Expression Analysis
   Expression Profile
   Differential Expression
   Correlation of Expression
Methylation Analysis
   Methylation Profile
   Differential Methylation
Survival Analysis
   Survival Plot
   Clinical Association
   Differential Clinical Parameter
Oncovirus Analysis 
   Expression Profile
   Methylation Profile
   Differential Expression
   Differential Methylation
   Survival Plot
   -Gene Associated Analysis
   -Virus Associated Analysis
   Clinical Profile
   Differential Clinical Parameter
   Virus Profile
Mutation Analysis 
   Mutation Profile
   Significantly Mutated Genes
   Survival Plot
   Mutation Clincial Profile
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Expression Analysis
-Expression Profile
 

Compare gene expression level in cancer vs normal according to the selected cancer types by generating box plots, along with a table of gene information.
(RNA-Seq is normalized, using TPM to show the expression level.).

-You may enter single gene and select up to 3 cancers or enter up to 3 genes and select a single cancer. You can NOT enter multiple genes and select multiple cancers at the same time.  

  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest. You can enter 3 at most, separated by comma.
  • Cancer Selection: Select cancer by clicking on the one you are in interested in. Multiple cancer types may be selected, 3 at most, if there is only one gene input.
-Differential Expression
 
 Retrieve the list of genes that expression levels are most differential between normal and cancer samples .
  • Cancer selection: Select cancer by clicking on the one you are in interest. It can also be selected multiple.
  • Threshold: Setting the threshold to filter list of genes.
  • FDR Adjusted p-value:  Set custom FDR(False Discovery Rate) adjusted p-value (q-value). Return genes with a q-value equal to or lower than threshold.
  • |log2FC|: Set the log2 transformed fold change.(upregulated/downregulated)
-Correlation Expression
 
  Check pairwise correlation coefficients between gene expression levels. Scatter plots visualizing the correlation between gene expression log2 TPMs are generated along with a table of gene information. (RNA-Seq data is normalized using log2 transformed TPM.)
  • GeneA, GeneB:  Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest.
  • Cancer Selection:  Select cancer by clicking on the one you are in interest.Multiple cancer types may be selected, 3 at most.
Methylation Analysis
-Methylation Profile
 

Compare gene methylation levels in cancer vs normal samples of the selected cancer types. Position plots are generated along with a table of gene information
(RNA-Seq is normalized, using TPM data to show the methylation level.)

-You can enter single gene and select 3 cancers at most or enter 3 genes at most and select single cancer. You can NOT enter multiple genes and select multiple cancers at the same time. 

  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter 3 at most, separated by comma.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.It can also be selected multiple, 3 at most.
-Differential methylation

Getting the list of genes that are most differential between normal and cancer, in terms of gene methylation.
(Methylation data is measured by Infinium HumanMethylation450K BeadChip)
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can also be selected Multiple.
  • Gene regionSelect the region of gene that you are interested (Promoter, GeneBody, Promoter+GeneBody)
  • ThresholdSetting the threshold to filter list of genes.
  • FDR Adjusted p-valueSet custom p-value.
  • ΔβSet custom beta difference value (beta value is to show the methylation level).
Survival Analysis
-Survival Plots
 
Performing Survival analysis of gene of interest related to the cancer, based on Gene expression or methylation. It creates table of gene info, significant clinical parameter, and the survival plots showing percent survival vs time.
  • Gene:Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter multiple, separated by Comma.(Limit 3).
  • Gene expression/methylationSelect either expression or methylation to show gene profile.
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can also be selected Multiple.(Limit 3)
  • ThresholdSetting the threshold to get certain gene up to customized threshold.
  • Cutoff(%)Set expression or methylation threshold. Higher than this threshold are considered as the higher cohort and lower will be the low cohorts
-Clinical Association
 

