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GRNInfer specifications
Information
| Unique identifier | OMICS_24034 |
|---|---|
| Name | GRNInfer |
| Alternative names | Gene Regulatory Network Inference, GNR |
| Software type | Application/Script |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Computer skills | Advanced |
| Version | 1.0 |
| Stability | Stable |
| Maintained | Yes |
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Maintainers
- person_outline Luonan Chen
- person_outline Dong Xu
- person_outline Xiang-Sun Zhang
Publication for Gene Regulatory Network Inference
GRNInfer citations
(6)Application of network construction to estimate functional changes to insulin receptor substrates 1 and 2 in Huh7 cells following infection with the hepatitis C virus
[…] The gene networks of the top 50 significantly differentially expressed genes between Huh7 and HCV-Huh7 cells were constructed using GRNInfer (digbio.missouri.edu/grninfer/) and GVedit version 2.38 (portableapps.com/node/38245) tools. GRNInfer () is a linear programming and decomposition algorithm for calculating gene networks from […]
Pathway mapping and development of disease specific biomarkers: protein based network biomarkers
[…] d algorithms ,. Computational programs were developed to integrate selected genes or proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics, such as GRNInfer , MDCinfer , TRNInfer , Samo , MNAligner , PTG , PRNA , NOA , differential dependency network (DDN) , WGCNA , SurvNet or DiME , each of them has its own advantages and strength on basis of s […]
Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy
[…] clopedia of Genes and Genomes (KEGG). Fisher's exact test was used to select each significant pathway, and the significance threshold was defined by the p value . Networks were reconstructed by using GRNInfer , . GRNInfer is a method based on linear programming and a decomposition procedure to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory […]
Role of clinical bioinformatics in the development of network based Biomarkers
[…] ed to integrate selected proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics. Those methodologies include gene regulatory network inference tool (GRNInfer), gene regulatory network reconstruction tool with compound targets (nGNTInfer), inferring transcriptional regulatory networks from high-throughput data (nTRNInfer), inferring protein-protein […]
Inferring gene regulatory networks from asynchronous microarray data with AIRnet
[…] s instead of correlation of absolute values. (1) (2)The Dialogue for Reverse Engineering Assessments and Methods (DREAM) organization creates benchmark data and metrics for evaluating the accuracy of gene regulatory network inference algorithms []. Table shows example data for generating influence vectors. The columns represent different microarray samples for the DREAM knockout experiment. In th […]
Integrative Decomposition Procedure and Kappa Statistics for the Distinguished Single Molecular Network Construction and Analysis
[…] We, respectively, constructed the interaction network of the above 51 genes in healthy tissues and that in tumor using GRNInfer [] and GVedit tools and selected the ATF2-centered downstream subnetworks. With comparison of these ATF2-centered subnetworks, we can get a more clear perception of the notable differences be […]
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