Limits...
Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.

Li C, Han J, Yao Q, Zou C, Xu Y, Zhang C, Shang D, Zhou L, Zou C, Sun Z, Li J, Zhang Y, Yang H, Gao X, Li X - Nucleic Acids Res. (2013)

Bottom Line: Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases.This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway.Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.

ABSTRACT
Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.

Show MeSH

Related in: MedlinePlus

Schematic overview of Subpathway-GM.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3643575&req=5

gkt161-F1: Schematic overview of Subpathway-GM.

Mentions: Subpathway-GM has been implemented as a freely available web-based and R-based tool (http://bioinfo.hrbmu.edu.cn/SubpathwayGM). Figure 1 depicts the schematic overview of Subpathway-GM. The step-by-step method is provided in Supplementary Text. The users inputs interesting the genes and metabolites of interest, and metabolic subpathways can then be identified mainly through: (i) mapping genes and metabolites of interest to graphs of pathways after graph-based reconstruction of metabolic pathways; (ii) locating subpathways within pathways according to signature nodes; (iii) evaluating the statistical significance of subpathways. The method is described in more detail later in the text.Figure 1.


Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.

Li C, Han J, Yao Q, Zou C, Xu Y, Zhang C, Shang D, Zhou L, Zou C, Sun Z, Li J, Zhang Y, Yang H, Gao X, Li X - Nucleic Acids Res. (2013)

Schematic overview of Subpathway-GM.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643575&req=5

gkt161-F1: Schematic overview of Subpathway-GM.
Mentions: Subpathway-GM has been implemented as a freely available web-based and R-based tool (http://bioinfo.hrbmu.edu.cn/SubpathwayGM). Figure 1 depicts the schematic overview of Subpathway-GM. The step-by-step method is provided in Supplementary Text. The users inputs interesting the genes and metabolites of interest, and metabolic subpathways can then be identified mainly through: (i) mapping genes and metabolites of interest to graphs of pathways after graph-based reconstruction of metabolic pathways; (ii) locating subpathways within pathways according to signature nodes; (iii) evaluating the statistical significance of subpathways. The method is described in more detail later in the text.Figure 1.

Bottom Line: Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases.This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway.Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.

ABSTRACT
Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.

Show MeSH
Related in: MedlinePlus