Table 1 Mutation frequencies of genes in pathways
Pathway | Number of non-silent somatic mutations | Mutation frequency (%, n = 96) | Mutation frequency in GCB subtype (%, n = 36) | Mutation frequency in non-GCB subtype (%, n = 60) | P | FDR |
|---|---|---|---|---|---|---|
BCR signaling | ||||||
 CD79A | 2 | 2 | 3 | 2 | 1.000 | 1.000 |
 CD79B | 23 | 18 | 6 | 25 | 0.016 | 0.536 |
 BTK | 3 | 3 | 6 | 2 | 0.650 | 1.000 |
 CARD11 | 12 | 10 | 14 | 8 | 0.605 | 1.000 |
 MALT1 | 5 | 2 | 3 | 2 | 1.000 | 1.000 |
 BCL10 | 5 | 5 | 6 | 5 | 1.000 | 1.000 |
 PRKCB | 6 | 5 | 3 | 7 | 0.722 | 1.000 |
 TCF3 | 4 | 4 | 6 | 3 | 1.000 | 1.000 |
 ID3 | 0 | 0 | 0 | 0 | NA | NA |
TLR signaling | ||||||
 MYD88 | 20 | 21 | 22 | 20 | 0.795 | 1.000 |
NF-κB signaling | ||||||
 TNFAIP3 | 7 | 7 | 3 | 10 | 0.362 | 1.000 |
 TRAF2 | 2 | 1 | 0 | 2 | 1.000 | 1.000 |
 TRAF5 | 2 | 2 | 0 | 3 | 0.526 | 1.000 |
 MAP3K7 | 0 | 0 | 0 | 0 | NA | NA |
 IKBKB | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 TNFRSF11A | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 TRAF3 | 0 | 0 | 0 | 0 | NA | NA |
 BIRC3 | 4 | 4 | 8 | 2 | 0.291 | 1.000 |
 MAP3K14 | 1 | 1 | 3 | 0 | 0.375 | 1.000 |
 NFKBIA | 5 | 4 | 6 | 3 | 1.000 | 1.000 |
NOTCH signaling | ||||||
 NOTCH1 | 8 | 8 | 8 | 8 | 1.000 | 1.000 |
 NOTCH2 | 9 | 9 | 8 | 10 | 1.000 | 1.000 |
 SPEN | 18 | 17 | 14 | 18 | 0.572 | 1.000 |
 FBXW7 | 5 | 4 | 3 | 5 | 1.000 | 1.000 |
PI3K/AKT signaling | ||||||
 PIK3CA | 2 | 2 | 3 | 2 | 1.000 | 1.000 |
 PIK3CD | 1 | 1 | 3 | 0 | 0.375 | 1.000 |
 PIK3CG | 4 | 4 | 3 | 5 | 1.000 | 1.000 |
 PIK3R1 | 2 | 2 | 3 | 2 | 1.000 | 1.000 |
 PIK3R2 | 2 | 2 | 0 | 3 | 0.526 | 1.000 |
 AKT1 | 0 | 0 | 0 | 0 | NA | NA |
 AKT2 | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 AKT3 | 3 | 3 | 3 | 3 | 1.000 | 1.000 |
 PTEN | 10 | 7 | 11 | 5 | 0.478 | 1.000 |
 MTOR | 4 | 4 | 6 | 3 | 1.000 | 1.000 |
 SGK1 | 33 | 13 | 19 | 8 | 0.202 | 1.000 |
JAK/STAT signaling | ||||||
 JAK1 | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 JAK2 | 4 | 4 | 3 | 5 | 1.000 | 1.000 |
 JAK3 | 2 | 2 | 6 | 0 | 0.138 | 1.000 |
 STAT3 | 10 | 7 | 14 | 3 | 0.128 | 1.000 |
 STAT5A | 2 | 1 | 0 | 2 | 1.000 | 1.000 |
 STAT5B | 0 | 0 | 0 | 0 | NA | NA |
 STAT6 | 8 | 7 | 8 | 7 | 1.000 | 1.000 |
 SOCS1 | 86 | 24 | 28 | 22 | 0.497 | 1.000 |
 PTPN1 | 1 | 1 | 3 | 0 | 0.375 | 1.000 |
 MPL | 1 | 1 | 3 | 0 | 0.375 | 1.000 |
MAPK signaling | ||||||
 NRAS | 1 | 1 | 3 | 0 | 0.375 | 1.000 |
 KRAS | 0 | 0 | 0 | 0 | NA | NA |
 BRAF | 4 | 4 | 3 | 5 | 1.000 | 1.000 |
S1P2 signaling | ||||||
 GNA13 | 9 | 7 | 14 | 3 | 0.128 | 1.000 |
 S1PR2 | 4 | 4 | 3 | 5 | 1.000 | 1.000 |
Epigenetic regulation | ||||||
 ARID1A | 11 | 10 | 17 | 7 | 0.227 | 1.000 |
 CREBBP | 13 | 13 | 14 | 12 | 1.000 | 1.000 |
 EP300 | 6 | 5 | 3 | 7 | 0.722 | 1.000 |
 DNMT3A | 2 | 2 | 0 | 3 | 0.526 | 1.000 |
 EZH2 | 5 | 4 | 8 | 2 | 0.291 | 1.000 |
 HDAC1 | 2 | 2 | 6 | 0 | 0.138 | 1.000 |
 HDAC4 | 4 | 3 | 3 | 3 | 1.000 | 1.000 |
 HDAC7 | 5 | 3 | 6 | 2 | 0.650 | 1.000 |
 HIST1H1C | 12 | 9 | 19 | 3 | 0.024 | 0.536 |
 HIST1H1E | 27 | 18 | 28 | 12 | 0.045 | 0.7538 |
 IDH1 | 0 | 0 | 0 | 0 | NA | NA |
 IDH2 | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 KDM2B | 7 | 6 | 3 | 8 | 0.514 | 1.000 |
 KMT2C | 16 | 16 | 11 | 18 | 0.345 | 1.000 |
 KMT2D | 36 | 30 | 33 | 28 | 0.605 | 1.000 |
 MEF2B | 8 | 8 | 6 | 10 | 0.703 | 1.000 |
 MEF2C | 1 | 1 | 0 | 2 | 1.000 | 1.000 |
 SETD2 | 3 | 3 | 6 | 2 | 0.650 | 1.000 |
 TET2 | 16 | 11 | 17 | 8 | 0.363 | 1.000 |
Immunity | ||||||
 B2M | 11 | 10 | 17 | 7 | 0.227 | 1.000 |
 CD58 | 7 | 6 | 8 | 5 | 0.828 | 1.000 |
 CD70 | 14 | 11 | 11 | 12 | 1.000 | 1.000 |
 CIITA | 14 | 13 | 6 | 17 | 0.202 | 1.000 |
 TNFRSF14 | 11 | 10 | 22 | 3 | 0.010 | 0.536 |