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排序方式: 共有501条查询结果,搜索用时 31 毫秒
51.
Maochun Qin Biao Liu Jeffrey M Conroy Carl D Morrison Qiang Hu Yubo Cheng Mitsuko Murakami Adekunle O Odunsi Candace S Johnson Lei Wei Song Liu Jianmin Wang 《BMC bioinformatics》2015,16(1)
Background
Somatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencing (NGS) data still faces major challenges introduced by tumor sample characteristics, such as ploidy, heterogeneity, and purity. A simulated cancer genome with known SVs and CNVs can serve as a benchmark for evaluating the performance of existing somatic SV/CNV detection tools and developing new methods.Results
SCNVSim is a tool for simulating somatic CNVs and structure variations SVs. Other than multiple types of SV and CNV events, the tool is capable of simulating important features related to tumor samples including aneuploidy, heterogeneity and purity.Conclusions
SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterozygosity (LOH), and event break points, which is essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies. 相似文献52.
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Peterson SE Westra JW Rehen SK Young H Bushman DM Paczkowski CM Yung YC Lynch CL Tran HT Nickey KS Wang YC Laurent LC Loring JF Carpenter MK Chun J 《PloS one》2011,6(8):e23018
Human pluripotent stem cell (hPSC) lines have been considered to be homogeneously euploid. Here we report that normal hPSC--including induced pluripotent--lines are karyotypic mosaics of euploid cells intermixed with many cells showing non-clonal aneuploidies as identified by chromosome counting, spectral karyotyping (SKY) and fluorescent in situ hybridization (FISH) of interphase/non-mitotic cells. This mosaic aneuploidy resembles that observed in progenitor cells of the developing brain and preimplantation embryos, suggesting that it is a normal, rather than pathological, feature of stem cell lines. The karyotypic heterogeneity generated by mosaic aneuploidy may contribute to the reported functional and phenotypic heterogeneity of hPSCs lines, as well as their therapeutic efficacy and safety following transplantation. 相似文献
56.
We compared plastic responses to variation in the light environment for sympatric populations of native and exotic dandelion species, Taraxacum ceratophorum and Taraxacum officinale. Plasticity in leaf size, inflorescence height, reproductive phenology and dispersal-related traits were measured under experimentally altered light quality (red : far-red light ratio, R : FR) and light intensity (photosynthetically active radiation, PAR). To test whether differences in means and reaction norms of dispersal-related traits between species affected colonization potential, we created seed-dispersal models based on seed-fall rate and release height. Differences in plasticity between species were not systematic, but varied in direction and magnitude among traits. Taraxacum officinale produced larger leaves that exhibited greater plasticity in size under variable light intensity than T. ceratophorum. Plasticity in scape length at flowering occurred in relation to R : FR ratio in both species, but tended to be greater in T. ceratophorum. Seed-bearing scapes of T. officinale were taller and more canalized in height across light regimes than scapes of T. ceratophorum. Seeds of T. officinale were smaller than seeds of T. ceratophorum. Models predict greater dispersal in T. officinale within open and vegetated habitats. In contrast to the idea that plasticity promotes invasiveness, results suggest that the lack of plasticity in dispersal-related traits enhances the colonization potential of T. officinale. 相似文献
57.
Excess biglycan causes eyelid malformation by perturbing muscle development and TGF-alpha signaling 总被引:2,自引:0,他引:2
Hayashi Y Liu CY Jester JJ Hayashi M Wang IJ Funderburgh JL Saika S Roughley PJ Kao CW Kao WW 《Developmental biology》2005,277(1):222-234
Tissue morphogenesis during development is regulated by growth factors and cytokines, and is characterized by constant remodeling of extracellular matrix (ECM) in response to signaling molecules, for example, growth factors, cytokines, and so forth. Proteoglycans that bind growth factors are potential regulators of tissue morphogenesis during embryonic development. In this study, we showed that transgenic mice overexpressing biglycan under the keratocan promoter exhibited exposure keratitis and premature eye opening from noninfectious eyelid ulceration due to perturbation of eyelid muscle formation and the failure of meibomian gland formation. In addition, in vitro analysis revealed that biglycan binds to TGF-alpha, thus interrupting EGFR signaling pathways essential for mesenchymal cell migration induced by eyelid epithelium. The defects of TGF-alpha signaling by excess biglycan were further augmented by the interruption of the autocrine or paracrine loop of the EGFR signaling pathway of HB-EGF expression elicited by TGF-alpha. These results are consistent with the notion that under physiological conditions, biglycan secreted by mesenchymal cells serves as a regulatory molecule for the formation of a TGF-alpha gradient serving as a morphogen of eyelid morphogenesis. 相似文献
58.
Weiss MD Donnelly WH Rossignol C Varoqui H Erickson JD Anderson KJ 《Journal of molecular histology》2005,36(4):301-309
Summary System A is a highly regulated, Na+-dependent transporter that accepts neutral amino acids containing short, polar side chains. System A plays an important role
during rat development as decreased pup weights are observed in dams infused during gestation with a non-metabolizable System
A substrate. Given the potential importance of SNAT1 during development in the rat brain, we examined whether SNAT1 would
be present at an earlier gestation during organogenesis in multiple organs by immunohistochemistry and immunoblotting. SNAT1
protein was observed in the developing lungs, intestines, kidneys, heart, pancreas, and skeletal muscle of rats at prenatal
days 14, 17, 19, 21, and postnatal day 2 rats. SNAT1 protein expression decreased in the liver and intestine shortly after
birth and as the rat matured. SNAT1 expression was constant throughout development in the lungs and kidney and increased in
the heart from prenatal day 19 to postnatal day 2. Highest levels of expression in older animals were seen in organs undergoing
rapid cell division. 相似文献
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