Table 1. List of grade 3 PNST CISs.
This table is a combined list of CISs identified by the tdCIS method and the gCIS method. Twenty-two CIS were identified by both statistical analyses independently. p-values and q-values were generated as described by Sarver et al. 2012 and Brett et al. 2011. Prediction on gene function indicates if the T2/Onc insertion would cause transcriptional activation of a gene (“Drive” and “Drive N-terminal Truncation) or disrupt gene transcription (“Disrupt”) based on position and orientation of T2/Onc insertion to gene transcription.
| CIS-Associated Gene | % of Tumors with tdCIS | tdCIS P-Value library # | p-value for grade 3 PNST enrichment | % of Tumors with gCIS | gCIS q-Value library # | Prediction on gene function | Neurofibroma CIS | Human Homolog |
|---|---|---|---|---|---|---|---|---|
| Nf1 | 34.9 | 5.03 x 10−25 | 8.04 x 10−06 | 36.8 | 2.61 x 10−62 | Disrupt | X | NF1 |
| Pten | 30.2 | 3.21 x 10−41 | 3.85 x 10−06 | 31.1 | 0 | Disrupt | X | PTEN |
| Stag2 | 19.8 | 6.72 x 10−12 | - | 19.8 | 7.33 x 10−26 | Disrupt | X | STAG2 |
| Taok1 | 19.8 | 1.32 x 10−18 | 0.003062 | 19.8 | 6.41 x 10−49 | Disrupt | X | TAOK1 |
| Srgap2 | 16.0 | 2.90 x 10−05 | 0.001182 | 17.9 | 3.40 x 10−11 | Disrupt | X | SRGAP2 |
| Faf1 | 14.2 | 0.047642812 | 0.03222 | 17.9 | 3.05 x 10−06 | Disrupt | X | FAF1 |
| Crebbp | 16.0 | 1.20 x 10−07 | 0.002837 | 16.0 | 3.49 x 10−21 | Disrupt | X | CREBBP |
| Dyrk1a | 11.3 | 1.44 x 10−06 | 0.009831 | 11.3 | 1.48 x 10−09 | Disrupt | X | DYRK1A |
| Spag9 | 11.3 | 0.046952457 | - | 11.3 | 1.22 x 10−07 | Disrupt | X | SPAG9 |
| Ppp6r3 | 10.4 | 0.047173607 | - | 10.4 | 7.46 x 10−09 | Disrupt | X | PPP6R3 |
| Bmpr2 | 9.4 | 0.005118412 | - | 10.4 | 4.70 x 10−07 | Drive N-term truncation | - | BMPR2 |
| Cdk13 | 9.4 | 0.005118412 | 0.01161 | 10.4 | 2.57 x 10−08 | Disrupt | X | CDK13 |
| Ccny | 4.7 | 0.042667588 | - | 10.4 | 4.25 x 10−06 | Drive N-term truncation | X | CCNY |
| Copg2 | 8.5 | 0.048819435 | - | 8.5 | 7.08 x 10−05 | Disrupt | X | COPG2 |
| Eras | 8.5 | 1.46 x 10−08 | - | 8.5 | 1.20 x 10−74 | Drive N-term truncation | - | ERAS |
| gm9766 | 5.7 | 0.043383381 | - | 8.5 | 0.000234 | Disrupt | X | C6orf204 |
| Jak2 | 5.7 | 0.00127532 | - | 8.5 | 9.07 x 10−09 | Drive N-term truncation | X | JAK2 |
| Sec63 | 7.5 | 0.047985716 | - | 7.5 | 1.28 x 10−05 | Disrupt | - | SEC63 |
| Foxr2 | 6.6 | 3.27 x 10−05 | - | 7.5 | 7.96 x 10−22 | Drive | - | FOXR2 |
| Cnot1 | 5.7 | 0.043383381 | - | 7.5 | 7.14 x 10−05 | Disrupt | - | CNOT1 |
| 2610044O15Rik | 4.7 | 0.042667588 | - | 5.7 | 5.60 x 10−11 | Drive N-term truncation | - | - |
| Baz1b | 4.7 | 0.042667588 | 0.0309 | 5.7 | 0.000157 | Drive N-term truncation | - | BAZ1B |
| Cdc27 | 15.1 | 0.001665472 | - | - | - | Disrupt | - | CDC27 |
| Pcdh10 | 11.3 | 0.046952457 | - | - | - | Disrupt | - | PCDH10 |
| Top2b | 11.3 | 0.046952457 | - | - | - | Disrupt | X | TOP2B |
| Plaa | 8.5 | 0.048819435 | - | - | - | Disrupt | - | PLAA |
| Zfp521 | 8.5 | 0.048819435 | - | - | - | Drive N-term truncation | - | ZNF521 |
| Gdi2 | 7.5 | 0.047985716 | - | - | - | Disrupt | X | GDI2 |
| Gmds | 7.5 | 0.047985716 | - | - | - | Disrupt | - | GMDS |
| Gsk3b | 7.5 | 0.047985716 | - | - | - | Disrupt | X | GSK3B |
| Picalm | 6.6 | 0.049919619 | - | - | - | Disrupt | X | PICALM |
| Gria3 | 5.7 | 0.00127532 | - | - | - | Disrupt | - | GRIA3 |
| Jmy | 5.7 | 0.043383381 | - | - | - | Drive N-term truncation | - | JMY |
| Nf2 | 5.7 | 0.00127532 | - | - | - | Disrupt | X | NF2 |
