cBioportal survival analysis help

Question

[mfangli]

hello, every one! I am a newcomer. Recently, I try to use cBioportal to analyzie survival. For example, I want to find whether tumor sample expression of IL8,CXCR1,CXCR2 genes can infuence breast cancer patients prognosis. Select TCGA, Nature Communications 2016, mRNA microarray, z-score ± 2.00. Input IL8,CXCR1,CXCR2 gene list menu. The result show us that tumor sample expression of IL8,CXCR1,CXCR2 genes were stratified into 3 groups(upregulation, downregulation ,noalterlation). But the survival analysis is based on two groups (noalterlation,alterlation).The alterlation group should include upregulation and downregulation.If I want to compare upregulation group with noalterlation group, how shuould I do ？

Answer 1

[TriS]

if you have some R skills a way to do that is to calculate the "ntile" per each of those genes (i.e. top vs. bottom quartile/tercile etc..) and then compare patients that have high vs. low expression.

for exemple (in pseudocode):

# take quantiles high and low 
gene <-  expression levels of gene X 
g_high <- take top quartile 
g_low <- take low quartile

# define a class for the patients with high/low expression 
class <- if expression of X is >= g_high <- 1
      else
       if expression of X is <= g_low <- 2
     else
       class <- 0
 # keep only high and low, remove those in between 
ind_to_remove <- which class == 0 
alive_dead <- if dead <- 1 else <- 0

 # prepare your formula for analysis
myAnalysis <- surv(OS[-ind_to_remove], alive_dead[-ind_to_remove]) ~ class[-ind_to_remove]
 # run logrank test 
s_fit <- survfit(myAnalysis) 
s_diff <- survdiff(myAnalysis)
 # and cox hazard model 
cox <- coxph(myAnalysis)

 # plot KM 
plot(s)

you can always keep those in between (i.e. class == 0), up to you what to do with them

also, check this: Survival analysis of TCGA patients integrating gene expression (RNASeq) data

Answer 2

[Samuel Brady]

Unfortunately, there is no way to do this in cBioPortal. cBioPortal will call patients with either up-regulation OR down-regulation "altered," while those with a z-score between -2 and 2 "non-altered." This of course makes no sense.

If you'd like something simple, I'd use KM plotter. If you want more freedom you can download TCGA RNA-Seq and survival data from GDC Data Portal.