GRNInfer protocols

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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 in pipeline

2009
PMCID: 2758837
PMID: 19758441
DOI: 10.1186/1752-0509-3-93

[…] regression; cs: control strength; em: expectation-maximization; elu: elutriation; go: gene ontology; tf: transcription factor; tfa: transcription factor activity; nca: network component analysis; grninfer: gene regulatory network inference; rrna: ribosomal rna; utr: untranslated region; rnp: nucleolar ribonucleoprotein; rbps: rna binding proteins; rpm: random periods model., the authors […]


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GRNInfer in publications

 (10)
PMCID: 4991679
PMID: 27432476
DOI: 10.3892/mmr.2016.5527

[…] algorithm. the top 50 genes, including irs1/2, were used as target genes to determine the gene regulatory networks and next the sub-networks of irs1 and irs2 in hcv-huh7 and huh7 cells using gene regulatory network inference tool, an algorithm based on linear programming and the decomposition process. the irs1/2 sub-networks were divided into upstream/downstream groups […]

PMCID: 4439936
PMID: 26000042
DOI: 10.7150/jca.11404

[…] 48 different pearson mutual-positive-correlation epidermal growth factor receptor (egfr_1)-activatory molecular feedback, up- and down-stream network was constructed from 171 overlapping of 366 grninfer and 223 pearson under egfr_1 cc ≥0.25 in high lung adenocarcinoma compared with low human normal adjacent tissues. our identified egfr_1 inside-out upstream activated molecular network […]

PMCID: 4605476
PMID: 24064399
DOI: 10.3233/ACP-130084

[…] compared with lower human normal adjacent tissues from the corresponding comp-stimulated (≥0.25) or inhibited (pearson cc≤−0.25) overlapping molecules of pearson correlation coefficient (cc) and grninfer, respectively. comp complete different activated and inhibited (all no positive correlation, pearson cc< 0.25) mechanisms networks of higher lung adenocarcinoma and lower human normal […]

PMCID: 3576279
PMID: 23426651
DOI: 10.3892/ol.2013.1122

[…] with high expression (fold change ≥2) were identified and computed., amely-activated upstream regulation molecular networks in non-tumor hepatitis/cirrhotic tissues and hcc were constructed by grninfer () and published studies (–), and illustrated by gvedit tool, respectively., the biological processes of amely-activated upstream regulation networks in non-tumor hepatitis/cirrhotic tissues […]

PMCID: 3444843
PMID: 22997493
DOI: 10.1100/2012/428979

[…] go terms from the same activated pthlh go-molecular network of hcc compared with the corresponding activated go-molecular network of no-tumor hepatitis/cirrhotic tissues, and constructed network by grninfer [] and our articles [–] and illustrated by gvedit tool., biological processes and occurrence numbers of the same activated high expression (fold change ≥2) pthlh feedback-mediated cell […]


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GRNInfer institution(s)
Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan; Academy of Mathematics and Systems Science, CAS, Beijing, China; Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Institute of Systems Biology, Shanghai University, Shanghai, China
GRNInfer funding source(s)
Supported by project Bioinformatics, Bureau of Basic Science, CAS and by a USDA grant CSREES 2004–25,604-14,708.

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