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Molecular expression profiling with respect to KEGG hsa05219 pathway.

ABSTRACT: One of the most promising avenues for interpreting large datasets of molecular expression profiles involves pathway-based analysis. Pathways are collection of genes and proteins that perform a well-defined biological task. These pathways have been established through decades of molecular biology research and are collected in a variety of public pathway repositories (KEGG and Reactome Pathway database). Understanding the complexity of these pathways is critical for understanding normal biological conditions and disease states and also since the number of known pathways within the cells is significantly smaller than the number of genes that is typically profiled, the transformation of data from a gene-centric view to a pathway-centred one represents a dramatic reduction in the number of dimensions. Such reduction allows a biologist to interpret and understand the data in a manner that is not possible when it is viewed as a collection of individual genes.

SUBMITTER: Krishnappa R

PROVIDER: S-EPMC3223945 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Molecular expression profiling with respect to KEGG hsa05219 pathway.

Krishnappa Raghavendra R

Ecancermedicalscience 20110222

One of the most promising avenues for interpreting large datasets of molecular expression profiles involves pathway-based analysis. Pathways are collection of genes and proteins that perform a well-defined biological task. These pathways have been established through decades of molecular biology research and are collected in a variety of public pathway repositories (KEGG and Reactome Pathway database). Understanding the complexity of these pathways is critical for understanding normal biological ...[more]

PMID: 22276047

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Project description:BackgroundThe MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences.ResultsKEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally.ConclusionsKEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.

Dataset Information

Molecular expression profiling with respect to KEGG hsa05219 pathway.

Publications

Molecular expression profiling with respect to KEGG hsa05219 pathway.

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