Literature DB >> 21870222

Bioinformatic approaches to metabolic pathways analysis.

Stuart Maudsley1, Wayne Chadwick, Liyun Wang, Yu Zhou, Bronwen Martin, Sung-Soo Park.   

Abstract

The growth and development in the last decade of accurate and reliable mass data collection techniques has greatly enhanced our comprehension of cell signaling networks and pathways. At the same time however, these technological advances have also increased the difficulty of satisfactorily analyzing and interpreting these ever-expanding datasets. At the present time, multiple diverse scientific communities including molecular biological, genetic, proteomic, bioinformatic, and cell biological, are converging upon a common endpoint, that is, the measurement, interpretation, and potential prediction of signal transduction cascade activity from mass datasets. Our ever increasing appreciation of the complexity of cellular or receptor signaling output and the structural coordination of intracellular signaling cascades has to some extent necessitated the generation of a new branch of informatics that more closely associates functional signaling effects to biological actions and even whole-animal phenotypes. The ability to untangle and hopefully generate theoretical models of signal transduction information flow from transmembrane receptor systems to physiological and pharmacological actions may be one of the greatest advances in cell signaling science. In this overview, we shall attempt to assist the navigation into this new field of cell signaling and highlight several methodologies and technologies to appreciate this exciting new age of signal transduction.

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Year:  2011        PMID: 21870222      PMCID: PMC4698828          DOI: 10.1007/978-1-61779-160-4_5

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  60 in total

1.  Nonparametric methods for identifying differentially expressed genes in microarray data.

Authors:  Olga G Troyanskaya; Mitchell E Garber; Patrick O Brown; David Botstein; Russ B Altman
Journal:  Bioinformatics       Date:  2002-11       Impact factor: 6.937

2.  Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.

Authors:  Ritu Pandey; Raghavendra K Guru; David W Mount
Journal:  Bioinformatics       Date:  2004-05-14       Impact factor: 6.937

3.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

4.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

5.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors:  P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal:  Mol Biol Cell       Date:  1998-12       Impact factor: 4.138

6.  Identification of a gene expression signature associated with recurrent disease in squamous cell carcinoma of the head and neck.

Authors:  Matthew A Ginos; Grier P Page; Bryan S Michalowicz; Ketan J Patel; Sonja E Volker; Stefan E Pambuccian; Frank G Ondrey; George L Adams; Patrick M Gaffney
Journal:  Cancer Res       Date:  2004-01-01       Impact factor: 12.701

7.  Gene expression signatures that predict radiation exposure in mice and humans.

Authors:  Holly K Dressman; Garrett G Muramoto; Nelson J Chao; Sarah Meadows; Dawn Marshall; Geoffrey S Ginsburg; Joseph R Nevins; John P Chute
Journal:  PLoS Med       Date:  2007-04       Impact factor: 11.069

8.  EcoCyc: a comprehensive database resource for Escherichia coli.

Authors:  Ingrid M Keseler; Julio Collado-Vides; Socorro Gama-Castro; John Ingraham; Suzanne Paley; Ian T Paulsen; Martín Peralta-Gil; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

9.  Gonadal transcriptome alterations in response to dietary energy intake: sensing the reproductive environment.

Authors:  Bronwen Martin; Michele Pearson; Randall Brenneman; Erin Golden; William Wood; Vinayakumar Prabhu; Kevin G Becker; Mark P Mattson; Stuart Maudsley
Journal:  PLoS One       Date:  2009-01-07       Impact factor: 3.240

10.  Network-based analysis of affected biological processes in type 2 diabetes models.

Authors:  Manway Liu; Arthur Liberzon; Sek Won Kong; Weil R Lai; Peter J Park; Isaac S Kohane; Simon Kasif
Journal:  PLoS Genet       Date:  2007-06       Impact factor: 5.917

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  17 in total

1.  Mining disease fingerprints from within genetic pathways.

Authors:  Ahmed Ragab Nabhan; Indra Neil Sarkar
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

Review 2.  Translating in vitro ligand bias into in vivo efficacy.

Authors:  Louis M Luttrell; Stuart Maudsley; Diane Gesty-Palmer
Journal:  Cell Signal       Date:  2017-05-07       Impact factor: 4.315

3.  Exploring G protein-coupled receptor signaling networks using SILAC-based phosphoproteomics.

Authors:  Grace R Williams; Jennifer R Bethard; Mary N Berkaw; Alexis K Nagel; Louis M Luttrell; Lauren E Ball
Journal:  Methods       Date:  2015-07-06       Impact factor: 3.608

4.  Informatic deconvolution of biased GPCR signaling mechanisms from in vivo pharmacological experimentation.

Authors:  Stuart Maudsley; Bronwen Martin; Jonathan Janssens; Harmonie Etienne; Areta Jushaj; Jaana van Gastel; Ann Willemsen; Hongyu Chen; Diane Gesty-Palmer; Louis M Luttrell
Journal:  Methods       Date:  2015-05-16       Impact factor: 3.608

Review 5.  Trespassing cancer cells: 'fingerprinting' invasive protrusions reveals metastatic culprits.

Authors:  Richard L Klemke
Journal:  Curr Opin Cell Biol       Date:  2012-09-11       Impact factor: 8.382

6.  Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC).

Authors:  Sung-Soo Park; Wells W Wu; Yu Zhou; Rong-Fong Shen; Bronwen Martin; Stuart Maudsley
Journal:  J Proteomics       Date:  2012-05-07       Impact factor: 4.044

7.  GIT2 acts as a potential keystone protein in functional hypothalamic networks associated with age-related phenotypic changes in rats.

Authors:  Wayne Chadwick; Bronwen Martin; Megan C Chapter; Sung-Soo Park; Liyun Wang; Caitlin M Daimon; Randall Brenneman; Stuart Maudsley
Journal:  PLoS One       Date:  2012-05-14       Impact factor: 3.240

8.  Short Report: Using Targeted Urine Metabolomics to Distinguish Between Manganese Exposed and Unexposed Workers in a Small Occupational Cohort.

Authors:  Kayla A Carter; Christopher D Simpson; Daniel Raftery; Marissa G Baker
Journal:  Front Public Health       Date:  2021-05-20

9.  Textrous!: extracting semantic textual meaning from gene sets.

Authors:  Hongyu Chen; Bronwen Martin; Caitlin M Daimon; Sana Siddiqui; Louis M Luttrell; Stuart Maudsley
Journal:  PLoS One       Date:  2013-04-30       Impact factor: 3.240

10.  VennPlex--a novel Venn diagram program for comparing and visualizing datasets with differentially regulated datapoints.

Authors:  Huan Cai; Hongyu Chen; Tie Yi; Caitlin M Daimon; John P Boyle; Chris Peers; Stuart Maudsley; Bronwen Martin
Journal:  PLoS One       Date:  2013-01-07       Impact factor: 3.240

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