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Table 1 Common Insertion Sites (CISs) in Medulloblastomas and Cerebellum Controls

From: Identification of a neuronal transcription factor network involved in medulloblastoma development

Gene Chr CIS width N I GKC p-value Other genes Inferred MOA CGC MB- Mut MB- CIS
A. Medulloblastomas
Nfia 4 28.6 20 27 <1E-14 - Loss - - Ptch
Atxn2 5 25 6 6 <1E-14 - ? - - -
Tead1 7 19.1 6 7 3.9E-14 - Gain - - Ptch
Tgif2 2 0.8 3 4 0.0006 - Gain - - -
Crebbp 16 37.1 5 5 0.0009 - Loss S Y Ptch
Dscr3 16 18.3 5 6 0.0009 - Loss - - -
CIS13:72336914 13 44.3 5 6 0.0042 n/a n/a n/a n/a n/a
Pten* 19 50.2 4 5 0.0046 - Loss S/G Y Both
Itgbl1 14 43.4 5 5 0.0062 Fgf14 ? - - -
Nfib 4 24.7 7 9 0.0071 - Gain S - Ptch
Myt1l 12 67.2 8 10 0.0089 Pxdn,Tpo,Sntg2 Loss - - -
Ankrd5 2 1071.3 8 15 0.0092 Plcb4, Pak7,Snap25 ? - - -
Slit3 11 494.3 8 12 0.012 - Loss - - -
Tmem45b 9 58.4 4 5 0.019 - ? - - -
Sfi1 11 51 5 6 0.021 - Loss - - Both
CIS15:70979306 15 20.3 4 4 0.028 n/a n/a n/a n/a n/a
Fgf13 X 23.5 3 4 0.026 - Gain - - -
CIS3:147532546 3 140.5 4 7 0.043 n/a n/a n/a n/a n/a
L3mbtl4 17 221.6 7 7 0.043 Tmem200c Loss - - -
Adcy5 16 127.1 4 6 0.044 Ptblb Loss - - -
B. Cerebellum controls
Faf1 4 41.7 4 4 0.01 - ?    
l7Rn6 7 10 3 3 0.018 Ccdc81 ?    
CIS6:31346217_240k 6 844 6 8 0.045 n/a n/a    
Ric3 7 99 4 4 0.035 Tub ?    
CIS9:68415409_240k 9 1738 9 11 0.016 n/a n/a    
  1. Genes associated with CISs, the chromosomes to which they map, and the genomic extent of each CIS are shown. GKC p-values are from the Genome Kernel Convolution analysis (see Methods). The number of tumours (N) and T2Onc insertions (I) which define each GKC CIS, together with other genes within the CIS interval, are also shown. The position and orientation of SB insertions can be used to infer the mode of action (MOA) of insertion (e.g. [28]). Most of the CISs have insertions distributed throughout the genes they identify, and in both orientations, suggesting loss of function (Loss). Both of the CIS genes which have proven tumour suppressor activity (Pten and Crebbp) show this pattern. An excess of inserts in the 5’ end of a gene, and in a +ve orientation with respect to transcription, implies upregulation of expression (Gain) through SB enhancer function [34]. CGC – Genes known to cause cancer due to somatic (S) or germline (G) mutations from the Cancer Genome Census (http://www.sanger.ac.uk/genetics/CGP/Census/). MB-Mut – Somatic mutations previously identified in MB [11, 12, 14, 15]. MB-CIS – previously identified as an MB CIS [30] in either the Ptch model (Ptch) or the Ptch and p53 model (both). *Pten, was also identified as a CIS within haematological tumours (data not shown) but is included here as it is a known MB gene. For details, see Methods.