| Dip2c | - | - | - | 17.9 | 9.86 x 10−05 | Disrupt | X | DIP2C |
| Dmd | - | - | - | 16.0 | 1.61 x 10−05 | Disrupt | X | DMD |
| Zswim6 | - | - | - | 11.3 | 1.40 x 10−06 | Disrupt | X | ZSWIM6 |
| Kdm6a | - | - | - | 10.4 | 6.11 x 10−05 | Disrupt | X | KDM6A |
| Eml4 | - | - | - | 9.4 | 9.21 x 10−05 | Disrupt | - | EML4 |
| Trip12 | - | - | - | 9.4 | 9.41 x 10−05 | Disrupt | X | TRIP12 |
| Npepps | - | - | - | 7.5 | 3.95 x 10−06 | Drive | - | NPEPPS |
| Ptpn14 | - | - | - | 7.5 | 0.000211 | Disrupt | - | PTPN14 |
| Setd5 | - | - | - | 7.5 | 0.000103 | Disrupt | X | SETD5 |
| Smc1a | - | - | - | 7.5 | 6.93 x 10−11 | Disrupt | - | SMC1A |
| Strn3 | - | - | - | 7.5 | 0.000448 | Disrupt | X | STRN3 |
| 5830433M19Rik | - | - | - | 6.6 | 0.000103 | Disrupt | - | C9orf82 |
| Cpne3 | - | - | - | 6.6 | 5.75 x 10−06 | Disrupt | - | CPNE3 |
| Eif4enif1 | - | - | - | 6.6 | 1.24 x 10−08 | Disrupt | X | EIF4ENIF1 |
| Map3k4 | - | - | - | 6.6 | 7.51 x 10−05 | Disrupt | - | MAP3K4 |
| Ppp2r2a | - | - | - | 6.6 | 1.18 x 10−05 | Disrupt | X | PPP2R2A |
| Ptch1 | - | - | - | 6.6 | 1.28 x 10−09 | Disrupt | X | PTCH1 |
| Rab2a | - | - | - | 6.6 | 0.000438 | Disrupt | X | RAB2A |
| Sec24b | - | - | - | 6.6 | 0.000117 | Disrupt | - | SEC24B |
| Sppl3 | - | - | - | 6.6 | 0.000178 | Disrupt | - | SPPL3 |
| Atl2 | - | - | - | 5.7 | 9.72 x 10−05 | Disrupt | - | ATL2 |
| Fam168b | - | - | - | 5.7 | 5.81 x 10−10 | Drive N-term truncation | X | FAM168B |
| Maea | - | - | - | 5.7 | 4.65 x 10−08 | Disrupt | X | MAEA |
| Mark2 | - | - | - | 5.7 | 4.48 x 10−05 | Disrupt | X | MARK2 |
| Shfm1 | - | - | - | 5.7 | 1.17 x 10−08 | Drive N-term truncation | - | SHFM1 |
| Txndc11 | - | - | - | 5.7 | 0.000367 | Disrupt | X | TXNDC11 |
| Ube2l3 | - | - | - | 5.7 | 4.32 x 10−06 | Disrupt | X | UBE2L3 |
| Ccm2 | - | - | - | 4.7 | 0.000296 | Disrupt | - | CCM2 |
| Cntfr | - | - | - | 4.7 | 3.66 x 10−09 | Disrupt | - | CNTFR |
| Gosr1 | - | - | - | 4.7 | 8.84 x 10−05 | Disrupt | - | GOSR1 |
| Klf13 | - | - | - | 4.7 | 7.38 x 10−05 | Disrupt | - | KLF13 |
| Myst2 | - | - | - | 4.7 | 0.000131 | Disrupt | - | KAT7 |
| Nr1d2 | - | - | - | 4.7 | 0.000131 | Disrupt | X | NR1D2 |
| Plekhb2 | - | - | - | 4.7 | 1.55 x 10−06 | Disrupt | - | PLEKHB2 |
| Rab12 | - | - | - | 4.7 | 6.99 x 10−08 | Disrupt | - | RAB12 |
| Zbtb10 | - | - | - | 4.7 | 0.000292 | Disrupt | - | ZBTB10 |
| Zfp217 | - | - | - | 4.7 | 7.38 x 10−06 | Drive N-term truncation | - | ZNF217 |
| 2310044G17Rik | - | - | - | 3.8 | 4.37 x 10−06 | Drive | - | KIAA1737 |
| Cdkn2a | - | - | - | 3.8 | 0.000128 | Disrupt | - | CDKN2A |
| Ddx3x | - | - | - | 3.8 | 3.07 x 10−05 | Disrupt | - | DDX3X |
| Manbal | - | - | - | 3.8 | 0.000157 | Drive | - | MANBAL |
| Mycn | - | - | - | 3.8 | 8.71 x 10−12 | Disrupt | - | MYCN |
| Pabpc1l | - | - | - | 3.8 | 5.76 x 10−05 | Drive | - | PABPC1L |
| Prdx1 | - | - | - | 3.8 | 2.27 x 10−05 | Disrupt | - | PRDX1 |
| Psmc1 | - | - | - | 3.8 | 1.66 x 10−08 | Disrupt | - | PSMC1 |
| Sntn | - | - | - | 3.8 | 4.48 x 10−05 | Disrupt | - | SNTN |
| 2610507I01Rik | - | - | - | 2.8 | 1.41 x 10−06 | Drive | - | - |
| Ifng | - | - | - | 2.8 | 0.000154 | Drive | - | IFNG |
| Igsf8 | - | - | - | 2.8 | 1.14 x 10−07 | Drive | - | IGSF8 |
| Mir1b | - | - | - | 2.8 | 0.000125 | Disrupt | - | MIR206 |
| Mir99a | - | - | - | 2.8 | 1.61 x 10−05 | Drive | - | MIR99A |
| P4hb | - | - | - | 2.8 | 0.000167 | Disrupt | - | P4HB |
| Trip10 | - | - | - | 2.8 | 0.000104 | Disrupt | - | TRIP10 |