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primary topic: Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses

Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses
type: Article
abstract: Background: Scientists in pharmaceutical as well as academic research work together to solve the challenging puzzle from the basic causes of disease at the level of genes, proteins and cells up to a marketed new drug. Analyses of mode of action (MoA) of new chemical entities (NCEs) are a very important step in the development of new drugs. One distinguishes between effects induced by modulating the compounds’ actual target protein (on-target effects) and effects induced by additional, possibly unknown targets (off-target effects). Quite often knowledge about either of these effects is limited. Since MoA is mainly triggered by the interplay of proteins or signaling cascades, investigating the change and subsequent influence of the changed molecules in a protein interaction (PI) network is a promising initial step to further analyses. As more and more data from diverse sources becomes available, the integration of this knowledge is important for generating a deeper insight into biology. In addition, expression experiments based on disease tissue and/or compound treatment are frequently conducted to get insight into transcriptional changes that could explain compounds’ MoA. Status quo: MoA could be analyzed by investigating those parts of a PI network that show changes based on compound treatment. Mathematical or graph theoretical in silico methods to identify interesting parts of a network based on different criteria are widely used. Criteria range from detection of highly connected subgraphs to subgraphs maximizing weights assigned to parts of the network under investigation. These methods can be transferred to biology and can be used to, e. g. identify condition responsive subnetworks on various types of molecular networks. Present questions addressed mainly focus on the detection of subnetworks enriched in information from functional genomics, e.g. differentially expressed genes. They neglect the existence of distance regulatory functions on the post-transcriptiona…
date: 2012
status: published
author list: authors
type: EPrint
type: DoctoralThesisEPrint
is part of: repository
has document: Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (PDF)
has document: Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
subject: 004 Informatik

Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (PDF)
type: Document
has file: schmid.pdf
has part: schmid.pdf

Ramona Schmid
type: Person
given name: Ramona
family name: Schmid

Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
type: Document
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Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
type: Document
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Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
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Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
type: Document
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Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (Other)
type: Document
is version of: Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses (PDF)
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https://archiv.ub.uni-heidelberg.de/volltextserver/13830/
title: HTML Summary of #13830 Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses
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primary topic: Analyzing Compounds’ Mode of Action - A Use Case for New Approaches Utilizing Protein Interaction Networks and Prior Knowledge to Complement State-of-the-Art Gene Expression Analyses

004 Informatik
type: Concept
preferred label: 004 Data processing Computer science @en