Gastric Cancer Portal (Cancer Research Li X.C. et al)

Gastric Cancer Portal:

Xiangchun Li, William KK Wu, Rui Xing et al. Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability. Cancer Research 2016

Related materials of my PhD thesis - 2016年丙申年【猴年】

Significantly mutated genes in regular-mutated gastric cancer

Click on a gene name to see additional annotations. MutSigCV/CL/FN were used.

Significant by CV/CL/FN

48.4% of all patients

Significant by CV/FN

13.8% of all patients

Significant by CV/CL/FN

11.6% of all patients

Significant by CV/CL

8.4% of all patients

Significant by CL only

7.3% of all patients

Significant by CV only

7.0% of all patients

Significant by CV/CL

6.8% of all patients

Significant by CV/CL/FN

6.2% of all patients

Significant by CL only

5.7% of all patients

Significant by CV/CL

5.7% of all patients

Significant by CV/CL

4.4% of all patients

Significant by CV only

4.4% of all patients

Significant by CL only

3.7% of all patients

Significant by CL only

3.7% of all patients

Significant by CV/CL/FN

3.3% of all patients

Significant by CL only

3.3% of all patients

Significant by CL only

3.1% of all patients

Significant by CV only

3.1% of all patients

Significant by CV/FN

3.1% of all patients

Significant by CL only

3.1% of all patients

Significant by CV

2.4% of all patients

Significant by CV/FN

2.4% of all patients

Significant by CV only

2.2% of all patients

Significant by CV only

2.0% of all patients

Significant by CV only

2.0% of all patients

Significant by CV only

1.8% of all patients

Significant by CV only

1.8% of all patients

Significant by CV only

1.8% of all patients

Significant by CL only

1.3% of all patients

Significant by FN only

1.1% of all patients

Significant by CL only

1.1% of all patients

Significant in my pnas.1422640112

2.64% of all patients

Significantly mutated genes in hyper-mutated gastric cancer

Click on a gene name to see additional annotations. MutSigCV/CL/FN were used. Only SNVs were included

Significant by CV/FN

30.3% of all patients

Significant by CV/FN

23.6%% of all patients

Significant by CV/CL

16.9%% of all patients

Significant by CV/CL

2.2% of all patients

Mutational signatures operative in 544 exomes of gastric cancer

Click on mutational signature and hover your mouse over to see detail information.

Mutational signature 1

Operative in 11.9% RGC and 10.1% HGC

Mutational signature 2

Operative in 59.3% RGC and 82% HGC

Mutational signature 3

Operative in 0.7% RGC and 3.4% HGC

Mutational signature 4

Operative in 2% RGC and 80.9% HGC

Mutational signature 5

Operative in 1.1% RGC and 51.7% HGC

Mutational signature 6

Operative in 70.8%% RGC and 10.1% HGC

Mutational signature 7

Operative in 0.4%% RGC and 80.9% HGC

Mutational exposures

Pie chart representation

Compare with nature paper Alexandrov L. B. et al

21 mutational signatures

Cosine similarity

Mutational signatures operative in 100 WGS of gastric cancers

Click on mutational signature and hover your mouse over to see detail information.

Stability & Reconstruction error

Optimal mutation signature number = 9

Mutational signature 1

Operative in 11.9% RGC and 10.1% HGC

Mutational signature 2

Operative in 59.3% RGC and 82% HGC

Mutational signature 3

Operative in 0.7% RGC and 3.4% HGC

Mutational signature 4

Operative in 2% RGC and 80.9% HGC

Mutational signature 5

Operative in 1.1% RGC and 51.7% HGC

Mutational signature 6

Operative in 70.8%% RGC and 10.1% HGC

Mutational signature 7

Operative in 0.4%% RGC and 80.9% HGC

Mutational signature 8

Operative in 0.4%% RGC and 80.9% HGC

Mutational signature 9

Operative in 0.4%% RGC and 80.9% HGC

Mutational exposures

Pie chart representation

Mutation distribution

Scatter plot ordered by cluster ID

Compare with nature paper Alexandrov L. B. et al

21 mutational signatures

Cosine similarity

Main and supplementary figures

Click on a mutational signature to see corresponding main figures.

Overall mutational spectra

Mutational spectra of RGC & HGC

Mutational & APOBEC signature in RGC vs. HGC.

SMG & molecular. subtypes et al.

Mutation plot of PIK3CA in RGC vs. HGC

CDH1 mutations as a prognosticator in DGC

Altered pathways in GC

Druggable target marked with red star

Mutational burden clustering

Clustering based on dynamic programming

Signature deciphering

Metrics of signature deciphering

Kernal PCA for mutational exposures

Survival analysis of C1/2

KM survival analysis of C1/C2 in DGC and HGC

C1/2 in validation cohort

Prognosis of C1/2 in validation cohort

CDH1 in validation cohort

Prognosis of CDH1 mutation(s) in validation cohort

MSig in RGC vs HGC

Importance scores of mutational signatures

Total visited times