市民社会のプレーヤー交代劇と政治-仁平典宏の<贈与のパラドックス>論を読み解く-

千葉大学大学院人文社会科学研究科研究プロジェクト報告書第257集『都市コミュニティにおける相互扶助と次世代育成』水島治郎 編Sustainable Urban Communities: Communality and Generativity Report on the Research Projects No.25

Determinants of protein function revealed by combinatorial entropy optimization-0

<p><b>Copyright information:</b></p><p>Taken from "Determinants of protein function revealed by combinatorial entropy optimization"</p><p>http://genomebiology.com/2007/8/11/R232</p><p>Genome Biology 2007;8(11):R232-R232.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2258190.</p><p></p>torial entropy difference [Equation 6]) by systematic exploration of different clusterings (horizontal axis) and of different values of the granularity parameter (vertical axis). The overall minimum (circle in red area, lower right, = 0.68, value of normalized contrast function -187) determines which protein is in which subfamily and which residues contribute most to the specificity patterns across the subfamilies. Here, the value landscape (color contours, values normalized by the number of residues [283 columns] in the alignment) was computed for a multiple alignment of 390 protein kinases [36] with 0.

Determinants of protein function revealed by combinatorial entropy optimization-1

<p><b>Copyright information:</b></p><p>Taken from "Determinants of protein function revealed by combinatorial entropy optimization"</p><p>http://genomebiology.com/2007/8/11/R232</p><p>Genome Biology 2007;8(11):R232-R232.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2258190.</p><p></p>r) for the actual (solid line) and randomized (dashed line) multiple alignment of 390 protein kinase sequences [36]. Deviations from the linear fit to the entropy curve define the specificity region (yellow, about 20 residues, conserved in subfamilies but varying between subfamilies) and conserved region (blue, about 50 residues, conserved across all subfamilies). The randomized alignment, obtained by independently shuffling residues in each column of the original alignment, serves as a point of reference. The shuffling does not affect the residue content in the columns, but it washes out the subfamily distinctions. The greater the differences between the native and the randomized entropy curves, the more reliable the corresponding prediction of specificity residues. To automate visual parsing of the extreme ends of the entropy plots, we perform a simple linear fit to the central region, covering a fraction = 0.5 to 0.7 (depending on the length of the alignment) of the sequence length (horizontal range). The line segment is centered at a point corresponding to the best linear fit. To identify the turning points at the extremes, we compute the root mean square deviation from a simple line in the central region and record the points outside of the central region where the curve deviates by more than from the extrapolated line segment. In most cases, this simple procedure is in agreement with visual identification of downturn and upturn at the extremes. A reasonable subset of specificity residues (low end of entropy difference) and conserved residues (high end) can then be read off from the horizontal axis of the entropy plot

Association analysis of genetic variants in DNA repair genes with the risk of major NHL subtypes.

<p>DLBCL = diffuse large B-cell lymphoma; FL = follicular lymphoma; SLL/CLL = small lymphocytic lymphoma/chronic lymphocytic leukemia; OR = odds ratio; CI = confidence interval.</p

Association analysis of genetic variants in DNA repair genes with the risk of NHL.

<p>OR = odds ratio; CI = confidence interval.</p

The results of association analysis, displayed as Manhattan plot, after imputation of 28 SNPs genotyped in both stage 1 and 2, which tag 11 DNA repair genes that showed association with NHL risk in our study.

<p>The SNPs and genes are ordered by chromosomal position (x-axis). The associations are displayed as –log₁₀(p-value) for each SNP. Red dots represent fifteen tagging SNPs that were genotyped in our study and were associated with NHL risk. Green dots represent tagging SNPs that were genotyped in our study and that showed no association with NHL. Blue markers represent SNPs imputed by IMPUTE from 1KG. The red dotted line defines the threshold of p-value <0.05. * indicates an associated SNP with a putatively functional impact; non-synonymous coding change or SNP mapping in: transcription factor binding site, H3K4Me1 chromatin mark, DNaseI hypersensitivity cluster, 5′UTR, 3′UTR.</p

Association analysis of rs1805812 x rs625245 interactions between <i>MRE11A</i> and <i>NBS1</i> with the risk of NHL.

<p>OR = odds ratio; CI = confidence interval.</p

Putatively functional SNPs imputed from the ATM locus associated with the risk of NHL.

<p>OR = odds ratio; CI = confidence interval; TFBS = transcription factor binding site; UTR = untranslated region.</p><p>*Correlated tSNP for rs228595 is rs611646; all other SNPs are correlated with the tSNP rs419716.</p

Additional file 12: Figure S9A and B. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

CLPB-NADSYN1 gene fusion in patient P0002. a Long-range PCR confirms CLPB-NADSYN1 gene fusion. b Genomic breakpoint of CLPB-NADSYN1 gene fusion. (ZIP 150 kb

Additional file 3: Figure S1. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

A decision tree approach to predict drug response based on genetic alterations. (PPTX 96 kb