The home page contains two figures to help users understand our database. The left figure is a conceptual graph illustrating the process of tumor evolution. For conveniently browsing the somatic events in each different evolutionary stage, the user can click the hyperlink embedded in the figure. For example , after clicking the 'early' link, the search engine will run and return the results containing a table showing all early-specific somatic events recorded in the database (as figure below shows).
The right figure in the home page shows a human body, some common cancers are marked as abbreviations to facilitate the user to quickly browse evolutionary stage-specific somatic events in the clicked cancer type (as figure below shows).
The browse page is built based on different hierarchical classification of cancer and somatic events. To browse somatic genomic events data in various evolutionary stage, please click the menu 'Browse'(1 in figure below). To browse the entries related a particular cancer (for example Glioblastoma), please click 'Cancer'(2 in figure below), then choose the tissue origin 'CNS/Brain' and corresponding cancer 'Glioblastoma' (3,4 in figure below).The related entries will be show on the right panel (5 in figure below).
Silimarly, the user can browse all entries associated with an interested somatic event (Gene or Chromosomal events) in a similar way (as figure below showing, taking the gene 'ABL1' for example).
The SEECancer allow users to search evolutionary stage-specific somatic events in more than 80 cancer types.
To search interested entries in the database, select the menu 'EvolutionaryStage'. SEECancer proveds functions of 'search' by gene/events or cancer or by evolutionary stages (as figure below shows).
The user can also search by combination of different key words. Input your candidate key words into corresponding blanks then click the 'search' button.
Here, we take 'Breast cancer' as an example to explain how to search somatic events in a particular evolutionary stage. First please click the menu 'EvolutionaryStage' (1 in figure below). Next, choose 'breast cancer' in the 'Cancer Type' search box (2 in figure below), and choose the 'early specific' in the 'Evolutionary stage' box (3 in figure below), then click Search button (4 in figure below). After finishing 4 steps above, the system will return a table showing all entries about somatic events specifically occurred in early development of breast cancer (5 in figure below).
SEECancer results are organized in a data table, with a somatic event record on each line containing Gene/Event, cancer Type, Variant Type, Evolutionary stage, Object of Study and Supported Papers. Users can click the 'more details' to view detailed information of the particular somatic events.
Users can obtain detailed information on each deposited somatic event by clicking on the 'more details' link of the data table, which opens a new page containing comprehensive information of the single record.
SEECancer provedes the page 'TemporalOrder' (1 in figure below) to query the temporal sequence of somatic gene alterations in a particular cancer. The user can search by cancer or by gene. In addition, the system also support searching by combination of gene and cancer type. Input the queried gene (The current version of SEECancer only supported searching by 'gene' term, not chromosomal alteration), then choose an interested cancer (2 in figure below). The search engine will run and return all recorded alterations related to the queried gene in the selected cancer (3 in figure below).
Please choose one somatic event you want to query then click the hyperlink under the column of 'Temporal order', The SEECancer will return two graphs that present the recorded antecedent events (left in figure below) and subsequent events (right in figure below) of the queried gene alteration, respectively.
The size of edge in the temporal tree represents the confidence of each temporal relationship. Specifically, 0.5 represents order events collected from one patients; 0.6 represents order events supported by at least two patients; 0.7 represents order events inferred from the bioinformatic prediction which usually involved more than 10 patients; 0.8 represents order events simultaneously inferred from the bioinformatic prediction and collected from individual patient.
SEECaner also provides a module to display the global network view of the collected temporal sequences for user selected cancer (figure below). Please click the hyperlink "Global view", then choose an interested cancer.
If the user want to obtain all the deposited temporal relationships, please download the related data 'temporal sequence' in the 'Download' page.
To download data in the database, select the menu 'Download'. SEECancer provides downloadable file in TXT format. The users can download all data in SEECancer, including six files about evolutionary stage-specific somatic events and one temporal order file.