Lung Adenocarcinoma: Mutation Analysis (MutSig)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.

Working with individual set: LUAD.

Number of patients in set: 148

Input

The input for this pipeline is a set of individuals with the following files associated for each:

1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

2. A .wig file that contains information about the coverage of the sample.

Summary

Significantly mutated genes (q ≤ 0.1): 84

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 1

Genes with clustered mutations (&le 3 aa apart): 1

Significantly mutated genesets: 74

Significantly mutated genesets: (excluding sig. mutated genes): 0

Results
Breakdown of Mutations by Type

Table 1.  Get Full Table Table representing breakdown of mutations by type.

type count
Frame_Shift_Del 38
Frame_Shift_Ins 18
In_Frame_Del 3
Missense_Mutation 2126
Nonsense_Mutation 154
Nonstop_Mutation 2
Silent 702
Splice_Site_DNP 1
Splice_Site_Del 1
Splice_Site_Ins 5
Splice_Site_SNP 68
Total 3118
Breakdown of Mutation Rates by Category Type

Table 2.  Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category n N rate rate_per_mb relative_rate
A->T 609 67502974 9e-06 9 0.54
C->(A/T) 908 77308830 0.000012 12 0.7
A->(C/G) 447 67502974 6.6e-06 6.6 0.4
C->G 160 77308830 2.1e-06 2.1 0.12
indel+null 286 144811804 2e-06 2 0.12
double_null 6 144811804 4.1e-08 0.041 0.0025
Total 2416 144811804 0.000017 17 1
Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1. 

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2. 

Significantly Mutated Genes

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 84. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 332193 35 29 35 7 11 11 4 1 6 2 3.7e-14 3.5e-11
2 KEAP1 kelch-like ECH-associated protein 1 73604 24 24 23 0 2 14 2 1 5 0 4.1e-14 3.5e-11
3 MYH2 myosin, heavy chain 2, skeletal muscle, adult 223101 18 18 18 4 6 8 3 1 0 0 1.2e-11 6.7e-09
4 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 149027 11 10 6 1 0 4 5 2 0 0 7.4e-11 3.1e-08
5 EPHA6 EPH receptor A6 155112 16 16 16 1 6 6 2 0 2 0 1.4e-10 4.6e-08
6 MYH1 myosin, heavy chain 1, skeletal muscle, adult 254227 16 16 16 5 3 7 3 0 3 0 1.7e-10 4.8e-08
7 ZAN zonadhesin 379001 25 20 22 5 7 6 5 1 4 2 2.2e-10 5.4e-08
8 PTPRC protein tyrosine phosphatase, receptor type, C 155693 11 11 11 3 4 4 1 0 2 0 1.1e-08 2.3e-06
9 FBN2 fibrillin 2 (congenital contractural arachnodactyly) 334477 18 17 18 2 11 4 1 0 2 0 1.4e-08 2.5e-06
10 MYH8 myosin, heavy chain 8, skeletal muscle, perinatal 226905 15 15 15 1 5 4 3 0 3 0 1.5e-08 2.5e-06
11 OLFM4 olfactomedin 4 60982 10 9 9 0 3 4 2 0 1 0 6.2e-08 9.4e-06
12 CHRNA1 cholinergic receptor, nicotinic, alpha 1 (muscle) 55117 6 6 6 0 2 0 0 2 2 0 1.2e-07 0.000016
13 OR10Z1 olfactory receptor, family 10, subfamily Z, member 1 50712 9 9 9 1 1 3 2 3 0 0 2.3e-07 3e-05
14 PCDHGA3 protocadherin gamma subfamily A, 3 122105 12 11 12 3 4 5 1 2 0 0 5.4e-07 0.000064
15 THEMIS 77473 8 8 8 0 5 2 1 0 0 0 1.4e-06 0.00016
16 DND1 dead end homolog 1 (zebrafish) 50800 4 4 1 2 0 0 0 0 4 0 3.2e-06 0.00034
17 CLEC4F C-type lectin domain family 4, member F 69502 6 6 6 1 1 2 2 0 1 0 3.9e-06 0.00039
18 FCRL2 Fc receptor-like 2 59122 7 7 7 1 3 4 0 0 0 0 5.3e-06 0.00049
19 FOXI1 forkhead box I1 45005 5 5 5 1 1 2 1 1 0 0 6.4e-06 0.00056
20 PCDHGA1 protocadherin gamma subfamily A, 1 121583 8 8 8 3 0 7 0 1 0 0 6.8e-06 0.00057
21 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 148970 9 9 9 2 4 1 2 0 2 0 0.000013 0.001
22 MEGF10 multiple EGF-like-domains 10 131444 9 9 9 2 2 2 5 0 0 0 0.000014 0.001
23 F2RL2 coagulation factor II (thrombin) receptor-like 2 44276 5 5 5 0 1 2 1 1 0 0 0.000015 0.0011
24 LSP1 lymphocyte-specific protein 1 40652 5 5 5 0 2 2 0 0 1 0 0.000018 0.0013
25 TRHDE thyrotropin-releasing hormone degrading enzyme 124301 11 9 11 2 2 4 0 5 0 0 0.000021 0.0014
26 RBM10 RNA binding motif protein 10 113954 5 5 5 1 0 0 0 0 5 0 0.000033 0.0021
27 ZNF665 zinc finger protein 665 77288 6 6 6 0 0 2 1 3 0 0 0.000043 0.0027
28 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide 48750 6 6 6 0 2 4 0 0 0 0 5e-05 0.003
29 RGS22 regulator of G-protein signaling 22 147859 7 7 7 1 2 0 2 2 1 0 0.000074 0.0042
30 DST dystonin 789876 18 16 18 1 1 8 6 1 2 0 0.000074 0.0042
31 TKTL1 transketolase-like 1 69055 4 4 4 1 0 0 2 0 2 0 0.000084 0.0045
32 NRCAM neuronal cell adhesion molecule 152536 9 8 9 1 1 4 2 0 2 0 0.000085 0.0045
33 TAP2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) 90232 6 6 6 0 1 2 1 1 1 0 0.000088 0.0045
34 WNK3 WNK lysine deficient protein kinase 3 203681 7 6 7 0 3 1 1 0 2 0 0.00011 0.0055
35 FCRL3 Fc receptor-like 3 110546 8 8 8 3 0 4 2 1 1 0 0.00012 0.0055

