Cancer Driver LncRNA Prediction Software

ExInAtor is a pipeline for discovering cancer driver lncRNAs, using maps of point mutations.

Latest version of ExInAtor here: https://github.com/alanzos/ExInAtor/

You can find the paper here: http://www.nature.com/articles/srep41544

Below are a summary of the top drivers discovered by ExInAtor, discovered with a false discovery rate (FDR) cutoff of 0.1.

Legend: Known cancer genes from CRL are marked in bold face. “Pc” – PanCancer. Ex mut: Number of exonic mutations; Ex len: total exonic length of gene (bp); Intr mut: Number of background mutations; Intr length: background region length for gene (bp); Pval: uncorrected P-value; Qval: Q-value, equivalent to False Discovery Rate; Ex mut rate: Exonic mutation rate (mutations per kb); Intr mut rate: Background mutation rate (mutations per kb); Ratio: Ratio of mutation ratio in exonic and background regions; Super_pc: Super pancancer – all cancers combined.

Cancer

Gene
Name

Gene
ID

Ex
mut

Ex
len

Intr
mut

 

Intr
len

Pval

Qval

Ex
mut rate

Intr
mut rate

Ratio

Breast

AP000469.2

ENSG00000224832

9

238824

2

1176908

4.38E-06

5.05E-03

3.77E-02

1.70E-03

22.2

Stad

PCA3

ENSG00000225937

10

392190

20

2702680

2.86E-03

5.49E-02

2.55E-02

7.40E-03

3.4

KICH

RP11-308N19.1

ENSG00000234323

1

26384

1

2437289

2.13E-02

6.39E-02

3.79E-02

4.10E-04

92.4

Stad

SAMMSON

ENSG00000240405

5

208795

1

697899

3.14E-03

5.49E-02

2.39E-02

1.43E-03

16.7

GBM

lncRNA-ATB

ENSG00000244306

4

314168

4

1347296

4.68E-02

9.36E-02

1.27E-02

2.97E-03

4.3

Super_Pc

NEAT1

ENSG00000245532

163

25316741

16

5559984

4.98E-04

2.19E-02

6.44E-03

2.88E-03

2.2

Pc_TCGA

NEAT1

ENSG00000245532

96

11497239

7

2524993

9.28E-04

4.08E-02

8.35E-03

2.77E-03

3.0

PRAD

RP11-455B3.1

ENSG00000248202

7

16573

1

380379

1.70E-09

1.19E-08

4.22E-01

2.63E-03

160.7

KICH

RP11-332J15.1

ENSG00000249734

3

8277

15

314985

1.03E-02

6.39E-02

3.62E-01

4.76E-02

7.6

Breast

RP11-707A18.1

ENSG00000250125

6

485395

9

6908893

2.38E-04

9.16E-02

1.24E-02

1.30E-03

9.5

KICH

RP11-6C14.1

ENSG00000250488

1

5369

1

687929

1.54E-02

6.39E-02

1.86E-01

1.45E-03

128.1

Super_Pc

MALAT1

ENSG00000251562

83

9683213

40

7768392

4.45E-03

9.79E-02

8.57E-03

5.15E-03

1.7

Breast

RP11-1101K5.1

ENSG00000253434

6

165285

19

4878981

1.28E-04

7.38E-02

3.63E-02

3.89E-03

9.3

HNSC

RP11-354A14.1

ENSG00000254689

3

12579

4

697784

1.84E-04

8.14E-02

2.38E-01

5.73E-03

41.6

BRCA

RP11-189E14.4

ENSG00000261623

9

352599

1

1252991

9.53E-06

9.25E-03

2.55E-02

7.98E-04

32.0

SKCM

BCAR4

ENSG00000262117

6

50458

8

533056

6.81E-04

2.11E-02

1.19E-01

1.50E-02

7.9