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排序方式: 共有59条查询结果,搜索用时 15 毫秒
31.
Roel GW Verhaak Frank JT Staal Peter JM Valk Bob Lowenberg Marcel JT Reinders Dick de Ridder 《BMC bioinformatics》2006,7(1):105-15
Background
Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. 相似文献32.
33.
Hinke F van Thuijl Ilari Scheinin Daoud Sie Agusti Alentorn Hendrik F van Essen Martijn Cordes Ruth Fleischeuer Anja M Gijtenbeek Guus Beute Wimar A van den Brink Gerrit A Meijer Miek Havenith Ahmed Idbaih Khê Hoang-Xuan Karima Mokhtari Roel GW Verhaak Paul van der Valk Mark A van de Wiel Jan J Heimans Eleonora Aronica Jaap C Reijneveld Pieter Wesseling Bauke Ylstra 《Genome biology》2014,15(9)
Background
The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behavior and can thereby complement the prognostically favorable 1p/19q co-deletion.Results
Genome-wide, 50 base pair single-end sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analyzed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors.Conclusions
CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0471-6) contains supplementary material, which is available to authorized users. 相似文献34.
The ability of particular cell surface glycoproteins to recycle and become
exposed to individual Golgi enzymes has been demonstrated. This study was
designed to determine whether endocytic trafficking includes significant
reentry into the overall oligosaccharide processing pathway. The Lec1
mutant of Chinese hamster ovary (CHO) cells lack N -
acetylglucosaminyltransferase I (GlcNAc-TI) activity resulting in surface
expression of incompletely processed Man5GlcNAc2 N -linked
oligosaccharides. An oligosaccharide tracer was created by exoglycosylation
of cell surface glycoproteins with purified porcine GlcNAc-TI and
UDP-[3H]GlcNAc. Upon reculturing, all cell surface glycoproteins that
acquired [3H]GlcNAc were acted upon by intracellular mannosidase II, the
next enzyme in the Golgi processing pathway of complex N -linked
oligosaccharides (t1/2= 3-4 h). That all radiolabeled cell surface
glycoproteins were included in this endocytic pathway indicates a common
intracellular compartment into which endocytosed cell surface glycoproteins
return. Significantly, no evidence was found for continued oligosaccharide
processing consistent with transit through the latter cisternae of the
Golgi apparatus. These data indicate that, although recycling plasma
membrane glycoproteins can be reexposed to individual Golgi-derived
enzymes, significant reentry into the overall contiguous processing pathway
is not evident.
相似文献
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The sensitivity of tissue autoradiography can be doubled and the number of false negative cells nearly eliminated by interposing thin tissue sections between two layers of photographic emulsion. A mouse was given 50 μc of tritiated thymidine (SA 2,500 c/M) intraperitoneally and killed 1.5 hr later. A portion of the small bowel was removed, fixed and embedded in methacrylate in the usual way. Sections 2 μ thick were cut and allowed to flatten on water at 40° C. Some sections were used to make conventional single emulsion auto-radiographs and other sections were interposed between two layers of emulsion by first coating slides with NTB 3 emulsion, picking up the sections from a water bath at 18° C, drying, soaking 1 min in benzene, drying, and then dipping again in NTB 3 emulsion. They were exposed at 4° C in a low humidity, 100% CO2 atmosphere for 10 days, developed and covered in the usual way. There was an average of 20.16 ± 1.4 grains per labelled cell in the double emulsion group compared with 10.6 ± 0.9 grains in the single emulsion group. In the double emulsion autoradiographs there were 55.1 ± 1.65 labelled cells per unit area as compared with 39.8 2 2.0 in the single emulsion group. 相似文献
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Comparative docking is based on experimentally determined structures of protein-protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similarity of target monomers to template complexes significantly expands structural coverage of the interactome. Template-based docking by structure alignment can be performed for the entire structures or by aligning targets to the bound interfaces of the experimentally determined complexes. Systematic benchmarking of docking protocols based on full and interface structure alignment showed that both protocols perform similarly, with top 1 docking success rate 26%. However, in terms of the models' quality, the interface-based docking performed marginally better. The interface-based docking is preferable when one would suspect a significant conformational change in the full protein structure upon binding, for example, a rearrangement of the domains in multidomain proteins. Importantly, if the same structure is selected as the top template by both full and interface alignment, the docking success rate increases 2-fold for both top 1 and top 10 predictions. Matching structural annotations of the target and template proteins for template detection, as a computationally less expensive alternative to structural alignment, did not improve the docking performance. Sophisticated remote sequence homology detection added templates to the pool of those identified by structure-based alignment, suggesting that for practical docking, the combination of the structure alignment protocols and the remote sequence homology detection may be useful in order to avoid potential flaws in generation of the structural templates library. 相似文献
40.
The type and the amount of end products resulting from sulfite reduction catalysed by a single partially purified desulfoviridin preparation from Desulfovibrio gigas were shown to depend upon the enzymic assay conditions employed. Both manometric and spectrophotometric assays were used, with reduced methyl viologen serving as the electron donor in each system. Trithionate, thiosulfate, tetrathionate and sulfide were identified as possible end products. In the manometric assays, sulfide production was favoured by high reduced methyl viologen concentrations, low sulfite concentrations and a pH value of 7.0 as opposed to 6.0. In the spectrophotometric assays, results approaching the stoichiometric conversion of sulfite to sulfide were obtained only at high initial reduced methyl viologen concentrations. 相似文献