Note:

N - number of sequenced bases in this gene across the individual set.

n - number of (nonsilent) mutations in this gene across the individual set.

npat - number of patients (individuals) with at least one nonsilent mutation.

nsite - number of unique sites having a non-silent mutation.

nsil - number of silent mutations in this gene across the individual set.

n1 - number of nonsilent mutations of type: A->T .

n2 - number of nonsilent mutations of type: C->(A/T) .

n3 - number of nonsilent mutations of type: A->(C/G) .

n4 - number of nonsilent mutations of type: C->G .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

p = p-value (overall)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4.  Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 1. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 0 0 0 0 0 1 1
2 ACRBP acrosin binding protein 1 0 0 0 0 1 1
3 ACTR1A ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) 0 0 0 0 0 1 1
4 ADA adenosine deaminase 1 0 0 0 0 1 1
5 ADCY4 adenylate cyclase 4 2 0 0 0 0 1 1
6 ATP13A1 ATPase type 13A1 2 0 0 0 0 1 1
7 BRPF1 bromodomain and PHD finger containing, 1 4 0 0 0 0 1 1
8 BTAF1 BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa (Mot1 homolog, S. cerevisiae) 4 0 0 0 0 1 1
9 C22orf24 chromosome 22 open reading frame 24 0 0 0 0 0 1 1
10 C6orf150 chromosome 6 open reading frame 150 0 0 0 0 0 1 1

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist npairs3 npairs12
540 NRAP nebulin-related anchoring protein 10 2 1 1
274 FAT2 FAT tumor suppressor homolog 2 (Drosophila) 6 5 0 1
180 COL7A1 collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) 12 221 0 0
508 MXRA5 matrix-remodelling associated 5 14 248 0 0
830 TLN1 talin 1 6 460 0 0
213 DNAH5 dynein, axonemal, heavy chain 5 14 530 0 0
742 SH3TC2 SH3 domain and tetratricopeptide repeats 2 8 913 0 0
473 MDN1 MDN1, midasin homolog (yeast) 5 927 0 0
621 PDCD11 programmed cell death 11 4 1401 0 0
1 AAGAB 2 Inf 0 0

