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Protocols

PANDA specifications

Information


Unique identifier OMICS_08165
Name PANDA
Alternative name Passing Attributes between Networks for Data Assimilation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A motif prior, a set of known protein-protein interactions, and expression data.
Operating system Unix/Linux
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Guo-Cheng Yuan

Publications for Passing Attributes between Networks for Data Assimilation

PANDA citations

 (11)
library_books

Detecting phenotype driven transitions in regulatory network structure

2018
NPJ Syst Biol Appl
PMCID: 5908977
PMID: 29707235
DOI: 10.1038/s41540-018-0052-5

[…] k. For the noiseless version of this simulation, we inferred a regulatory network by integrating known human TF-binding sites with gene expression data in normal human fibroblasts using the algorithm PANDA (see Materials and Methods for further details). After thresholding the edge weights and applying CONDOR, a method for community detection in bipartite networks, we found that the baseline netwo […]

library_books

Regulatory network changes between cell lines and their tissues of origin

2017
BMC Genomics
PMCID: 5596945
PMID: 28899340
DOI: 10.1186/s12864-017-4111-x

[…] We reconstructed gene regulatory networks using PANDA, a message-passing model that integrates multiple types of genomic data and infers the network of interactions between TFs and their target genes []. PANDA starts with a prior regulatory network […]

library_books

An imprinted non coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

2017
PMCID: 5433149
PMID: 28506242
DOI: 10.1186/s13045-017-0465-4

[…] We used a method called PUMA (PANDA using MicroRNA Associations, Kuijjer et al., in preparation). This is a network reconstruction algorithm that models gene regulation by miRNAs and transcription factors and is an extension of ou […]

call_split

Estimating gene regulatory networks with pandaR

2017
Bioinformatics
PMCID: 5870629
PMID: 28334344
DOI: 10.1093/bioinformatics/btx139
call_split See protocol

[…] PANDA’s regulatory network model is fundamentally a bipartite graph in which TFs are connected to target genes. In PANDA’s message passing model, the edge weights are calculated based on the evidence […]

library_books

Gene regulatory pattern analysis reveals essential role of core transcriptional factors’ activation in triple negative breast cancer

2017
Oncotarget
PMCID: 5400636
PMID: 28423538
DOI: 10.18632/oncotarget.15749

[…] latory networks, integrative analyses show promising perspective in comprehending of pathophysiologic mechanisms and developing novel and precise therapies [, ]. Among the multiple integration tools, Passing Attributes between Networks for Data Assimilation (PANDA) has better performance and higher accuracy [–]. PANDA predicts TF-gene regulatory relationships by integrating information from protei […]

library_books

Therapeutic potential of targeting microRNA‐10b in established intracranial glioblastoma: first steps toward the clinic

2016
PMCID: 4772951
PMID: 26881967
DOI: 10.15252/emmm.201505495

[…] ed posttranscriptional repression (Lee et al, ; Grey et al, ; Moretti et al, ; Zhou & Rigoutsos, ), direct target up‐regulation through 5′UTR interaction has been reported (Tsai et al, ; Liu et al, ; Panda et al, ). Along with translational, a transcriptional regulation by miRNA through 5′UTR has been also observed (Liu et al, ). Of note, miR‐10a, the close homolog of miR‐10b distinct only in a si […]

Citations

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PANDA institution(s)
Dana-Farber Cancer Institute, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA; Brigham and Women’s Hospital, Boston, MA, USA; Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
PANDA funding source(s)
Supported by R01 HL089438, R01 HL111759 and P01 HL105339.

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