PFSNet protocols

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PFSNet specifications

Information


Unique identifier OMICS_19444
Name PFSNet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

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This tool is not available anymore.

Publication for PFSNet

PFSNet in pipeline

2016
PMCID: 4838159
PMID: 27035224
DOI: 10.3892/mmr.2016.5007

[…] (,) using the limma package (version 3.22.1; fred hutchinson cancer research center). degs were identified with the cutoff value of fdr<0.05 and |log (fold change)|>1 (,)., paired fuzzy snet (pfsnet) () is a powerful method to identify smaller parts of pathways termed subnetworks. comparison with previously published methods shows that significant subnetworks (and the genes therein) […]

PFSNet in publications

 (3)
PMCID: 5656635
PMID: 29070875
DOI: 10.1038/s41598-017-13174-w

[…] astrogliosis was induced with il1β. within 24 hours of il1β induction, astrocytes acquired reactive characteristics. transcriptome analysis of over 40000 transcripts of genes and analysis with pfsnet subnetwork revealed upregulation of chemokines and axonal permissive factors including fgf2, bdnf, and ngf. in addition, most genes regulating axonal inhibitory molecules, including robo1 […]

PMCID: 4838159
PMID: 27035224
DOI: 10.3892/mmr.2016.5007

[…] included 36 pc tissue samples and 16 normal samples. limma package in r language was used to screen differentially expressed genes (degs), which were grouped as up- and downregulated genes. then, pfsnet was applied to perform subnetwork analysis for all the degs. moreover, gene ontology (go) and reactome pathway enrichment analysis of up- and downregulated genes was performed, followed […]

PMCID: 4678536
PMID: 26666224
DOI: 10.1186/s13062-015-0098-x

[…] shifts are more unstable, and less reliable. their rank shifts are likely more due to chance than to phenotype-specific changes. in earlier work on genomics, we’ve also shown that in methods e.g. pfsnet and fsnet, using the top 20 % with complexes/subnets is an optimal alpha cutoff., the fdr adjusted analyses reflect stability of analysis against low to high fdr levels given the same qpsp […]

PFSNet institution(s)
School of Computing, National University of Singapore, Singapore
PFSNet funding source(s)
Supported by National University of Singapore; and Singapore Ministry of Education (tier-2 grant MOE2012-T2-1-061).

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