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 74. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 HSA04530_TIGHT_JUNCTION Genes involved in tight junction ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK 13 ACTN3(2), CDK4(1), EPB41L1(3), MYH1(16), MYH2(18), MYH4(8), MYH6(8), MYH8(15) 1811589 71 56 71 23 18 34 10 2 7 0 6.7e-15 3.1e-12
2 ARENRF2PATHWAY Nrf1 and nrf2 are transcription factors that bind to antioxidant response elements (AREs), promoters of genes involved in oxidative damage control. CREB1, FOS, FXYD2, JUN, KEAP1, MAFF, MAFG, MAFK, MAPK1, MAPK14, MAPK8, NFE2L2, PRKCA, PRKCB1 1 KEAP1(24) 73604 24 24 23 0 2 14 2 1 5 0 4.1e-14 9.8e-12
3 HSA04514_CELL_ADHESION_MOLECULES Genes involved in cell adhesion molecules (CAMs) ALCAM, CADM1, CADM3, CD2, CD22, CD226, CD274, CD276, CD28, CD34, CD4, CD40, CD40LG, CD58, CD6, CD80, CD86, CD8A, CD8B, CD99, CDH1, CDH15, CDH2, CDH3, CDH4, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CNTN1, CNTN2, CNTNAP1, CNTNAP2, CTLA4, ESAM, F11R, GLG1, HLA-A, HLA-A29.1, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-E, HLA-F, HLA-G, ICAM1, ICAM2, ICAM3, ICOS, ICOSLG, ITGA4, ITGA6, ITGA8, ITGA9, ITGAL, ITGAM, ITGAV, ITGB1, ITGB2, ITGB7, ITGB8, JAM2, JAM3, L1CAM, MADCAM1, MAG, MPZ, MPZL1, NCAM1, NCAM2, NEGR1, NEO1, NFASC, NLGN1, NLGN2, NLGN3, NRCAM, NRXN1, NRXN2, NRXN3, OCLN, PDCD1, PDCD1LG2, PECAM1, PTPRC, PTPRF, PTPRM, PVR, PVRL1, PVRL2, PVRL3, SDC1, SDC2, SDC3, SDC4, SELE, SELL, SELP, SELPLG, SIGLEC1, SPN, VCAM1, VCAN 16 CD22(2), CDH1(2), CDH3(1), CDH5(2), CNTN1(7), ITGAL(7), NLGN2(3), NRCAM(9), PTPRC(11), PVRL1(1) 1551279 45 38 45 18 13 15 6 3 8 0 5.4e-12 7.1e-10
4 BLYMPHOCYTEPATHWAY B cells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion proteins, and other factors on their cell surface. CD80, CR1, CR2, FCGR2B, HLA-DRA, HLA-DRB1, ICAM1, ITGAL, ITGB2, PTPRC, TNFRSF5 2 ITGAL(7), PTPRC(11) 291192 18 16 18 4 8 4 3 0 3 0 9e-12 7.1e-10
5 TCYTOTOXICPATHWAY Cytotoxic T cells release perforin and granzyme to lyse foreign cell targets and express Fas ligand to promote Fas-induced apoptosis. CD2, CD28, CD3D, CD3E, CD3G, CD3Z, CD8A, ICAM1, ITGAL, ITGB2, PTPRC, THY1, TRA@, TRB@ 2 ITGAL(7), PTPRC(11) 291192 18 16 18 4 8 4 3 0 3 0 9e-12 7.1e-10
6 THELPERPATHWAY Helper T cells coordinate the actions of B cells, macrophages, and other immune cells via surface molecules such as T cell receptor/CD3 and their characteristic marker CD4. CD2, CD28, CD3D, CD3E, CD3G, CD3Z, CD4, ICAM1, ITGAL, ITGB2, PTPRC, THY1, TRA@, TRB@ 2 ITGAL(7), PTPRC(11) 291192 18 16 18 4 8 4 3 0 3 0 9e-12 7.1e-10
7 CARDIACEGFPATHWAY Cardiac hypertrophy, a response to high blood pressure, is stimulated by GPCR ligands such as angiotensin II that activate the EGF pathway. ADAM12, AGT, AGTR2, ARHA, EDN1, EDNRA, EDNRB, EGF, EGFR, FOS, HRAS, JUN, MYC, NFKB1, PLCG1, PRKCA, PRKCB1, RELA 1 EGFR(11) 149027 11 10 6 1 0 4 5 2 0 0 7.4e-11 3.2e-09
8 CBLPATHWAY Activated EGF receptors undergo endocytosis into clathrin-coated vesicles, where they are recycled to the membrane or ubiquitinated by Cbl. CBL, CSF1R, EGF, EGFR, GRB2, MET, PDGFRA, PRKCA, PRKCB1, SH3GLB1, SH3GLB2, SH3KBP1, SRC 1 EGFR(11) 149027 11 10 6 1 0 4 5 2 0 0 7.4e-11 3.2e-09
9 EEA1PATHWAY The FYVE-finger proteins EEA1 and HRS are localized to endosome membranes and regulate sorting and ubiquitination in the vesicle transport system. EEA1, EGF, EGFR, HGS, RAB5A, TF, TFRC 1 EGFR(11) 149027 11 10 6 1 0 4 5 2 0 0 7.4e-11 3.2e-09
10 ERBB3PATHWAY Neuregulins bind to the receptor tyrosine kinases ErbB3 and ErbB4, surface-localized receptors whose overexpression induces tumor formation. EGF, EGFR, ERBB3, NRG1, UBE2D1 1 EGFR(11) 149027 11 10 6 1 0 4 5 2 0 0 7.4e-11 3.2e-09

