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PAGER: constructing PAGs and new PAG-PAG relationships for network biology.

Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY - Bioinformatics (2015)

Bottom Line: To help users assess each PAG's biological relevance, we developed a cohesion measure called Cohesion Coefficient (CoCo), which is capable of disambiguating between biologically significant PAGs and random PAGs with an area-under-curve performance of 0.98.PAGER database was set up to help users to search and retrieve PAGs from its online web interface.PAGER enable advanced users to build PAG-PAG regulatory networks that provide complementary biological insights not found in gene set analysis or individual gene network analysis.

View Article: PubMed Central - PubMed

Affiliation: Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China.

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Example of calculation of each Cohesion measure
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btv265-F2: Example of calculation of each Cohesion measure

Mentions: To evaluate the biological relevance of PAGs, we developed three PAG cohesion measures, i.e. Cohesion by Interaction enrichment (CoI), Cohesion by Triangle enrichment (CoT) and CoCo. Conventional tests such as chi-square, hypergeometric test or Fisher’s exact test have all been used to assess gene-set enrichment results. However, none of these statistical tests may generate true statistical P-values in practice (Huang da et al., 2009). Therefore, for simplicity of calculation, we calculate all three cohesion measures based on signed probability mass function of hypergeometric distribution. Mathematical notations are defined as the following: Π is the set of genes in the reference PPI database; i and j are PAG indexes; Ii or Ij is the set of PPIs in PAGi and PAGj, respectively; IΠ is the set of all PPIs in the referenced database; Ti or Tj is the set of PPI triangles in PAGi and PAGj, respectively given IΠ; TΠ is the set of all PPI triangles in Π. For an overview of how each cohesion measure is calculated, refer to the illustrated example shown in Figure 2.Fig. 2.


PAGER: constructing PAGs and new PAG-PAG relationships for network biology.

Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY - Bioinformatics (2015)

Example of calculation of each Cohesion measure
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4553834&req=5

btv265-F2: Example of calculation of each Cohesion measure
Mentions: To evaluate the biological relevance of PAGs, we developed three PAG cohesion measures, i.e. Cohesion by Interaction enrichment (CoI), Cohesion by Triangle enrichment (CoT) and CoCo. Conventional tests such as chi-square, hypergeometric test or Fisher’s exact test have all been used to assess gene-set enrichment results. However, none of these statistical tests may generate true statistical P-values in practice (Huang da et al., 2009). Therefore, for simplicity of calculation, we calculate all three cohesion measures based on signed probability mass function of hypergeometric distribution. Mathematical notations are defined as the following: Π is the set of genes in the reference PPI database; i and j are PAG indexes; Ii or Ij is the set of PPIs in PAGi and PAGj, respectively; IΠ is the set of all PPIs in the referenced database; Ti or Tj is the set of PPI triangles in PAGi and PAGj, respectively given IΠ; TΠ is the set of all PPI triangles in Π. For an overview of how each cohesion measure is calculated, refer to the illustrated example shown in Figure 2.Fig. 2.

Bottom Line: To help users assess each PAG's biological relevance, we developed a cohesion measure called Cohesion Coefficient (CoCo), which is capable of disambiguating between biologically significant PAGs and random PAGs with an area-under-curve performance of 0.98.PAGER database was set up to help users to search and retrieve PAGs from its online web interface.PAGER enable advanced users to build PAG-PAG regulatory networks that provide complementary biological insights not found in gene set analysis or individual gene network analysis.

View Article: PubMed Central - PubMed

Affiliation: Indiana University School of Informatics and Computing, Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, Purdue University Center for Cancer Research, West Lafayette, IN 47906 and Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China.

Show MeSH
Related in: MedlinePlus