AR2–3 | ENSG00000266999.1 | lnc-RDM1–1 | ENSG00000261235.1 | lnc-MPHOSPH6–1 | ENSG00000241684.1 | ADAMTS9-AS2 |
| ENSG00000229124.2 | VIM-AS1 | ENSG00000267348.2 | GEMIN7-AS1 | ENSG00000272264.1 | lnc-TPD52–1 | ENSG00000251179.1 | TMEM92-AS1 | ENSG00000263400.2 | |
| ENSG00000258910.2 | LINC01956 | ENSG00000263214.1 | lnc-ZSCAN10–3 | ENSG00000263874.1 | ENSG00000249700.4 | SRD5A3-AS1 | ENSG00000267532.2 | lnc-SLC16A11–7 | |
| ENSG00000246334.2 | PRR7-AS1 | ENSG00000248360.3 | LINC00504 | ENSG00000230838.1 | LINC01614 | ENSG00000257086.1 | lnc-PPP1R14B-1 | ENSG00000262097.1 | LINC02185 |
| ENSG00000272524.1 | lnc-KLF11–3 | ENSG00000235106.4 | lnc-BRD3OS-1 | ENSG00000263466.1 | lnc-FBXO47–2 | ENSG00000273257.1 | lnc-SRD5A3–1 | ENSG00000267047.1 | lnc-SLC16A11–7 |
| ENSG00000258938.1 | lnc-RALGAPA1–1 | ENSG00000263011.1 | lnc-ZNF205–1 | ENSG00000228265.1 | RALY-AS1 | ENSG00000235491.1 | LINC01889 | ENSG00000235904.1 | RBMS3-AS3 |
| ENSG00000224167.1 | lnc-FAM19A3–2 | ENSG00000225361.3 | PPP1R26-AS1 | ENSG00000261005.1 | lnc-MLLT6–1 | ENSG00000204603.2 | LINC01257 | ENSG00000255090.1 | MIR100HG |
| ENSG00000227392.1 | HPN-AS1 | ENSG00000205913.2 | SRRM2-AS1 | ENSG00000228613.1 | lnc-PXDN-3 | ENSG00000234378.1 | lnc-LAPTM4A-2 | ENSG00000269936.2 | CARMN |
| ENSG00000215866.3 | LINC01356 | ENSG00000231439.3 | WASIR2 | ENSG00000250917.1 | lnc-AHCY-1 | ENSG00000257588.1 | lnc-RACGAP1–1 | ENSG00000267069.1 | lnc-CIDEA-1 |
| ENSG00000254035.1 | lnc-ZNF454–1 | ENSG00000261801.1 | LOXL1-AS1 | ENSG00000260228.1 | lnc-SLC38A8–2 | ENSG00000231298.2 | MANCR | ENSG00000254847.1 | lnc-DKK3–2 |
| ENSG00000237517.4 | lnc-DGCR6–6 | ENSG00000268913.1 | lnc-KCNK6–1 | ENSG00000203635.2 | lnc-PXDN-1 | ENSG00000236345.1 | lnc-PHF3–1 | ENSG00000215386.6 | MIR99AHG |
| ENSG00000254615.2 | lnc-OXR1–1 | ENSG00000259459.1 | LINC02568 | ENSG00000253917.3 | lnc-OTOP1–6 | ENSG00000248359.1 | lnc-CCDC125–6 | ENSG00000226005.3 | lnc-PFKP-16 |
| ENSG00000272192.1 | lnc-MTFR1–1 | ENSG00000261664.1 | TTC39A-AS1 | ENSG00000263975.1 | lnc-PCGF2–1 | ENSG00000266222.1 | lnc-HOXB1–1 | ENSG00000249669.3 | CARMN |
| ENSG00000229891.1 | LINC01315 | ENSG00000268204.1 | lnc-PCP2–1 | ENSG00000257702.3 | lnc-TTC31–4 | ENSG00000204832.5 | ST8SIA6-AS1 | ENSG00000244513.2 | lnc-ARL6IP5–1 |
| ENSG00000261175.1 | LINC02188 | ENSG00000260810.1 | lnc-DGLUCY-1 | ENSG00000226853.2 | lnc-SCRN3–1 | ENSG00000214546.3 | lnc-PPP1R1B-1 | ENSG00000228962.1 | HCG23 |
