CLC

The Cancer LncRNA Census is an continous effort to identify and catalogue lncRNA genes which have been causally implicated in cancer. The original census and analysis was published in bioRxiv (http://biorxiv.org/content/early/2017/06/20/152769).

CLC can be used for two main analysis:

a) Analysis of the genomic and functional properties of cancer related lncRNAs, that distinguish them from the rest of lncRNAs.

b) Sensitivity and precision analysis of lncRNA cancer driver prediction methods like ExInAtor (https://www.nature.com/articles/srep41544), in order to check the percentage of candidates that have prior evidence of cancer relationship.

Please send suggestions for new cancer related lncRNAs or any comments to Andrés Lanzós (andres.lanzos@crg.eu).

Download CLC table using the following links:
CLC_table.doc
CLC_table.xlsx

Name as published GENCODE ID Oncogene (o) or Tumour Supp (t) Evidence level Cancer type – Homogenised Cancer type – From reference Date added PMID reference
AATBC ENSG00000215458 o tv bladder BC 11 august 2016 25473900
ADAMTS9-AS2 ENSG00000241684 t t neuroepithelial glioma 11 august 2016 24833086
AFAP1-AS1 ENSG00000272620 o ptv nasopharyngeal; colon; liver; esophageal; lung NPC; CRC; HCC; ESCC; NSCLC; lung 6 june 2016 26246469; 27261589; 26892468; 26756568; 26463625; 26245991
ANRIL ENSG00000240498 o gs neuroepithelial; breast; skin; blood; thyroid glioma; breast; basal cell carcinoma; melanoma; lymphoblastic leukaemia; glioma; thyroid cancer 19 april 2016 19578367; 20453838; 19578363; 20386740; 21414664; 27507052
AOC4P ENSG00000260105 t ptv liver HCC 11 august 2016 26160837
AP001631.9 ENSG00000236663 o t stomach GC 11 august 2016 26261500
APTR ENSG00000214293 t t neuroepithelial glioblastoma 11 august 2016 24748121
BANCR ENSG00000278910 ot ptv thyroid; esophageal; bladder; skin; lung; colon; retinoblastoma; stomach PTC; ESCC; BC; melanoma; NSCLC; CRC; LC; retinoblastoma; GC 11 august 2016 27462868; 27470379; 27514530; 22581800; 24655544; 25013510; 25661343; 25894373; 26054683
BCAR4 ENSG00000262117 o pt breast breast 19 april 2016 21506106
CASC15 ENSG00000272168 o pst neuroepithelial; skin neuroblastoma; melanoma 6 june 2016 26100672; 26016895
CCAT1 ENSG00000247844 o gpt lymph; lung; blood; breast; liver; gallbladder multiple myeloma; lung; AML; breast; HCC; GBC 19 april 2016 27363682; 27212446; 26923190; 26225650; 25569100
CRNDE ENSG00000245694 o ptv neuroepithelial; neuroepithelial; ovarian; colon medulloblastoma; glioma; ovarian; CRC 19 april 2016 27383309; 27058823; 7042112; 26231038
CTBP1-AS ENSG00000280927 o t prostate prostate 11 august 2016 23644382
DANCR ENSG00000226950 o tp prostate; colon; liver prostate; CRC; HCC 11 august 2016 27191265; 26617879; 25964079
DBH-AS1 ENSG00000225756 o t liver HCC 11 august 2016 26393879
DLEU1 ENSG00000176124 t s blood; lymph; head_and_neck CLL; multiple myeloma; HNSC 19 april 2016 23047824; 12461754;
DLEU2 ENSG00000231607 t s blood; lymph; head_and_neck CLL; multiple myeloma; HNSC 19 april 2016 23047824; 12461754;
DRAIC ENSG00000245750 t tp prostate prostate 11 august 2016 25700553
