Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks Export

@article{citeulike:2529270, abstract = {10.1101/gr.226602 We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or more genes in a pathway would be significantly altered in a given experiment by chance alone. This method has been validated on diauxic shift experiments and reproduces well known effects of carbon source on yeast metabolism. The analysis is implemented with , one of the tools of , a new statistical package for the analysis of whole-genome expression data. Results from multiple experiments can be compared, reducing the analysis from the full set of individual genes to a limited number of pathways of interest. The pathways are visualized with , an open-source visualization software package, and the relationship between genes in the pathways can be examined in detail using , the second program of the package. This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned. [Supplementary materials are available at and.]}, address = {Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA.}, author = {Grosu, Paul and Townsend, Jeffrey P. and Hartl, Daniel L. and Cavalieri, Duccio}, citeulike-article-id = {2529270}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.226602}, citeulike-linkout-1 = {http://genome.cshlp.org/content/12/7/1121.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/12/7/1121.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/12097350}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=12097350}, comment = {They have used fold-change values and then run singed fisher exact test on these values to decide which of the 92 metabolic KEGG's pathways are significantly differently expressed in two experiments. }, day = {1}, doi = {10.1101/gr.226602}, issn = {1088-9051}, journal = {Genome Research}, keywords = {kegg, microarray, pathway}, month = {July}, number = {7}, pages = {1121--1126}, posted-at = {2009-07-10 21:00:10}, priority = {0}, title = {Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks}, url = {http://dx.doi.org/10.1101/gr.226602}, volume = {12}, year = {2002} }

TY - JOUR ID - citeulike:2529270 L3 - citeulike-article-id:2529270 N2 - 10.1101/gr.226602 We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or more genes in a pathway would be significantly altered in a given experiment by chance alone. This method has been validated on diauxic shift experiments and reproduces well known effects of carbon source on yeast metabolism. The analysis is implemented with , one of the tools of , a new statistical package for the analysis of whole-genome expression data. Results from multiple experiments can be compared, reducing the analysis from the full set of individual genes to a limited number of pathways of interest. The pathways are visualized with , an open-source visualization software package, and the relationship between genes in the pathways can be examined in detail using , the second program of the package. This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned. [Supplementary materials are available at and.] IS - 7 JF - Genome Research SN - 1088-9051 AD - Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA. EP - 1126 TI - Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks VL - 12 SP - 1121 KW - kegg KW - microarray KW - pathway N1 - They have used fold-change values and then run singed fisher exact test on these values to decide which of the 92 metabolic KEGG's pathways are significantly differently expressed in two experiments. AU - Grosu, Paul AU - Townsend, Jeffrey AU - Hartl, Daniel AU - Cavalieri, Duccio PY - 2002/07/01/ UR - http://dx.doi.org/10.1101/gr.226602 ER -