| ENSG00000234899.5 | lnc-SLC39A11–10 | ENSG00000230314.2 | ELOVL2-AS1 | ENSG00000213793.3 | lnc-ZNF320–1 | ENSG00000230033.1 | lnc-NOM1–1 | ENSG00000255248.2 | MIR100HG |
| ENSG00000251161.2 | lnc-VPS18–1 | ENSG00000267715.1 | lnc-REEP6–1 | ENSG00000234703.1 | lnc-CLIC6–3 | ENSG00000272663.1 | lnc-LHCGR-2 | ENSG00000226237.1 | GAS1RR |
| ENSG00000272430.1 | lnc-SYT15–3 | ENSG00000250101.1 | lnc-FAM153C-5 | ENSG00000232679.1 | LINC01705 | ENSG00000237883.1 | DGUOK-AS1 | ENSG00000231246.1 | lnc-ST7L-2 |
| ENSG00000257718.1 | CPNE8-AS1 | ENSG00000260219.1 | lnc-MYLPF-1 | ENSG00000259802.1 | lnc-CMBL-1 | ENSG00000236921.1 | lnc-CDKN2B-1 | ENSG00000248869.1 | LINC02511 |
| ENSG00000215190.4 | lnc-RAB23–53 | ENSG00000236703.1 | MYB-AS1 | ENSG00000266040.1 | lnc-EPOP-2 | ENSG00000255118.1 | lnc-SCGB1D4–1 | ENSG00000260947.1 | lnc-PRSS3–2 |
| ENSG00000272620.1 | lnc-SORCS2–1 | ENSG00000260136.1 | lnc-SCNN1B-1 | ENSG00000250081.1 | lnc-ADAMTS6–1 | ENSG00000262973.1 | lnc-ABI3–6 | ENSG00000237560.1 | LINC01497 |
| ENSG00000226419.2 | SLC16A1-AS1 | ENSG00000264589.1 | MAPT-AS1 | ENSG00000232940.1 | ENSG00000254966.1 | AC103974.1 | ENSG00000263586.1 | HID1-AS1 | |
| ENSG00000267287.1 | lnc-NFATC1–1 | ENSG00000249684.1 | lnc-FAM153C-5 | ENSG00000236591.1 | lnc-ZC3H12D-2 | ENSG00000259702.1 | lnc-PGPEP1L-60 | ENSG00000245812.2 | LINC02202 |
| ENSG00000253348.1 | lnc-KCNMB1–3 | ENSG00000254231.1 | lnc-SLC7A13–1 | ENSG00000263931.1 | lnc-MARCH10–1 | ENSG00000240497.2 | lnc-TMEM212–1 | ENSG00000238120.1 | LINC01589 |
| ENSG00000270170.1 | NCBP2-AS2 | ENSG00000268049.1 | AC012313.2 | ENSG00000228221.1 | LINC00578 | ENSG00000273328.1 | lnc-KRBOX1–1 | ENSG00000230587.1 | LINC02580 |
| ENSG00000233654.1 | lnc-MFSD6–1 | ENSG00000263105.1 | lnc-SRL-1 | ENSG00000244300.2 | GATA2-AS1 | ENSG00000273237.1 | lnc-HNRNPA2B1–14 | ENSG00000272316.1 | lnc-RAB23–53 |
| ENSG00000257271.1 | KIRREL3-AS1 | ENSG00000260954.1 | lnc-PTX4–2 | ENSG00000254854.1 | lnc-RNF26–1 | ENSG00000225243.1 | lnc-MYOC-1 | ENSG00000272143.1 | FGF14-AS2 |
| ENSG00000237976.1 | lnc-PSMB4–1 | ENSG00000228133.2 | lnc-DPH1–1 | ENSG00000231482.2 | lnc-PXDN-2 | ENSG00000226733.1 | lnc-C6orf141–2 | ENSG00000232079.2 | LINC01697 |
| ENSG00000253164.1 | lnc-ATP6V1B2–3 | ENSG00000228043.1 | lnc-NXPH2–3 | ENSG00000228950.1 | lnc-RHOB-1 | ENSG00000234072.1 | lnc-SNX17–1 | ENSG00000261625.1 | lnc-MRGPRF-1 |
