API for ToPP

Example for Univariate analysis api in ToPP.

http://www.biostatistics.online/topp/result.php?action=survival&&ca=TCGA-LIHC&variable=EZH2&timic=years&confint=FALSE&risktable=TRUE&HRR=TRUE&low=000000&high=ff0000&survmedianline=hv&cutoff=Median&customhigh=&customlow=&datatype=Gene_expression&survivaltype=OS&conditions=no&conditiongene=&Methylationhigh=&Methylationlow=&cli=no&clinicalcut=&diffexp=yes

Example for Multivariate Analysis api in ToPP.

http://www.biostatistics.online/topp/result.php?action=survival1&&ca=TCGA-LIHC&genelist=EZH2,CDH1,APP1,HIF1A&timic=years&confint=FALSE&risktable=TRUE&HRR=TRUE&low=000000&high=ff0000&survmedianline=hv&cutoff=Median&customhigh=&customlow=&datatype=Gene_expression&survivaltype=OS&direction=none&conditions=no&conditiongene=&cli=no&clinicalcut=

Example for Pan-cancer analysis api in ToPP.

http://www.biostatistics.online/topp/result.php?action=survivalpancancer&ca=TCGA-LIHC;TCGA-KIRP;TCGA-CHOL&variable=EZH2&timic=years&confint=FALSE&risktable=TRUE&HRR=TRUE&low=000000&high=ff0000&survmedianline=hv&cutoff=Median&customhigh=&customlow=&datatype=Gene_expression&survivaltype=OS&conditions=no&conditiongene=&Methylationhigh=&Methylationlow=&cli=no&clinicalcut=&cpg=&pathway=

Example for Combination analysis api in ToPP.

http://www.biostatistics.online/topp/result.php?action=4group&&ca=TCGA-LIHC&variable1=CYP2B6&variable2=TP53&timic=years&confint=FALSE&risktable=TRUE&groupc1=dc143c&groupc2=4169e1&groupc3=cd853f&groupc4=3cb371&survmedianline=hv&cutoff=Median&datatype1=Gene_expression&datatype2=Mutation&survivaltype=OS

Parameters

• ca:TCGA-LIHC,Tumor type,all the types can be found here
• variable:EZH2,Gene symbol
• datatype:Gene_expression.Data tpye for the dataset your selected. datatype can only be one of the following
• survivaltype:OS,Survival tpye can only be one of the following
• cutoff:Median,The cutoff value for continuous variable can only be one of the following
• Methylationhigh:0.6,The high thread for cutoff value should be in range(0-1)
• Methylationlow:0.2,The low thread for cutoff value should be in range(0-1)
• conditions:Mutation_1,The generic conditions for subgroup selection,such as Mutation_1,_0,Methylation_high,_low,CNA_gain,_loss
• conditiongene:TP53, The gene for generic conditions,only in gene symbol.
• diffexp:yes,Different expression between tumor and normal tissue.value can be yes or no.
• cli:gender,Clinical conditions for subgroup selection such as gender,race,tumor_status,sample_type
• clinicalcut:female,Value for clinical condition.
• risktable:TRUE,Show the risk table for KM plot. value can be TRUE or FALSE
• timic:years,Timec for survival data,value can be days,months,years
• survmedianline:hv,Show the survival median line for KM plot. value can be hv or none
• confint:TRUE,Show the 95% confint for KM plot. value can be TRUE or FALSE
• HRR:TRUE,Show the HRR for KM plot. value can be TRUE or FALSE
• high:FF0000,Identify the group color for high group
• low:000000,Identify the group color for low group
• customhigh:0.75,Custom cutoff % for high group
• customlow:0.25,Custom cutoff % for low group
• pathway:1,Top ten pathways related with tumor,and 1 for RTK.RAS.pathway;2 for Nrf2.pathway;3 for TGFbeta.pathway;4 for PI3K.pathway;5 for Wnt.pathway;6 for Myc.pathway;7 for P53.pathway;8 for Cell.cycle.pathway;9 for Hippo.pathway;10 for Botch.pathway;
• genelist:EZH2,CDH1,APP1,HIF1A,Gene list in Multivariate Analysis

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