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Systems analysis of small signaling modules relevant to eight human diseases.

ABSTRACT: Using eight newly generated models relevant to addiction, Alzheimer's disease, cancer, diabetes, HIV, heart disease, malaria, and tuberculosis, we show that systems analysis of small (4-25 species), bounded protein signaling modules rapidly generates new quantitative knowledge from published experimental research. For example, our models show that tumor sclerosis complex (TSC) inhibitors may be more effective than the rapamycin (mTOR) inhibitors currently used to treat cancer, that HIV infection could be more effectively blocked by increasing production of the human innate immune response protein APOBEC3G, rather than targeting HIV's viral infectivity factor (Vif), and how peroxisome proliferator-activated receptor alpha (PPAR?) agonists used to treat dyslipidemia would most effectively stimulate PPAR? signaling if drug design were to increase agonist nucleoplasmic concentration, as opposed to increasing agonist binding affinity for PPAR?. Comparative analysis of system-level properties for all eight modules showed that a significantly higher proportion of concentration parameters fall in the top 15th percentile sensitivity ranking than binding affinity parameters. In infectious disease modules, host networks were significantly more sensitive to virulence factor concentration parameters compared to all other concentration parameters. This work supports the future use of this approach for informing the next generation of experimental roadmaps for known diseases.

SUBMITTER: Benedict KF

PROVIDER: S-EPMC3033523 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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Systems analysis of small signaling modules relevant to eight human diseases.

Benedict Kelly F KF Mac Gabhann Feilim F Amanfu Robert K RK Chavali Arvind K AK Gianchandani Erwin P EP Glaw Lydia S LS Oberhardt Matthew A MA Thorne Bryan C BC Yang Jason H JH Papin Jason A JA Peirce Shayn M SM Saucerman Jeffrey J JJ Skalak Thomas C TC

Annals of biomedical engineering 20101204 2

Using eight newly generated models relevant to addiction, Alzheimer's disease, cancer, diabetes, HIV, heart disease, malaria, and tuberculosis, we show that systems analysis of small (4-25 species), bounded protein signaling modules rapidly generates new quantitative knowledge from published experimental research. For example, our models show that tumor sclerosis complex (TSC) inhibitors may be more effective than the rapamycin (mTOR) inhibitors currently used to treat cancer, that HIV infection ...[more]

PMID: 21132372

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Project description:BackgroundScientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.Principal findingsWe developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.ConclusionsFor the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.AvailabilityThe gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download.

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Systems analysis of small signaling modules relevant to eight human diseases.

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Systems analysis of small signaling modules relevant to eight human diseases.

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