EGFLAM-AS1/lncRNA-LOWEG ENSG00000249491 t t stomach GC 11 august 2016 26537802
EGFR-AS1 ENSG00000224057 o t liver HCC 11 august 2016 26271667
EGOT ENSG00000235947 t pg breast breast 11 august 2016 26159853; 23535729
Epist ENSG00000249082 t t esophageal ESCC 11 august 2016 26158411
EWSAT1 ENSG00000212766 o t ewing_sarcoma ewing sarcoma 11 august 2016 25401475
FAL1 ENSG00000228126 o sv ovarian ovarian 19 april 2016 25203321
FENDRR ENSG00000268388 t pt stomach GC 11 august 2016 25167886
FER1L4 ENSG00000088340 t t stomach GC 11 august 2016 26306906
FOXCUT ENSG00000280916 o pt breast; esophageal basal-like breast cancer; ESCC 11 august 2016 25516208; 25031703
FTX ENSG00000230590 ot ptv liver; colon HCC; CRC 11 august 2016 27065331; 26629053
GAPLINC ENSG00000266835 o pt stomach; colon gastric; CRC 19 april 2016 25277524; 27259250
GAS5 ENSG00000234741 t gpt breast; kidney; prostate; pancreas; bladder; lung; stomach; liver; colon; cervical; ovarian; endometrial; bladder breast; renal cell carcinoma; prostate; pancreatic; BC; NSCLC; GC; HCC; CRC; cervical; stomach; ovarian; endometrial; bladder transitional cell carcinoma 19 april 2016 18836484; 23676682; 24026436; 24069260; 24357161; 24884417; 25120813; 25326054; 25400758; 25959498; 26163879; 26503132; 26511107; 26548923
GHET1 ENSG00000281189 o pt stomach; bladder; colon GC; bladder; CRC 4 july 2016 24397586; 27131316
H19 ENSG00000130600 ot gtv ovarian; thyroid; bladder; gallbladder; nasopharyngeal; colon; stomach; breast; lung; neuroepithelial; esophageal; kidney; prostate; pancreas; blood; neuroepithelial; choriocarcinoma HGSC; thyroid; BC; GBC; NPC; CRC; GC; breast; NSCLC; glioblastoma; esophageal; CCRCC; ovarian; prostate; pancreatic; leukemia; glioma; choriocarcinoma; HCC 19 april 2016 27193186; 27093644; 27091055; 27073719; 27040767; 27027436; 26931432; 26886624; 26722426; 26274999; 26171017; 25866221; 25205099; 24988946; 24920070; 24685695; 24466011; 23711233; 17786216
HEIH ENSG00000278970 o tv liver HCC 19 april 2016 21769904
HNF1A-AS1 ENSG00000241388 o tv liver; lung; esophageal HCC; LUAD; EAC 11 august 2016 7084450; 25863539; 24000294
HOTAIR ENSG00000228630 o gptv cervical; ovarian; blood; colon; kidney; nasopharyngeal; lung; head_and_neck; breast; neuroepithelial; liver; stomach; thyroid; oral; urothelial; bone; gallbladder; esophageal; endometrial; skin; pancreas cervical; EOC; DLBCL; CRC; colon; ovarian; TCC; NPC; NSCLC; HNSCC; breast; AML; glioma; liver; GC; glioblastoma; PTC; HCC; OSCC; UC; OS; renal carcinoma; GBC; ESCC; EC; melanoma; pancreatic 19 april 2016 27229487; 27166268; 27122348; 27069543; 26962687; 26826873; 26781446; 26717040; 26707824; 26592246; 26577852; 26261618; 26183397; 26172293; 26136075; 26111795; 27549736; 27301338; 26036760; 25994132; 25728753; 25149152; 24953832; 24788237; 24285342; 23862139; 22614017; 22258453
HOTAIRM1 ENSG00000233429 ot pt colon; PML; blood CRC; PML; AML 11 august 2016 27307307; 24824789; 26436590
HOTTIP ENSG00000243766 o gpt lung; stomach; prostate; colon; bone; lung; pancreas NSCLC; GC; prostate; CRC; OS; lung; pancreatic 20 april 2016 27347311; 27103834; 27064878; 26678886; 26617868; 26265284; 25912306; 26729200
