69 research outputs found
CMS: A web-based system for visualization and analysis of genome-wide methylation data of human cancers
DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters.Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework.CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible at: http://cbbiweb.uthscsa.edu/KMethylomes/
SIDEKICK: Genomic data driven analysis and decision-making framework
<p>Abstract</p> <p>Background</p> <p>Scientists striving to unlock mysteries within complex biological systems face myriad barriers in effectively integrating available information to enhance their understanding. While experimental techniques and available data sources are rapidly evolving, useful information is dispersed across a variety of sources, and sources of the same information often do not use the same format or nomenclature. To harness these expanding resources, scientists need tools that bridge nomenclature differences and allow them to integrate, organize, and evaluate the quality of information without extensive computation.</p> <p>Results</p> <p>Sidekick, a genomic data driven analysis and decision making framework, is a web-based tool that provides a user-friendly intuitive solution to the problem of information inaccessibility. Sidekick enables scientists without training in computation and data management to pursue answers to research questions like "What are the mechanisms for disease X" or "Does the set of genes associated with disease X also influence other diseases." Sidekick enables the process of combining heterogeneous data, finding and maintaining the most up-to-date data, evaluating data sources, quantifying confidence in results based on evidence, and managing the multi-step research tasks needed to answer these questions. We demonstrate Sidekick's effectiveness by showing how to accomplish a complex published analysis in a fraction of the original time with no computational effort using Sidekick.</p> <p>Conclusions</p> <p>Sidekick is an easy-to-use web-based tool that organizes and facilitates complex genomic research, allowing scientists to explore genomic relationships and formulate hypotheses without computational effort. Possible analysis steps include gene list discovery, gene-pair list discovery, various enrichments for both types of lists, and convenient list manipulation. Further, Sidekick's ability to characterize pairs of genes offers new ways to approach genomic analysis that traditional single gene lists do not, particularly in areas such as interaction discovery.</p
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Combined treatment of rapamycin and dietary restriction has a larger effect on the transcriptome and metabolome of liver
Rapamycin (Rapa) and dietary restriction (DR) have consistently
been shown to increase lifespan. To investigate whether Rapa
and DR affect similar pathways in mice, we compared the effects
of feeding mice ad libitum (AL), Rapa, DR, or a combination of
Rapa and DR (Rapa + DR) on the transcriptome and metabolome
of the liver. The principal component analysis shows that Rapa
and DR are distinct groups. Over 2500 genes are significantly
changed with either Rapa or DR when compared with mice fed
AL; more than 80% are unique to DR or Rapa. A similar
observation was made when genes were grouped into pathways;
two-thirds of the pathways were uniquely changed by DR or
Rapa. The metabolome shows an even greater difference
between Rapa and DR; no metabolites in Rapa-treated mice were
changed significantly from AL mice, whereas 173 metabolites
were changed in the DR mice. Interestingly, the number of genes
significantly changed by Rapa + DR when compared with AL is
twice as large as the number of genes significantly altered by
either DR or Rapa alone. In summary, the global effects of DR or
Rapa on the liver are quite different and a combination of Rapa
and DR results in alterations in a large number of genes and
metabolites that are not significantly changed by either manipulation
alone, suggesting that a combination of DR and Rapa
would be more effective in extending longevity than either
treatment alone.Keywords: metabolome, rapamycin, transcriptome, dietary restrictio
Charge confinement effect in cuprate superconductors: an explanation for the normal-state resistivity and pseudogap
The fact that the stripe phase and pseudogap in the cuprate superconductors
occur in the same doping regime is emphasized. A model based on charge
confinement in self-organized nanometer-scale stripe fragments is proposed
to understand various generic features of the normal-state energy gap
including the magnitude of the gap, its anti-correlation with the
superconducting gap, and the d-wave symmetry in its K-dependence.
This model also provides a basis for understanding other anomalous normal-state
properties such as the linear temperature dependence of electrical resistivity
Profitability of Wood Production of Generating Bioenergy
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Verfahren zur Herstellung von enantimerenangereicherten Aminen
Doderer K, Wienand W, Gröger H, Rollmann C. Verfahren zur Herstellung von enantimerenangereicherten Aminen. 2009
High temperature superconducting Josephson junctions in a stacked bicrystal geometry
Bicrystal grain boundary Josephson junctions were fabricated in a stack of two layers of YBa2Cu3Oχ separated by epitaxial SrTiO3. Weak link behavior was observed in the bridges formed in both layers that had similar shunted-junction characteristics but significantly different critical currents. Characteristic voltages up to 1.9 mV were measured at 4.5 K. The resonant structure was seen in the current–voltage characteristics of the upper-layer junctions, and interactions between junctions in the two layers were evident
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