NDLI: Using pathway modules as targets for assay development in xenobiotic screening

Please wait, while we are loading the content...

Hydrophilic interaction and reversed-phase ultraperformance liquid chromatography TOF-MS for serum metabonomic analysis of myocardial infarction in rats and its applications

Specific in situ discrimination of amyloid fibrils versusα-helical fibres by the fluorophore NIAD-4

Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli

Molecular, kinetic and thermodynamic characterization of Mycobacterium tuberculosis orotate phosphoribosyltransferase

More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis

¹H NMR-based metabonomics study on serum of renal interstitial fibrosis rats induced by unilateral ureteral obstruction

Effects of intermittent media replacement on the gene expression of differentiating neural progenitor cells

A synthetic heparan sulfate oligosaccharide library reveals the novel enzymatic action of d-glucosaminyl 3-O-sulfotransferase-3a

Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon-beta in high cell density fed batch cultures using time course transcriptomic data

iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites

Analysis of the Fragile X mental retardation protein isoforms 1, 2 and 3 interactions with the G-quadruplex forming semaphorin 3F mRNA

Pro-oxidant and antioxidant effects of N-acetylcysteine regulate doxorubicin-induced NF-kappa B activity in leukemic cells

The reconstruction and analysis of tissue specific human metabolic networks

Back cover

Molecular BioSystems Vol -7

Molecular BioSystems Vol -6

Molecular BioSystems Vol -5

Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

Molecular BioSystems Vol -2

Using pathway modules as targets for assay development in xenobiotic screening

Content Provider	Royal Society of Chemistry (RSC)
Author	Elloumi, Fathi Shah, Imran Knudsen, Thomas B. Judson, Richard S. Mortensen, Holly M.
Copyright Year	2012
Abstract	Toxicology and pharmaceutical research is increasingly making use of high throughout-screening (HTS) methods to assess the effects of chemicals on molecular pathways, cells and tissues. Whole-genome microarray analysis provides broad information on the response of biological systems to chemical exposure, but is not practical to use when thousands of chemicals need to be evaluated at multiple doses and time points, as well as across different tissues, species and life-stages. A useful alternative approach is to identify a focused set of genes that can give a coarse picture of systems-level responses and that can be scaled to the evaluation of thousands of chemicals and diverse biological contexts. We demonstrate a computational approach to select in vitro expression assay targets that are informative and broadly distributed in biological pathway space, using the concept of pathway modularity. Canonical pathways are decomposed into subnetworks (modules) of functionally-related genes based on rules such as co-regulated expression, protein-protein interactions, and coordinated physiological activity. Pathway modules are constructed using these rules but are then restricted by the bounds of canonical pathways. We demonstrate this approach using a subset of genes associated with tumor development and cancer progression. Target genes were identified for assay development, and then validated by using independent, published microarray data. The result is a targeted set of genes that are sensitive predictors of whether a chemical will perturb each pathway module. These selected genes could then form the basis for a battery to test for pathway-chemical interactions under many biological contexts using throughput expression-based assays.
Starting Page	531
Ending Page	542
Page Count	12
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	8
Issue Number	2
Journal	Molecular BioSystems
DOI	10.1039/c1mb05303e
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Microarray Biological pathway Cancer
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Screening of the prognostic targets for breast cancer based co-expression modules analysis.

Integrating Multiple Microarray Data for Cancer Pathway Analysis Using Bootstrapping K-S Test

Cell-Based Assays for High-Throughput Screening

Integrating Multiple Microarray Data for Cancer Pathway Analysis Using Bootstrapping K-S Test

Cyclin-Dependent Kinases as Drug Targets for Cell Growth and Proliferation Disorders. A Role for Systems Biology Approach in Drug Development. Part I—Cyclin-Dependent Kinases as Drug Targets in Cancer

Screening and functional pathway analysis of genes associated with pediatric allergic asthma using a DNA microarray

A novel paradigm for potential drug-targets discovery: quantifying relationships of enzymes and cascade interactions of neighboring biological processes to identify drug-targets

Comprehensive analysis of the long noncoding RNA HOXA11-AS gene interaction regulatory network in NSCLC cells

Quantitative Pathway Modeling and Analysis in Cancer

Using pathway modules as targets for assay development in xenobiotic screening

Similar Documents

Screening of the prognostic targets for breast cancer based co-expression modules analysis.

Integrating Multiple Microarray Data for Cancer Pathway Analysis Using Bootstrapping K-S Test

Cell-Based Assays for High-Throughput Screening

Integrating Multiple Microarray Data for Cancer Pathway Analysis Using Bootstrapping K-S Test

Cyclin-Dependent Kinases as Drug Targets for Cell Growth and Proliferation Disorders. A Role for Systems Biology Approach in Drug Development. Part I—Cyclin-Dependent Kinases as Drug Targets in Cancer

Screening and functional pathway analysis of genes associated with pediatric allergic asthma using a DNA microarray

A novel paradigm for potential drug-targets discovery: quantifying relationships of enzymes and cascade interactions of neighboring biological processes to identify drug-targets

Comprehensive analysis of the long noncoding RNA HOXA11-AS gene interaction regulatory network in NSCLC cells

Quantitative Pathway Modeling and Analysis in Cancer

Using pathway modules as targets for assay development in xenobiotic screening