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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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PAG ID standard naming convention and three types of PAGs
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btv265-F1: PAG ID standard naming convention and three types of PAGs

Mentions: We follow the PAG ID standard naming convention as shown in Figure 1. Every PAG begins with a three-letter-code followed by six digits. The first letter position is used to signify the PAG data type category. The second letter position is used to signify the PAG derivation category. The third letter position is used to signify PAG relationship details. The human-readable naming convention may make it easy for end users to understand how the PAGs are constructed.Fig. 1.


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)

PAG ID standard naming convention and three types of PAGs
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

btv265-F1: PAG ID standard naming convention and three types of PAGs
Mentions: We follow the PAG ID standard naming convention as shown in Figure 1. Every PAG begins with a three-letter-code followed by six digits. The first letter position is used to signify the PAG data type category. The second letter position is used to signify the PAG derivation category. The third letter position is used to signify PAG relationship details. The human-readable naming convention may make it easy for end users to understand how the PAGs are constructed.Fig. 1.

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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Related in: MedlinePlus