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.
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-Differential Expression |
Retrieve the list of genes that expression levels are most differential between normal and cancer samples
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Cancer selection: Select
cancer by clicking on the one you are in
interest. It can also be selected multiple.
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Threshold: Setting
the threshold to filter list of genes.
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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.
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|log2FC|: Set
the log2 transformed fold
change.(upregulated/downregulated)
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-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.)
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GeneA, GeneB:
Select gene input format (Gene symbol,Gene Accession,NCBI Gene ID) and enter your gene of interest.
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Cancer Selection:
Select cancer by clicking on the one you are in interest.Multiple cancer types may be selected.
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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.
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-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)
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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.
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-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).
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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".
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-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".
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-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".
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-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".
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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.
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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.
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-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.
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-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.
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-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.
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-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.
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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.
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-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.
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-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)
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-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).
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-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.
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-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.
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-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.
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-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.
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-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.
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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.
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-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.
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-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.
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