Function 1: Search Potential Cancer Markers

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(a) The query form of Function 1. Users can specify the cancer type, analysis stages, and the significance threshold to obtain the list of differentially expressed genes or isoforms.
(b) The differentially expressed gene list or isoform list for the given cancer type and stages.
(c) The link to the detail information for the selected gene or isoform between the selected 2 stages.
(d) The differentially expressed gene/isoform list can be download as a plain text file for further processing.
(e) The users can filter the transcript list to check only coding transcripts or non-coding transcripts. This filter only appears in the ”DE isoforms” mode.

Function 2: Search Potentially Induced Cancers

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(a) The search form of Function 2. Users can input a gene/transcript isoform name and the significance threshold to obtain the list of cancer types that may be potentially induced by the differential expression of the input gene/isoform.
(b) The table of cancer types in which the input gene/isoform shows differential expression between two stages.
(c) The link to the detail information for the selected gene or isoform between the specified 2 stages.
(d) The potentially induced cancer type list and the differential expression of the input gene/isoform can be downloaded in a plain text file.

Detail page of the gene-level or isoform marker

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In the detail page of a selected isoform or gene, the detailed comparison of FPKM values between the selected two stages is shown. In this figure, a differentially expressed isoform detail page is used as an example. The results are similar for a differentially expressed gene detail page.
(a) The FPKM values comparison summary for the isoform.
(b) A link to the survival analysis of the selected isoform is provided.
(c) A boxplot visualizes the stage comparison of the selected isoform/gene.
(d) In the isoform detail tab, a visualization exon map of the alternative spliced transcripts is implemented for users to investigate the relationship between different splice isoforms.
(e) In the isoform detail tab, a tabular summary of isoform switching test results are provided for identifying differential isoform usage.
(f) The related gene tab can be clicked to view the comparison summary of the related gene of the specified isoform.

Function 3: Survival Analysis

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(a) The query form of Function 3. Users can input a gene/transcript isoform name and a cancer type to perform the survival analysis using the RNA-seq FPKM expression values.
(b) The threshold and cancer stages for the high expression group and the low expression group can be specified.
(c)(d) The survival curves of the high expression and low expression groups and the log-rank test p-value.

Function 4: Stage Comparison Plot

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(a) The query form of Function 4. Users can input a gene/transcript isoform name, a cancer type, and stages to visualize the RNA-seq FPKM expression value comparison between different stages.
(b) The comparison results between the primary tumor samples and the normal group.
(c) The boxplot and the average values are provided.
(d) Clinical data filtering for the specified gene/isoform.
(e) The plot can be downloaded in the .png format.