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Data released on November 03, 2017

Supporting data for "ProphTools: General Prioritization Tools for Heterogeneous Biological Networks"

Navarro, C; Martínez, V; Blanco, A; Cano, C (2017): Supporting data for "ProphTools: General Prioritization Tools for Heterogeneous Biological Networks" GigaScience Database. http://dx.doi.org/10.5524/100369 RIS BibTeX Text

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest, or they lack flexibility to analyse user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk With Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform Cross-Validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long non-coding RNAs (lncRNAs) to disease prioritization.

Contact Submitter

Related manuscripts:

doi: 10.1093/gigascience/gix107

Additional information:

http://genome.ugr.es:9000/prophnet

https://github.com/cnluzon/prophtools

https://hub.docker.com/r/cnluzon/prophtools/

Keywords:

network analysis prioritization heterogeneous networks long non-coding rnas 

Software, Network-Analysis

http://gigadb.org/images/data/cropped/100369.jpg

Funding:

  • Funding body - Consejería de Economía Innovación Ciencia y Empleo Junta de Andalucía
  • Award ID - PI-0710-2013
  • Awardee - AB Morón
  • Funding body - European Commission
  • Comment - European Regional Development Fund
  • Awardee - AB Morón
  • Funding body - Dirección General de Investigación Científica y Técnica
  • Award ID - TIN2013-41990-R
  • Awardee - AB Morón
  • Funding body - Ministerio de Educación Cultura y Deporte
  • Award ID - FPU12_01875
  • Awardee - CN Luzón

Files: (FTP site) Table Settings

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File NameSample IDFile TypeFile FormatSizeRelease Date 
otherarchive26.67 MB2017-10-12
otherarchive2.86 GB2017-10-12
GitHub archivearchive418 KB2017-10-12
otherarchive2.86 GB2017-10-12
ReadmeTEXT2.62 KB2017-10-12
Tabular DataUNKNOWN38.77 KB2017-10-12
Tabular DataUNKNOWN16.15 KB2017-10-12
Displaying 1-7 of 7 File(s).

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