| ENSG00000228109.1 | MELTF-AS1 | ENSG00000238122.1 | lnc-NBPF4–1 | ENSG00000261039.1 | LINC02544 | ENSG00000265282.1 | lnc-CYB561–1 | ENSG00000253864.1 | CARMN |
| ENSG00000267480.1 | lnc-MPPE1–10 | ENSG00000260009.1 | LINC02130 | ENSG00000227857.2 | lnc-TSPAN1–1 | ENSG00000261712.1 | lnc-KIAA1024–1 | ENSG00000243243.1 | lnc-TFEC-2 |
| ENSG00000263893.2 | lnc-SOX9–5 | ENSG00000253959.1 | LINC01863 | ENSG00000233818.1 | lnc-CHAF1B-2 | ENSG00000259933.2 | ENSG00000225731.1 | lnc-WDR4–5 | |
| ENSG00000254148.3 | lnc-SLC39A11–10 | ENSG00000251169.2 | LINC01843 | ENSG00000224189.2 | HAGLR | ENSG00000225833.1 | lnc-BMX-1 | ENSG00000229645.4 | lnc-SYNE3–1 |
| ENSG00000228639.2 | lnc-SLC39A11–10 | ENSG00000272933.1 | lnc-ARL3–1 | ENSG00000249917.2 | LINC00536 | ENSG00000258689.1 | LINC01269 | ENSG00000227467.3 | LINC01537 |
| ENSG00000245614.2 | DDX11-AS1 | ENSG00000271420.1 | lnc-TCEA3–1 | ENSG00000230479.1 | lnc-CHAF1B-3 | ENSG00000242540.2 | lnc-SOX11–1 | ENSG00000238018.1 | lnc-RTN4–3 |
| ENSG00000260420.1 | LINC02182 | ENSG00000248399.1 | lnc-CFAP99–1 | ENSG00000267493.2 | CIRBP-AS1 | ENSG00000261123.1 | lnc-NTHL1–1 | ENSG00000224318.1 | CHL1-AS2 |
| ENSG00000232803.1 | SLCO4A1-AS1 | ENSG00000268895.1 | A1BG-AS1 | ENSG00000223387.2 | LINC02068 | ENSG00000228288.2 | PCAT6 | ENSG00000272777.1 | lnc-ADH5–1 |
| ENSG00000229692.3 | SOS1-IT1 | ENSG00000262869.1 | lnc-SMG6–4 | ENSG00000264007.1 | lnc-SSH2–1 | ENSG00000245080.4 | MIR3150BHG | ENSG00000231943.3 | PGM5P4-AS1 |
| ENSG00000232445.1 | LNCPRESS1 | ENSG00000263244.1 | lnc-PMM2–6 | ENSG00000267013.1 | LINC01929 | ENSG00000249199.1 | lnc-MYO10–2 | ENSG00000178947.8 | SMIM10L2A |
| ENSG00000224930.2 | ENSG00000224698.1 | lnc-NBPF6–1 | ENSG00000260766.1 | lnc-PIGM-1 | ENSG00000254248.1 | lnc-TP53INP1–2 | ENSG00000226833.1 | lnc-TRMT61B-1 | |
| ENSG00000272825.1 | lnc-FAM207A-2 | ENSG00000267277.1 | lnc-EPOR-2 | ENSG00000267118.1 | lnc-CCL4–3 | ENSG00000253217.1 | lnc-SPAG1–1 | ENSG00000255850.1 | RXYLT1-AS1 |
| ENSG00000224717.1 | lnc-CDK18–1 | ENSG00000261742.1 | LINC00922 | ENSG00000264112.1 | lnc-VEZF1–1 | ENSG00000258616.1 | LINC02303 | ENSG00000180769.4 | WDFY3-AS2 |
| ENSG00000251136.4 | lnc-NBN-1 | ENSG00000234918.1 | lnc-ZNF33A-13 | ENSG00000260162.2 | lnc-BANP-14 | ENSG00000248161.1 | lnc-SLC39A8–1 | ENSG00000267107.2 | PCAT19 |
