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Peak intersection analysis used intersectBed (Quinlan and Hall, 2010 ) between Eed +/+ and Eed −/− RING1B peaks.
Peak intersection analysis used intersectBed (Quinlan and Hall, 2010) with CpG island data downloaded from UCSC mm9 table browser.
Moreover, our peak intersection analysis showed that FUS and EWS ChIP-seq peaks often overlap, which altogether supeakss a functioftencoverlapion or redundancy of these proteins.
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Thus, we performed an intersection analysis of the top ~5% of transcripts from the three groups.
Peak intersection was performed by BEDTools-Version-2.16.2 BEDTools-Version-2.16.2 BEDTools-Version-2.16.2
This paper attempts to improve intersection analysis through parallel computing.
Moreover, several modifications were proposed to optimize the procedure of intersection analysis.
The essence of intersection analysis is quantifying the spatial relation between two individual fractures.
The workflow of the intersection analysis is essentially an enumeration process in which each pair of fractures is selected and successively tested against intersection.
We chose transcripts that were either statistically significant by t tests or intersection analysis.
Of nine transcripts identified by intersection analysis, 33% were validated by qPCR (three human transcripts only: C11orf75, RAB31, and DUSP4).
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