Get the gene expression and methylation profile in the specific clinical parameter that user choose.
  • Gene Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter multiple, separated by Comma.(Limit 3)
  • Cancer Selection Select Cancer by clicking on the one you are in interest
  • Clinical Parameter Select the parameter
  • Gene expression/methylation Select to show list of genes in terms of expression or methylation.
-Differential Clinical Parameter
 
Get the list of differential genes expression or methylation that are significant in Analysis of variance (ANOVA) tests, in selected clinical parameter.
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can also be selected Multiple.
  • Clinical ParametersSelect the clinical paramter.
  • Gene expression/methylationSelect to show list of genes in terms of expression or methylation.
  • ThresholdSetting the threshold to get certain gene up to customized threshold.
  • p-valueSet custom pvalue.
Oncovirus Analysis
-Expression Profile
 

Compare gene expression level in viral vs non-viral cancer according to the selected cancer types, by generating box plots. Also it will generate the table of gene information.
(RNA-Seq is normalized using TPM to show the expression level.)

-You can enter single gene and select 3 cancers at most or enter 3 genes at most and select single cancer. You can NOT enter multiple genes and select multiple cancers at the same time. 

  • Virus type: Select the virus in your interest.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter 3 at most, separated by comma.
  • Cancer Selection: Select cancer by clicking on the one you are in interest. It can also be selected multiple, 3 at most.
-Methylation Profile
 

Compare gene methylation level in viral vs non-viral cancer according to the selected cancer, by generating probe position plot and the table of gene information.
(RNA-Seq is normalized using TPM to show the methylation level)

-You can enter single gene and select 3 cancers at most or enter 3 genes at most and select single cancer. You can NOT enter multiple genes and select multiple cancers at the same time. 

  • Virus type: Select the virus in your interest.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter 3 at most, separated by comma.
  • Cancer Selection: Select cancer by clicking on the one you are in interest. It can also be selected multiple, 3 at most
-Differential Expression
 
Getting the list of genes that are most differential between virus and non-virus infected cancer, in terms of gene 
expression.
  • Virus type(s): Select the virus in your interest.
  • Cancer selection: Select cancer by clicking on the one you are in interest. It can also be selected multiple.
  • Threshold: Setting the threshold to filter list of genes.
  • FDR Adjusted p-value: Set custom p value.
  • |log2FC|: Set the log2 transformed fold change.(log2(median(viral)/log2(median(non-viral)))
-Differential Methylation
 
Getting the list of genes that are most differential between virus and non-virus, in terms of gene methylation.

(Methylation data is measured by Infinium HumanMethylation450K BeadChip)
  • Virus type(s): Select the virus in your interest.
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can also be selected Multiple.
  • Gene regionSelect the region of gene that you are interested (Promoter, GeneBody, Promoter+GeneBody)
  • ThresholdSetting the threshold to filter list of genes.
  • FDR Adjusted p-valueSet custom p-value.
  • ΔβSet custom beta difference value (beta value is to show the methylation level).
-Survival Plots
GeneAssociated Survival Plots
 
Performing survival analysis in gene of interest which is associated with virus, based on gene expression or methylation. It creates table of gene info, and the survival plots showing percent survival vs time.
  • Virus type(s): Select the virus in your interest.
  • Gene:Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter multiple, separated by Comma.(Limit 3).
  • Gene expression/methylationSelect either expression or methylation to show gene profile.
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can also be selected up to 3 (Limit 3).
  • ThresholdSetting the threshold to get certain gene up to customized threshold.
  • Cutoff(%)Set expression or methylation threshold. Higher than this threshold are considered as the high cohort and lower will be the low cohorts
Virus Associated Survival Plots
 

Performing Survival analysis based on virus vs non-virus. The survival plots showing percent survival vs time.
  • Virus type(s): Select the virus in your interest.
  • Cancer SelectionSelect cancer by clicking on the one you are in interest. It can be selected up to 3 (Limit 3).
  • ThresholdSetting the threshold to get certain gene up to customized threshold.
  • Cutoff(%)Set expression or methylation threshold. Higher than this threshold are considered as the high cohort and lower will be the low cohorts
-Clinical Association
 
