ArticleNucleic acids research2009
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Integrative metabolome and lipidome analyses of plasma in neovascular macular degeneration.Heliyon · 2023Article
- Principles and methods of integrative genomic analyses in cancer.Nature reviews. Cancer · 2014Review
- Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by orthologs of Agamous-like15 and Agamous-like18.Plant physiology · 2014Article
- AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response.BMC systems biology · 2013Article
- Identification of aberrant pathways and network activities from high-throughput data.Briefings in bioinformatics · 2012Review
- Novel approach to meta-analysis of microarray datasets reveals muscle remodeling-related drug targets and biomarkers in Duchenne muscular dystrophy.PLoS computational biology · 2012Article
- Critical assessment of human metabolic pathway databases: a stepping stone for future integration.BMC systems biology · 2011Article
- Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses.BMC plant biology · 2011Article
- Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst.Nature protocols · 2011Article
- SEAS: a system for SEED-based pathway enrichment analysis.PloS one · 2011Article
- Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants.Plant physiology · 2009Article
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3 authors.
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Abstract
The post-genomic era presents us with the challenge of linking the vast amount of raw data obtained with transcriptomic and proteomic techniques to relevant biological pathways. We present an update of PathExpress, a web-based tool to interpret gene-expression data and explore the metabolic network without being restricted to predefined pathways. We define the Enzyme Neighbourhood (EN) as a sub-network of linked enzymes with a limited path length to identify the most relevant sub-networks affected in gene-expression experiments. PathExpress is freely available at: http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/.
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