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The promoter sequences (1.0 kb before the ATG site) of the highly up-regulated genes (≥50-fold) in Cypress (compared to LaGrue and Nipponbare) and Ilpumbyeo (compared to YR15965 and Nipponbare) identified in both SBS and MPSS libraries were analyzed using the 'PLACE Signal Scan Search' software http://www.dna.affrc.go.jp/htdocs/PLACE/.jp/htdocs/PLACE/
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The pairwise linkage disequilibrium (r) of SNPs in the region approximately 45 kb before and after the APC gene (chr5:112055101–112254554 (hg18)) and the APC CNV is depicted in Fig. 3.
We used SNP genotype data from all SNPs in the gene region including approximately 45 kb before and after the APC gene, and perform linkage disequilibrium analysis using Haploview 4.2 [28].
In order to prevent local regions of high linkage disequilibrium (LD) overwhelming the principal components, the training data were thinned to 1 SNP every 100 kb before choosing the number of principal components and computing.
In support of the PennCNV genotypes for this region, a distinct decrease in log R ratio values for the eight single copy subjects encompassing only the APC gene, compared to 100 kb before and after the gene, was evident on examination of the genotyping array data (Fig. 2).
The 3' end of 20-kb deletion is about 2.7-kb before the reported IRGM1 transcription start; and the deletion may affect the function of the IRGM1 gene promoter, causing decreased gene expression [7].
The 3 kb region before the coding region was amplified as a gene specific promoter (supplementary material Table S1).
Clone 408619 (ESTs: GB No. AI430291, AI429558) begins approximately 1.1 kb before exon 13 and continues through the exon and splices correctly to exon 14.
The selected regions are defined in a region of 5 kb before and after TSSs of gene list selections.
The mean sizes of successfully converted CNV were 62.1 kb (vs. 60.4 kb before conversion) and 43.7 kb (vs. 44.9 kb before conversion), respectively.
The number of heterogeneous distance classes in East Asia was five and two (60 70 and 70 80 kb) before and after Bonferroni correction, respectively.
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Justyna Jupowicz-Kozak
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