Get the gene expression and methylation profile in the specific clinical parameter related to viral cancer, to compare each stages, and the table of p-values from Analysis of variance (ANOVA) testsin the selected clinical parameter..
  • Virus Types Select virus of your interest
  • Gene Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter multiple, separated by Comma.(Limit 3)
  • Cancer Selection Select Cancer by clicking on the one you are in interest
  • Clinical Parameter Select the parameter
  • Gene expression/methylation Select to show list of genes in terms of expression or methylation.
-Differential Clinical Parameter
 
Get the differential genes related to viral-cancer based on expression or methylation that are significant in Analysis of variance (ANOVA) tests in the selected clinical parameter.
  • VirusSelect the virus of your interest
  • Cancer SelectionSelect cancer by clicking on the one you are in interest.
  • Clinical ParametersSelect the clinical paramter.
  • Gene expression/methylationSelect to show list of genes in terms of expression or methylation.
  • ThresholdSetting the threshold to get certain gene up to customized threshold.
  • p-valueSet custom pvalue.
Mutation Analysis
-Mutation Profile
  

Retrive somatic mutation profile of specific genes in selected cancer types and data types, by generating mutations plots. Also generate the table of gene information

-You can enter single gene and select 3 cancers at most or enter 3 genes at most and select single cancer. You can NOT enter multiple genes and select multiple cancers at the same time. 

  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter 3 at most, separated by comma.
  • Cancer Selection: Select cancer by clicking on the one you are in interest. It can also be selected multiple, 3 at most.
  • Data Type: Select the data type for somatic mutation analysis. Somatic mutations can be detected using either DNA-seq or RNA-seq alone, or by combining the results from both sequencing datasets, referred to as "DNA-seq + RNA-seq".
-Significantly Mutated Genes
 
 

Getting the list of genes that are most significantly mutated in certain cancer type. Significantly mutated genes (SMGs) were determined by DNDScv. .

  • Cancer selection: Select Cancer by clicking on the one you are in interest. It can also be selected multiple.
  • Threshold: Setting the threshold to filter list of genes.
  • p-value: Set cut-off for adjusted p value.
  • Mutation percentage: Set cut-off for mutation percentage. Mutation percentage was calculated as the number of patients with the mutation divided by the total number of patients examined.
  • Data Type: Select the data type for somatic mutation analysis. Somatic mutations can be detected using either DNA-seq or RNA-seq alone, or by combining the results from both sequencing datasets, referred to as "DNA-seq + RNA-seq".
-Survival Plot
 
 

Perform survival analysis on patients of specified cancer(s), stratified by mutation status of each patient. Survival plot showing percent survival vs time are provided.

  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest. You can enter 3 at most, separated by commas.
  • Cancer Selection: Select up to 3 cancer types of interest.
  • Data Type: Select the data type for somatic mutation analysis. Somatic mutations can be detected using either DNA-seq or RNA-seq alone, or by combining the results from both sequencing datasets, referred to as "DNA-seq + RNA-seq".
Mutation Clinical Profile
 
 

Get the somatic mutation profile in the specific clinical parameter that user choose and get the p-values from Fisher's exact test in the selected clinical parameter.

  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest. You can enter multiple, separated by Comma.(Limit 10).
  • Cancer selection: Select Cancer by clicking on the one you are in interest. It can also be selected multiple.
  • Clinical Parameter: Select the clincial parameter.
  • Data Type: Select the data type for somatic mutation analysis. Somatic mutations can be detected using either DNA-seq or RNA-seq alone, or by combining the results from both sequencing datasets, referred to as "DNA-seq + RNA-seq".
  • Cancer Selection:  Select cancer by clicking on the one you are in interest.Multiple cancer types may be selected, 3 at most.