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 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.
  • Cancer Selection: Select cancer by clicking on the one you are in interested in.
-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.
Proteomic Analysis
-Proteomic Profile

Compare gene protein expression levels in cancer vs normal samples according to the selected cancer types by generating box plots, along with a table of gene information.
  • Gene: 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 cancer type you are in interested in.
-Differential Proteomic Expression

Retrieve the list of genes that protein expression levels are most differential between normal and cancer samples.
  • Cancer selection: Select cancer type of interest from the drop-down menu.
  • 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 threshold. (upregulated/downregulated)
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.
  • Gene: 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 cancer type you are in interested in.
-Differential Methylation

Getting the list of genes whose methylation levels are most differential between normal and cancer samples.(Methylation data is measured by Infinium HumanMethylation450K BeadChip)
  • Cancer selection: Select cancer type of interest from the drop-down menu.
  • Gene region: Select the region of gene that you are interested (Promoter, GeneBody, Promoter+GeneBody).
  • 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.
  • Δβ: Set custom beta difference value (beta value is to show the methylation level).
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.
  • Gene: 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 cancer type you are in interested in.
  • 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 cancer type you are in interested in.
  • 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.
  • 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".
-Mutation Associated Survival Analysis

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 of interest.
  • Cancer Selection: Select cancer by clicking on the cancer type you are in interested in.
  • 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".
-Clinical Profile in Mutation

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.
  • Cancer Selection: Select cancer by clicking on the cancer type you are in interested in.
  • Clinical Parameter: Select clinical parameter which are from TCGA
  • 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".
Chromatin Accessibility
-Peak Analysis

Observe accessibility of geneomic regions in selected gene and tumor within fixed-width 501 bp peaks. Also providing pan-cancer level peak information
  • Gene: 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 cancer type you are in interested in.
Multiomic Analysis
-RNA Expression Relation to Mutation Status

Compare gene expression levels in different mutation status according to the selected cancer types by generating box plots, along with summary information.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Data Type: Select the mutation derived from either DNA-seq, RNA-seq, or both.
  • Comparison: Select how you want to make the comparison of expression on mutation status.
  • Cancer Selection: Select the tumor of interest.
-RNA Expression Relation to Mutation Location

Compare gene expression levels in different mutation location according to the selected cancer types by generating lollipop plot, along with summary information.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Data Type: Select the mutation derived from either DNA-seq, RNA-seq, or both.
  • Cancer Selection: Select the tumor of interest.
-Methylation Relation to Mutation Status

Compare gene methylation levels in different mutation status according to the selected cancer types by generating linear plot, along with summary information.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Data Type: Select the mutation derived from either DNA-seq, RNA-seq, or both.
  • Comparison: Select how you want to make the comparison of expression on mutation status.
  • Cancer Selection: Select the tumor of interest.
-Methylation Relation to Mutation Location

Compare gene methylation levels in different mutation location according to the selected cancer types by generating lollipop plot, along with summary information.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Data Type: Select the mutation derived from either DNA-seq, RNA-seq, or both.
  • Cancer Selection: Select the tumor of interest.
-Expression vs Methylation Correlation

Compare gene expression and methylation levels in selected gene and tumor, performing correlation analysis
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Methylation Region: Select which region to focus to get methylation
  • Cancer Selection: Select the tumor of interest.
Oncovirus Analysis
-Expression Profile

Compare gene expression level in viral vs non-viral cancer samples according to the selected cancer types by generating box plots, along with a table of gene information.(RNA-Seq data is normalized using TPM.)
  • Virus: Select virus in your interest.
  • Gene: 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.
-Methylation Profile

Compare gene methylation level in viral vs non-viral cancer samples according to the selected cancer types by generating box plots, along with a table of gene information.
    • Virus: Select virus in your interest.
    • Gene: 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.
-Differential Expression

Retrieve the list of genes that expression levels are most differential between viral and non-viral cancer samples.
  • Virus: Select virus in your interest.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • 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 threshold. (upregulated/downregulated)
-Differential methylation

Retrieve the list of genes whose methylation levels are most differential between viral and non-viral cancer samples.(Methylation data is measured by Infinium HumanMethylation450K BeadChip)
  • Virus: Select virus in your interest.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Gene region: Select the region of gene that you are interested (Promoter, GeneBody, Promoter+GeneBody).
  • 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.
  • |Δβ|: Set custom beta difference value (beta value is to show the methylation level).
-Survival Plots

Perform survival analysis on patients of specified viral-cancer or non-viral cancer, stratified by the expression or methylation levels of gene of interest. Survival plot showing percent survival vs time are provided in viral-cancer and non-viral cancer.
  • Virus: Select virus in your interest.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Threshold: Setting the threshold to filter list of genes.
  • Cutoff(%): Set expression or methylation threshold. Patients whose gene expression/methylation levels are higher than this threshold are considered as the higher cohort and lower will be the low cohorts.
-Virus Survival Plots

Performing Survival analysis based virus vs non-virus. The survival plot showing percent survival vs time.
  • Virus: Select virus in your interest.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Threshold: Setting the threshold to filter list of genes.
  • Cutoff(%): Set expression or methylation threshold. Patients whose gene expression/methylation levels are higher than this threshold are considered as the higher cohort and lower will be the low cohorts.
-Clinical Profile

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) tests in the selected clinical parameter.
  • Virus: Select virus in your interest.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Clinical Parameter: Select the clincial parameter.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
-Differential Clinical

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) tests in the selected clinical parameter.
  • Virus: Select virus in your interest.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Clinical Parameter: Select the clincial parameter.
  • 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.
-Virus Profile

Within the viral cancer, get the viral gene expression in the specific clinical parameter to compare each stages, and the table of p-values from Analysis of variance (ANOVA) tests in the selected clinical parameter.
  • Virus: Select virus in your interest.
  • Viral Gene Selection: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Clinical Parameter: Select the clincial parameter.
Clinical Analysis
-Survival Analysis

Perform survival analysis on patients of specified viral-cancer or non-viral cancer, stratified by the expression or methylation levels of gene of interest. Survival plot showing percent survival vs time are provided in viral-cancer and non-viral cancer.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Threshold: Setting the threshold to filter list of genes.
  • Cutoff(%): Set expression or methylation threshold. Patients whose gene expression/methylation levels are higher than this threshold are considered as the higher cohort and lower will be the low cohorts.
-Clinical Profile

Get the gene expression and methylation profile in the specific clinical parameter to compare each stages, and the table of p-values from Analysis of variance (ANOVA) tests in the selected clinical parameter.
  • Gene: Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene(s) of interest.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Clinical Parameter: Select the clincial parameter.
-Differential Genes in Clinical Parameter

Get the list of genes whose expression or methylation levels are significantly differential between patients stratified by the selected clinical parameter, as determined by Analysis of variance (ANOVA) tests.
  • Gene expression/methylation: Select the type of profile of gene to show in terms of expression or gene.
  • Cancer Selection: Select cancer by clicking on the one you are in interest.
  • Clinical Parameter: Select the clincial parameter.
  • 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.