排序方式: 共有56条查询结果,搜索用时 15 毫秒
31.
GW Patton R Stephens IA Sidorov X Xiao RA Lempicki DS Dimitrov RH Shoemaker G Tudor 《BMC bioinformatics》2006,7(1):81
Background
Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes. 相似文献32.
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33.
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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35.
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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Irma L. Geenen Felix F. Kolk Daniel G. Molin Allard Wagenaar Mathijs G. Compeer Jan H. Tordoir Geert W. Schurink Jo G. De Mey Mark J. Post 《PloS one》2016,11(1)
Background
Autologous arteriovenous (AV) fistulas are the first choice for vascular access but have a high risk of non-maturation due to insufficient vessel adaptation, a process dependent on nitric oxide (NO)-signaling. Chronic kidney disease (CKD) is associated with oxidative stress that can disturb NO-signaling. Here, we evaluated the influence of CKD on AV fistula maturation and NO-signaling.Methods
CKD was established in rats by a 5/6th nephrectomy and after 6 weeks, an AV fistula was created between the carotid artery and jugular vein, which was followed up at 3 weeks with ultrasound and flow assessments. Vessel wall histology was assessed afterwards and vasoreactivity of carotid arteries was studied in a wire myograph. The soluble guanylate cyclase (sGC) activator BAY 60–2770 was administered daily to CKD animals for 3 weeks to enhance fistula maturation.Results
CKD animals showed lower flow rates, smaller fistula diameters and increased oxidative stress levels in the vessel wall. Endothelium-dependent relaxation was comparable but vasorelaxation after sodium nitroprusside was diminished in CKD vessels, indicating NO resistance of the NO-receptor sGC. This was confirmed by stimulation with BAY 60–2770 resulting in increased vasorelaxation in CKD vessels. Oral administration of BAY 60–2770 to CKD animals induced larger fistula diameters, however; flow was not significantly different from vehicle-treated CKD animals.Conclusions
CKD induces oxidative stress resulting in NO resistance that can hamper AV fistula maturation. sGC activators like BAY 60–2770 could offer therapeutic potential to increase AV fistula maturation. 相似文献38.
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
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