HOXA-AS2 ENSG00000253552 o t stomach; blood GC; myeloid leukemia 11 august 2016 26384350; 23649634
HOXA11-AS ENSG00000240990 t gt ovarian EOC 11 august 2016 26430965
HULC ENSG00000251164 o gpt colon; liver; blood; bone CRC; HCC; DLBCL; osteosarcoma 19 april 2016 27496341; 27285757; 27044827; 26045809; 22493738
linc-ITGB1 / KIAA0125 ENSG00000226777 o tv breast; gallbladder breast; gallbladder 11 august 2016 26601916; 26448925
linc-JPH1 / CASC9 ENSG00000249395 o t head_and_neck; esophageal HNSCC; esophageal 17 june 2016 27323410; 27431358
linc-ROR ENSG00000258609 o tv breast; pancreas breast; pancreatic 20 april 2016 27449099; 26898939; 26883251
linc-UBC1 ENSG00000281406 o pt stomach; bladder GC; bladder 11 august 2016 25755750; 23688781
LINC00152 ENSG00000222041 o pt kidney; stomach; liver; breast CCRCC; GC; HCC; breast 11 august 2016 27186403; 26799422; 26540343
LINC00261 ENSG00000259974 t pt stomach GC 11 august 2016 27439973
LINC00467 ENSG00000153363 t t neuroepithelial neuroblastoma 11 august 2016 24586304
LINC00520 ENSG00000258791 o t breast breast 11 august 2016 27626181
LINC00963 ENSG00000204054 o t prostate prostate 11 august 2016 24691949
LINC00974 ENSG00000226629 o tv liver HCC 11 august 2016 25476897
LINC00982 ENSG00000177133 t pt stomach GC 11 august 2016 26334618
LINC01021 ENSG00000250337 t t colon CRC 11 august 2016 26183718
LINC01089/LIMT ENSG00000212694 t tv breast breast 11 august 2016 27485121
LINC01133 ENSG00000224259 ot pt lung; colon LSCC; NSCLC; CRC 11 august 2016 25908174; 26840083; 27443606
LINC01138 ENSG00000274020 o pt prostate prostate 11 august 2016 27556357
LINC01207 ENSG00000248771 o tv lung LUAD 11 august 2016 26693067
LINK-A ENSG00000215808 o tv breast breast 11 august 2016 26751287
LINP1 / PARROT ENSG00000223784 o st breast breast 2 may 2016 27111890
lncARSR ENSG00000233086 o t kidney renal 2 may 2016 27117758
lncRNA-ATB ENSG00000244306 o pt liver; stomach; pancreas; colon; breast; prostate; neuroepithelial HCC; GC; pancreatic; colon; breast; CRC; prostate carcinoma; glioma 20 april 2016 24768205; 25986864; 26482611; 26487301; 25871474; 27176634; 27267902
lncRNA-BGL3 ENSG00000260629 t tv blood CML 11 august 2016 24837367
lncRNA-EBIC ENSG00000262904 t t cervical cervical 11 august 2016 25007342
lncRNA-LET ENSG00000281183 t pt esophageal; nasopharyngeal; cervical; gallbladder; stomach ESCC; NPC; cervical; GBC; GC 11 august 2016 26935396; 26243049; 25755778; 25213660; 25674261
lncTCF7 ENSG00000249073 o t liver HCC; liver 11 august 2016 26452542; 25842979
lncUSMycN ENSG00000223850 t sv neuroepithelial neuroblastoma 11 august 2016 24906397
LOC728228 ENSG00000230176 o t lung lung 11 august 2016 25820656
LSINCT5 ENSG00000281560 o pt ovarian; breast ovarian; breast 11 august 2016 21532345; 25526476
LUADT1 ENSG00000196634 o t lung LUAD 31 May 2016 26291312
MA-linc1 ENSG00000245146 o pt lung; breast lung; breast 11 august 2016 26337085
