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The overall compaction level and intranuclear location varies as a function of gene density for both entire chromosomes [J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague,W.A. Bickmore, Differences in the localization and morphology of chromosomes in the human nucleus, J. Cell Biol. 145 (1999) 1119 1131] and specific chromosomal regions [N.L. Mahy, P.E.
Individual and average occurrence probabilities are shown as a function of gene and list vertex degrees.
Figure 2 shows the Kaplan-Meier analysis as a function of gene profile for homogeneous subsets of patients.
A three-way analysis of variance (ANOVA) measured genetic distance as a function of gene, year and within- versus between-region designation, testing whether underlying genetic distributions differ regionally.
Xiao and C.D. Town, personal communication) and having independent quantitative and qualitative evidence of strong antisense expression from tiling array experiments [58], [82], [83] clustered as a function of gene model quality.
We also plotted GC3 as a function of gene expression.
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The first of these involves the study of phenotypic variations in model organisms such as C. elegans, as a function of gene-knockouts or changes in environmental conditions.
CAI is assessing translation elongation efficiency as a function of genes' codon usage.
For visualization purposes, median intensity ratios from successive 19-gene sliding windows were plotted as a function of genes in chromosome order.
Specifically, with GSVA (Gene Set Variation Analysis) [ 53] we calculated sample-wise gene set enrichment scores as a function of genes inside and outside the gene set, analogously to a competitive gene set test (see Methods).
Read position was visualized by either Integrative Genomics Viewer (http://www.broadinstitute.org/igv/) [ 53, 54] or DNAPlotter (http://www.sanger.ac.uk/resources/software/dnaplotter/) [ 55] and multiple sites within a gene were then assessed together to generate estimates of essentiality as a function of genes.
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