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 SALMONELLAPATHWAY Salmonella induces membrane ruffling in infected cells via bacterial proteins including SipA, SipC, and SopE, which alter actin structure. ACTA1, ACTR2, ACTR3, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, CDC42, RAC1, WASF1, WASL 2 WASF1(3), WASL(2) 143371 5 5 5 0 0 1 0 3 1 0 0.021 1
2 HSA04664_FC_EPSILON_RI_SIGNALING_PATHWAY Genes involved in Fc epsilon RI signaling pathway AKT1, AKT2, AKT3, BTK, CSF2, FCER1A, FCER1G, FYN, GAB2, GRB2, HRAS, IL13, IL3, IL4, IL5, INPP5D, KRAS, LAT, LCP2, LYN, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6, MAP2K7, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK8, MAPK9, MS4A2, NRAS, PDK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCD, PRKCE, RAC1, RAC2, RAC3, RAF1, SOS1, SOS2, SYK, TNF, VAV1, VAV2, VAV3 4 LYN(2), MAP2K6(1), PIK3R5(4) 259509 7 7 7 3 2 2 2 1 0 0 0.023 1
3 VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS BCAT1, IARS, LARS, LARS2, PDHA1, PDHA2, PDHB 1 LARS(5) 146161 5 5 5 0 1 2 1 1 0 0 0.033 1
4 HSA04330_NOTCH_SIGNALING_PATHWAY Genes involved in Notch signaling pathway ADAM17, APH1A, CIR, CREBBP, CTBP1, CTBP2, DLL1, DLL3, DLL4, DTX1, DTX2, DTX3, DTX3L, DTX4, DVL1, DVL2, DVL3, EP300, GCN5L2, HDAC1, HDAC2, HES1, JAG1, JAG2, LFNG, LOC652788, MAML1, MAML2, MAML3, MFNG, NCOR2, NCSTN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NUMB, NUMBL, PCAF, PSEN1, PSEN2, PSENEN, PTCRA, RBPJ, RBPJL, RFNG, SNW1 4 ADAM17(1), HDAC2(3), PSENEN(1), RBPJL(2) 233940 7 7 7 1 2 3 1 1 0 0 0.039 1
5 RIBOFLAVIN_METABOLISM ACP1, ACP2, ACP5, ACPP, ACPT, ENPP1, ENPP3, FLAD1, RFK, TYR 1 ACP5(2) 40619 2 2 2 0 0 2 0 0 0 0 0.039 1
6 G1PATHWAY CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition. ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53 2 CDK4(1), SKP2(2) 99971 3 3 3 1 0 2 0 1 0 0 0.041 1
7 C21_STEROID_HORMONE_METABOLISM AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2 2 CYP11B1(2), CYP11B2(2) 130510 4 4 4 8 0 3 0 1 0 0 0.044 1
8 HSA00140_C21_STEROID_HORMONE_METABOLISM Genes involved in C21-steroid hormone metabolism AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2 2 CYP11B1(2), CYP11B2(2) 130510 4 4 4 8 0 3 0 1 0 0 0.044 1
9 HSA04630_JAK_STAT_SIGNALING_PATHWAY Genes involved in Jak-STAT signaling pathway AKT1, AKT2, AKT3, BCL2L1, CBL, CBLB, CBLC, CCND1, CCND2, CCND3, CISH, CLCF1, CNTF, CNTFR, CREBBP, CRLF2, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, EP300, EPO, EPOR, GH1, GH2, GHR, GRB2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL13RA2, IL15, IL15RA, IL19, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL9, IL9R, IRF9, JAK1, JAK2, JAK3, LEP, LEPR, LIF, LIFR, MPL, MYC, OSM, OSMR, PIAS1, PIAS2, PIAS3, PIAS4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIM1, PRL, PRLR, PTPN11, PTPN6, SOCS1, SOCS2, SOCS3, SOCS4, SOCS5, SOCS7, SOS1, SOS2, SPRED1, SPRED2, SPRY1, SPRY2, SPRY3, SPRY4, STAM, STAM2, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6, TPO, TSLP, TYK2 9 EPOR(1), IFNA16(2), PIAS4(1), PIK3R5(4), TSLP(1) 569379 9 9 9 1 3 3 1 0 2 0 0.046 1
10 ALTERNATIVEPATHWAY The alternative complement pathway is an antibody-independent mechanism of immune activation that results in cell lysis via the membrane attack complex. BF, C3, C5, C6, C7, C8A, C9, DF, PFC 1 C9(3) 68084 3 3 3 2 1 1 1 0 0 0 0.05 1
Methods & Data
Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset.[1]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 Ð 615 (2011)
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