| ENSG00000254607.2 | lnc-ST3GAL4–4 | ENSG00000215256.3 | DHRS4-AS1 | ENSG00000263655.1 | lnc-FBXO15–1 | ENSG00000225077.2 | LINC00337 | ENSG00000259134.1 | LINC00924 |
| ENSG00000261189.1 | lnc-CAGE1–1 | ENSG00000272335.1 | lnc-MRPS30–8 | ENSG00000249942.1 | lnc-BTC-5 | ENSG00000226207.1 | lnc-MMS22L-1 | ENSG00000225039.1 | LINC01058 |
| ENSG00000248846.2 | LINC02065 | ENSG00000263280.1 | lnc-PRSS22–1 | ENSG00000238123.1 | MID1IP1-AS1 | ENSG00000230212.2 | CBR3-AS1 | ENSG00000228649.4 | SNHG26 |
| ENSG00000237857.2 | lnc-FANCC-1 | ENSG00000260793.2 | lnc-TMUB2–1 | ENSG00000196421.3 | ENSG00000229272.1 | lnc-EIF3A-2 | ENSG00000229694.2 | LINC00484 | |
| ENSG00000225096.1 | lnc-PRIM2–7 | ENSG00000224577.1 | LINC01117 | ENSG00000227543.3 | SPAG5-AS1 | ENSG00000260209.1 | lnc-PUS3–1 | ENSG00000225655.1 | PGM5P3-AS1 |
| ENSG00000185904.7 | LINC00839 | ENSG00000260526.1 | lnc-TIFA-1 | ENSG00000226876.2 | lnc-KIF26B-2 | ENSG00000253417.1 | LINC02159 | ENSG00000230747.1 | lnc-SNRNP200–1 |
| ENSG00000226101.1 | LINC02097 | ENSG00000233621.1 | LINC01137 | ENSG00000261327.3 | lnc-CA5A-4 | ENSG00000235939.1 | lnc-C10orf71–1 | ENSG00000253552.3 | HOXA-AS2 |
| ENSG00000203362.2 | POLH-AS1 | ENSG00000271916.1 | lnc-CHDH-1 | ENSG00000265908.1 | lnc-PIPOX-5 | ENSG00000272894.1 | lnc-COL28A1–1 | ENSG00000267082.1 | lnc-ANGPTL8–1 |
| ENSG00000236663.1 | FRGCA | ENSG00000231868.1 | lnc-TNFRSF25–1 | ENSG00000254239.1 | lnc-SLC25A48–1 | ENSG00000260231.1 | KDM7A-DT | ENSG00000226031.1 | FGF13-AS1 |
| ENSG00000241155.1 | ARHGAP31-AS1 | ENSG00000272913.1 | lnc-TRIM43B-1 | ENSG00000153363.8 | LINC00467 | ENSG00000233342.1 | lnc-MAP3K4–2 | ENSG00000227591.1 | lnc-LAMB3–1 |
| ENSG00000272048.1 | lnc-DNMT3A-1 | ENSG00000273472.1 | lnc-ELMOD2–4 | ENSG00000258457.1 | lnc-PSMB11–1 | ENSG00000258829.1 | lnc-DIO2–5 | ENSG00000231999.2 | LRRC8C-DT |
| ENSG00000239445.1 | ST3GAL6-AS1 | ENSG00000223813.2 | lnc-CPVL-4 | ENSG00000264083.1 | lnc-PSMD11–1 | ENSG00000261472.1 | lnc-WWOX-1 | ||
| ENSG00000261521.1 | lnc-DSC2–1 | ENSG00000255367.1 | lnc-ART5–1 | ENSG00000242136.1 | lnc-ASAP2–4 | ENSG00000186594.8 | MIR22HG | ||
| ENSG00000237594.2 | lnc-SOD1–3 | ENSG00000270177.1 | lnc-TCF7–4 | ENSG00000268686.1 | lnc-TEAD2–1 | ENSG00000255471.1 | lnc-FZD4–1 | ||
| ENSG00000234753.1 | FOXP4-AS1 | ENSG00000267009.2 | lnc-ARSG-3 | ENSG00000224468.3 | LAMC1-AS1 | ||||