Tables from Webster et al manuscript.
GKC CIS Selection. Limiting the analysis to late stage clonal integrations, Gaussian Kernel Colvolution (CIMPL/KCRBM) identifies 311 CIS loci with a p-value <0.05.
Webster_et_al_Supplementary_Data_2-GKC_CIS_Selection.xlsx
Genome wide scan for selection. Genome wide scanning of subclonal mutation selection. A scanning 100kb window is moved across the genome in increments of 10kb. For each window the number of insertions in each class (early/late, forward strand/reverse strand, BCL2 transgenic/wild type, B cell/T cell) is counted and the likelihood of this distribution between groups is estimated using Fisher's exact test. By comparing neighboring windows p-value minima are identified (i.e. windows where the p-value is higher on either side). If a run of 2 or more minima are less than 100,000bp from each other all but the lowest minima will be discarded. For each of the remaining local p-value minima, to assign gene names the nearest peak identified by Gaussian kernel convolution (using the CIMPL/KCRBM packages) and the genes associated with this peak are identified. Each locus with a false discovery rate <0.05 is indicated.
Webster_et_al_Supplementary_Data_3-Genome_Scan.xlsx
Strand bias in early & late stage samples. Comparison of strand bias in early vs. late stage cohorts using equal numbers of integrations. The total number of early stage integrations is 81316. A subset of late 81316 stage integrations was randomly selected and regions with strand/orientation bias were identified using 100kb scanning windows across the entire genome. 16 late-stage loci were significant (FDR < 0.05) after correcting for multiple testing but no early stage loci were found to be significant.
Webster_et_al_Supplementary_Data_4-Orientation_Early&Late_Subsets.xlsx
Candidate genes. Combined list of all candidate genes implicated by one or more criteria in the genome wide scans of subclonal mutation selection.
Webster_et_al_Supplementary_Data_5-CandidateGenes.xlsx
Tab delimited text files.
| Filename | Filesize | Description |
|---|---|---|
| BCL2_specific.txt | 110021 | Loci with more mutations in BCL2 transgenic mice than wild type mice |
| WT_specific.txt | 106944 | Loci with more mutations in wild type mice than BCL2 transgenic mice |
| Late_specific.txt | 114352 | Loci with more mutations in late stage vs early mice |
| Strand_specific.txt | 114612 | Loci with a bias in strand orientation |
| Filename | Filesize | Description |
|---|---|---|
| insertsByDNASample_PW.txt | 226464641 | All retroviral insertions built by DNA sample |
| insertsByMouse_PW.txt | 220003062 | All retroviral insertions built by mouse |
| insertsByMouse_Late_PW.txt | 94571512 | Retroviral insertions from late stage lymphoma mice built by mouse |
| peaksTable.txt | 100837 | Peaks of high insertion site density as determined by gaussian kernel convolution of clonal insertions only |