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[…] been observed within chromosomal breakpoints. Ruiz-Herrera et al. also showed the correspondence between fragile site location and the positions of evolutionary breakpoints []. As stated by Ruiz-Herrera, microsatellites are known to be an additional underlying mechanism behind chromosomal instability, characterizing some fragile sites in human DNA, and in constitutional human chromosomal disorders. Not only are microsatellites repeats of varying length, but they have also been found to be particularly AT-rich []. Furthermore, palindromic AT-rich repeats are found to be related to human chromosomal aberrations [,]. We determined the associated GO terms (Gene Ontology) of the six motifs using GOMO [] (Gene Ontology for Motifs, from MEME suite []); the top GO term predictions are listed in Table . The association of the term “positive regulation of transcription from RNA polymerase II promoter” is very common to motifs 1 and 5. Motif 1 was also identified to be associated to a “negative regulation of transcription from RNA polymerase II promoter”. Interestingly, only a cellular component association was found for motif 3 and no association was found for motif 4. Additionally, three of six motifs were found to be associated to “transcription factor activity”. Comparing the motifs found within the inter-segment regions (ISRs), seventeen matches were computed searching the Uniprobe mouse database with TomTom []. Most motif matches were found for motif 2, including Zinc finger protein motifs, growth factor response motifs and homeodomains. In summary, an association to DNA, RNA and protein interaction as well as an influence on transcriptional regulation can be found for four of the six previously presented motifs. These motif characteristics are indicated not only by motif associations to GO terms but also by motif matches to validated and well known motifs. Motifs having neither a GO term prediction nor matching known motifs, may still by further analyses be shown to contribute to breakpoint prediction., Motifs found by motif search in 285 segments of the Tumor1 sample are depicted in Fi […]

Pipeline specifications

Software tools GOMo, MEME Suite, Tomtom
Databases UniPROBE