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GeneNet specifications

Information


Unique identifier OMICS_02696
Name GeneNet
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GeneNet

library_books

GeneNet in 2005

2005 Nucleic Acids Res
PMCID: 540031
PMID: 15608230
DOI: 10.1093/nar/gki077

GeneNet citations

 (24)
library_books

Downregulation of 15‐hydroxyprostaglandin dehydrogenase by interleukin‐1β from activated macrophages leads to poor prognosis in pancreatic cancer

2018
Cancer Sci
PMCID: 5797824
PMID: 29224225
DOI: 10.1111/cas.13467

[…] RT‐PCR was carried out using the TaqMan probe method. All primers and probe sets were designed by the Universal Probe Library Assay Design Center (Basel, Switzerland). All primers were synthesized by Genenet, and all probes were purchased from Roche Diagnostics (Basel, Switzerland).The quantitative RT‐PCR assay was carried out in the presence of 1 × LightCycler 480 Probes Master (Roche Diagnostics […]

library_books

ALK is a critical regulator of the MYC signaling axis in ALK positive lung cancer

2018
Oncotarget
PMCID: 5823650
PMID: 29507657
DOI: 10.18632/oncotarget.24260

[…] ntivirus production was performed by transfecting viral packaging vectors pCMV-VSV-G and pΔ8.9 into 293T cells using TransIT-293 reagent (Mirus) as previously described []. For the genome-wide screen GeneNet Lentiviral Human 50K library was used (pS1H1-H1 Puro; Systems Biosciences). shRNA vectors used for validation were sourced from TRC (pLKO.1). […]

call_split

Unraveling the human salivary microbiome diversity in Indian populations

2017
PLoS One
PMCID: 5590957
PMID: 28886168
DOI: 10.1371/journal.pone.0184515
call_split See protocol

[…] uently used in GUniFrac []. Calculation of alpha and beta diversity indices and rarefaction analyses were carried out by the ‘vegan’ package while partial correlation analyses was carried out by the ‘GeneNet’ package, both implemented in R [,]. To calculate the diversity indices for each sampling location, 10000 reads from 10 random samples from each population were utilized. For calculating indic […]

library_books

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co expression network and genome analyses

2017
BMC Genomics
PMCID: 5389088
PMID: 28403814
DOI: 10.1186/s12864-017-3678-6

[…] ach Pgt isolate’s dataset using the host and pathogen genes that showed differential expression either between Pgt isolate treatments or across time points over the course of infection. The R package geneNet was used to account for the non-scale free nature of the time-course data []. Partial correlations (edges) between the genes (nodes) identified by the algorithm implemented in geneNet were fil […]

library_books

High Content Genome Wide RNAi Screen Reveals CCR3 as a Key Mediator of Neuronal Cell Death

2016
eNeuro
PMCID: 5075945
PMID: 27822494
DOI: 10.1523/ENEURO.0185-16.2016

[…] ADP-ribose) polymerase, resulting in a more necrotic-like rather than apoptotic cell death which has been designated parthanatos. (; ).In this study, we performed a genome-wide screen using the mouse GeneNet Mouse 40K FIV lentiviral small, interfering RNA (siRNA) library. We identified 80 key mediators for DNA damage-induced neural cell death. Among these 80 genes, 66 have not been previously been […]

call_split

The Potential of the MAGIC TOM Parental Accessions to Explore the Genetic Variability in Tomato Acclimation to Repeated Cycles of Water Deficit and Recovery

2016
Front Plant Sci
PMCID: 4700940
PMID: 26779213
DOI: 10.3389/fpls.2015.01172
call_split See protocol

[…] fruit data, based on the residues of the linear regressions (elimination of the genotype effect) and performed independently for the control and for the WD treatments (P threshold < 0.001; GGMselect, GeneNet, and igraph packages; ; , and , respectively). Finally, clustering analysis was performed on leaf and fruit data (FactoMineR package; ). […]

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GeneNet institution(s)
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

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