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Yi Qiao Aaron R Quinlan Amir A Jazaeri Roeland GW Verhaak David A Wheeler Gabor T Marth 《Genome biology》2014,15(8)
Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0443-x) contains supplementary material, which is available to authorized users. 相似文献93.
Roel GW Verhaak Mathijs A Sanders Maarten A Bijl Ruud Delwel Sebastiaan Horsman Michael J Moorhouse Peter J van der Spek Bob Löwenberg Peter JM Valk 《BMC bioinformatics》2006,7(1):337-4
Background
Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata. 相似文献94.
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The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by high-resolution NRM spectroscopy. Here, we present strategies for the assignment of protein resonances from homonuclear nonselective 3D NOE-HOHAHA spectra. A notation for connectivities between protons, corresponding to cross peaks in 3D spectra, is introduced. We show how spin systems can be identified by tracing cross-peak patterns in cross sections perpendicular to the three frequency axes. The observable 3D sequential connectivities in proteins are tabulated, and estimates for the relative intensities of the corresponding cross peaks are given for alpha-helical and beta-sheet conformations. Intensities of the cross peaks in the 3D spectrum of pike III parvalbumin follow the predictions. The sequential-assignment procedure is illustrated for loop regions, extended and alpha-helical conformations for the residues Ala 54-Leu 63 of parvalbumin. NOEs that were not previously identified in 2D spectra of parvalbumin due to overlap are found. 相似文献
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Induction of ceruloplasmin synthesis by copper 总被引:2,自引:0,他引:2
P F Evans GW MAJORS W E Cornatzer 《Biochemical and biophysical research communications》1970,41(5):1120-1125
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