MALAT1 ENSG00000251562 ot tv thyroid; gallbladder; pancreas; tongue; ovarian; lung; stomach; breast; esophageal; neuroepithelial; cervical; oral; nasopharyngeal; kidney; colon; bone; lymph; bladder; liver thyroid; GBC; pancreatic; TSCC; ovarian; LUAD; GC; breast; ESCC; glioma; NSCLC; cervical; OSCC; NPC; KIRC; RCC; CRC; OS; myeloma; BC; liver; 19 april 2016 27470543; 27420766; 27371730; 27353727; 27313681; 27294002; 27259812; 27250026; 27015363; 26938295; 26884862; 26854446; 26522444; 26482776; 26461224; 25600645; 25446987; 25431257; 25369863; 24449823; 24468535
MEG3 ENSG00000214548 t gptv pancreas; gallbladder; lung; prostate; cervical; liver; pituitary; stomach; kidney; thyroid; colon; endometrial; breast; tongue; bladder; neuroepithelial pancreatic; GBC; lung; prostate; cervical; HCC; pituitary; GC; RCC; PTC; LUAD; CRC; EC; breast; TSCC; NSCLC; BC; glioma; 19 april 2016 26850851; 26812694; 26729200; 26610246; 26574780; 26444285; 26284494; 26253106; 26223924; 25997963; 25992654; 25636452; 27470401; 27166155; 24343426; 24098911; 23295831; 22234798
MIR100HG ENSG00000255090 o t blood AMKL 11 august 2016 25027842
MIR31HG ENSG00000171889 t pt stomach; pancreas; neuroepithelial GC; pancreatic ductal adenocarcinoma; glioblastoma 20 april 2016 26692098; 26549028; 26164206
MONC ENSG00000215386 o t blood AMKL 11 august 2016 25027842
MT1DP ENSG00000205361 t tv liver liver 11 august 2016 25261601
MYU ENSG00000261373 o t colon colon 11 august 2016 27568568
NBAT-1 ENSG00000260455 t pt neuroepithelial; kidney neuroblastoma; renal cell carcinoma 20 april 2016 25517750; 26097558
NcRAN ENSG00000163597 t pt bladder; neuroepithelial; colon bladder; neuroblastoma; CRC 19 april 2016 21147498; 19287950; 24519959
NEAT1 ENSG00000245532 o pst bladder; lung; breast; stomach; ovarian; liver; larynx; esophageal; neuroepithelial; colon BC; NSCLC; breast; gastric; ovarian; liver; laryngeal squamous cell cancer; ESCC; glioma; CRC; HCC; 19 april 2016 27384674; 27351135; 27147820; 27095450; 27075229; 27064257; 26822763; 26609486; 26582084; 26552600; 26191242
NKILA ENSG00000278709 t pt breast breast 20 april 2016 25759022
ODRUL ENSG00000260944 o t bone OS 11 august 2016 26408180
OVAL ENSG00000236719 o s ovarian ovarian 16 may 2016 24265805
PANDAR ENSG00000281450 ot pt bladder; breast; liver; lung; stomach bladder; breast; HCC; NSCLC; GC 11 august 2016 27206339; 26927017; 26054684; 26898439
PCA3 ENSG00000225937 o pt prostate prostate 19 april 2016 23130941
PCAN-R1 ENSG00000228288 o st prostate prostate 11 august 2016 23728290
PCAN-R2 ENSG00000231806 o st prostate prostate 11 august 2016 23728290
PCAT-1 ENSG00000253438 o gpt liver; prostate; lung; bladder; esophageal; colon HCC; prostate; NSCLC; bladder; ESCC; CRC 19 april 2016 27035680; 26823525; 26770456; 25934337; 23640607
PCAT18 ENSG00000265369 o t prostate prostate 6 june 2016 24519926
PCAT29 ENSG00000259641 t pt prostate prostate; 11 august 2016 25030374
PCAT5 ENSG00000280719 o t prostate prostate 6 june 2016 26282172
PCGEM1 ENSG00000227418 o gpt prostate prostate 19 april 2016 25200485; 23459097
PINT ENSG00000231721 t t colon CRC 19 april 2016 24070194
PlncRNA-1 ENSG00000236830 o t esophageal; prostate; liver ESCC; prostate; HCC 19 april 2016 22264502; 2433768; 26906068
