Starting Points at Home Page:

CanIsoNet offers two starting points to the user:

1) Browse Disease Type: The user can find 28 disease types to browse. In the table, the first column represents a PCAWG-Code used in the Pan-Cancer Analysis Whole Genome Project for 27 cancer types and one BioProject Accession Number for OIH. The second column corresponds to the name of the disease type. The third column indicates the data source (project).

2) Browse a Genes & Isoforms: The user can search for a specific gene name or ENST id, or corresponding transcript name. Isoform search leads the user to the Transcript Page while gene search leads the user to the Gene page.


Example Use Case: Browse Disease Type Click on any of the column to be directed into the disease page (Figure A).

Disease Page

Browsing by disease type directs users to a disease page. This page presents three main findings:
a. In the Figure B-left, you will see frequencies of the top ten most common dMDTs, which represents the proportion of the transcripts occurence across cancer samples. Some dMDTs are found in every sample, which makes them potential biomarkers for that cancer type.

b. In the Figure B-right: you will find the distribution of dMDT counts across samples of the cancer type selected which is also presented as a table on the bottom table of the page.

c. In the table below the figures, the user can find all different isoforms found as dMDTs in the cancer type of interest. The user can search for a specific isoform or sample.

Transcript Page

The transcript page contains the following information:
a. STRING-based transcript interaction network (Figure D):
- Up to 30 interactions of the protein of interest are shown in the network.
- The missing interactions upon isoform switching are shown as a thick black lines. The remaining interactions are seen as a thin grey lines.
- Proteins found in the ClinVar are highlighted in turquoise colours.

b.Statistics on the dMDT (Figure E-F): Number of missed and remaining interactions, network density score ( which estimates the density of interactions of a protein and its local neighborhood in the STRING interaction network), and disease types where the transcript is found as dMDT.

c.Figure G-top shows the table that includes the sample-based information for the interactions lost upon isoform switching: which interactions are lost in which sample.

d.Figure G-bottom shows the table that includes the cancer census genes, included if an interaction with the protein of interest is lost upon isoform switching.

Sample Page

In sample based page, the user can see the MDT-dMDT switch in the corresponding sample. Here, we also show the TPM counts for the MDTs and dMDTs in cancer sample along with the average TPM counts of MDTs and dMDTs in normal samples (Figure H). In addition, domain structure of MDT and dMDT are provided.