40 research outputs found
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
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YuZhenBiochemistryBiophysicsCombinedTreatmentRapamycin.pdf
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: transcriptome, rapamycin, metabolome, dietary restrictio
Recommended from our members
YuZhenBiochemistryBiophysicsCombinedTreatmentRapamycin_SupportingInformation.zip
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: transcriptome, dietary restriction, rapamycin, metabolom