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1. What is the definition of common integration sites(CISs)?

   Common Integration Sites (CISs) are the transposon insertion sites observed in small windows of genome by two or more tumors. The window sizes are determined by considering the likelihood of observing such occurrences by chance.

   We used following window sizes for approximately 1,000 insertion spots to limit false discovery rate:

   • a window size of 30 kb for CISs with 2 insertions
   • a window size of 50 kb for CISs with 3 insertions
   • a window size of 100 kb for CISs with 4 (or more)

   To determine the window sizes, we simulated random transposon insertions at TA sites in approximately 2Gb mouse genome by computer based on two characteristics of SB transposon (Vigdal et al., 2002: J Mol Biol.):

   • a small target site (TA in the case of SB transposon)
   • random integration (No preference of genes)

   This procedure is similar to that of the retrovirus random integration model (Suzuki et al., 2002: Nat. Genet.).

   However, there is a problem in this random SB transposition model, a local hopping. In germline cells, 50-80% of SB transpositions are located within 10-25 megabases of the donor site (Horie et al., 2001: Proc Natl Acad Sci U S A.). In somatic cells, the percentages of location transpositions are reduced, but researchers have to adjust the window sizes in donor site chromosomes.

2. Why is the candidate gene different from the gene in UCSC genome browser?

   Candidate genes are usually the nearest neighboring RefSeq gene from each integration sites. However, we do not apply this rule strictly toward common integration sites. We choose CIS candidate genes based on directions of insertions and gene functions. In addition, we may have missed the latest additions and modifications of gene definitions.

   If you notice a mistake, please contact to our help desk by e-mail.

3. How can I get the clone list of each chromosome?
   1. Visit Easy Search.
   2. Leave the text box blank.
   3. Uncheck the CIS only checkbox to view non-CIS clones.
   4. Select the chromosome of your interest from the selection bar.
   5. Select "Clone" from Display-by radio buttons.
   6. Click "Go". You will see the clone list in the chromosome ordered by the insertion position.
4. How can I get the tumor list of each model?
   1. Visit Model Search.
   2. Check the model of your interest in model checkboxes.
   3. Check "All" in tumor type checkboxes.
   4. Select "Tumor" from Display-by radio buttons.
   5. Click "Go". You can view the tumor name, model, strain, type, and the number of clones.
5. How did you add custom tracks in the UCSC genome browser?

   Please visit UCSC Genome Bioinformatics Homepage (http://genome.ucsc.edu). There is a step-by-step instruction how to create user custom tracks.