POU3F3/ LINC01158 ENSG00000233639 o t stomach; esophageal; colon; neuroepithelial GC; ESCC; CRC; glioma 6 june 2016 26807174; 26833746; 26510906; 25445282
PRAL ENSG00000279296 t st liver HCC 6 june 2016 26663434; 27275496
PTCSC3 ENSG00000259104 t gt thyroid PTC 11 august 2016 25562676; 22586128; 26274343
PVT1 ENSG00000249859 o st ovarian; breast; colon ovarian; breast; CRC 19 april 2016 17908964; 24196785
RMEL3 ENSG00000250961 o t skin melanoma 11 august 2016 27167340
SAMMSON ENSG00000240405 o tv skin melanoma 19 april 2016 27008969
schlap1 / LINC00913 ENSG00000281131 o tv prostate prostate 11 august 2016 24076601
SLNCR1 ENSG00000227036 o pt skin melanoma 19 april 2016 27210747
SNHG1 ENSG00000255717 o pt neuroepithelial; liver; lung neuroblastoma; HCC; NSCLC 11 august 2016 27517149; 27133041; 5818744
SNHG15 ENSG00000232956 o t stomach GC 11 august 2016 26662309
SOX2OT ENSG00000242808 o pt colon; lung; liver; breast; esophageal CRC; LUAD; HCC; breast; ESCC 11 august 2016 27353770; 26846097; 26097588; 25006803; 24105929
SPRY4-IT1 ENSG00000274721 o pt neuroepithelial; stomach; bladder; breast; esophageal; colon; skin; bone glioma; GC; bladder; breast; ESCC; CRC; melanoma; OS 19 april 2016 26464658; 26238992; 25973088; 25742952; 27460732; 2745341527391336 ;27391336; 27239436; 26982001
SUZ12P1 ENSG00000264538 o pt prostate prostate 11 august 2016 27556357
TCL6 ENSG00000187621 t t kidney CCRCC 19 april 2016 27494890
TERC ENSG00000270141 o gs neuroepithelial; blood; colon; cervical glioma; cervical intraepithelial neoplasia; ALL; CRC; cervical 19 april 2016 26017031; 22800828; 22390679; 21708826
TINCR ENSG00000223573 o t colon; esophageal; stomach CRC; ESCC; GC 19 april 2016 27009809; 26833746; 25728677
TRPM2-AS ENSG00000230061 o t prostate prostate 11 august 2016 24931166
TUG1 ENSG00000253352 ot gptv bone; lung; esophageal; liver; neuroepithelial; stomach; colon; bladder OS; NSCLC; ESCC; HCC; glioma; gastric; glioblastoma; CRC; bladder 11 august 2016 23725133; 24853421; 25366138; 26336870; 26748401; 26913601; 27345398; 27421138; 27460088
TUNAR / LINC00617 ENSG00000250366 o tv breast breast 6 june 2016 26207516
TUSC7 ENSG00000243197 t pt lung; liver; bone; stomach NSCLC; HCC; OS; GC 19 april 2016 27158360; 27002617; 26781978; 25765901
TUSC8 / XLOC_010588 ENSG00000237361 t pt cervical cervical 19 april 2016 24667250
UCA1 / CUDR ENSG00000214049 o t bladder; liver bladder; liver; 19 april 2016 18501714; 27167190
WT1-AS ENSG00000183242 t pt liver HCC 11 august 2016 26462627
XIST ENSG00000229807 ot tv neuroepithelial; blood; lung; breast glioblastoma; hematological; NSCLC; breast; 19 april 2016 25578780; 23415223; 27501756; 27248326
ZEB1-AS1 ENSG00000237036 o pt liver; esophageal HCC; ESCC 11 august 2016 26073087; 26617942
ZFAS1 ENSG00000177410 o pst colon; stomach; liver CRC; GC; HCC 6 june 2016 27461828; 27246976
ZXF1 ENSG00000180139 o pt lung LUAD 11 august 2016 24721325
RMRP ENSG00000269900 o tv stomach GC 7 november 2016 27192121
SNHG6 ENSG00000245910 o ptv liver HCC 7 november 2016 27530352