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GeneAnalytics specifications

Information


Unique identifier OMICS_14215
Name GeneAnalytics
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data The input species, a gene set that contains 300 or fewer genes
Output data Analysed genes, tissues and cells analysis, disease analysis, pathway, GO terms, phenotypes and compound analysis
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainer


  • person_outline Gil Stelzer

Additional information


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Publication for GeneAnalytics

GeneAnalytics citations

 (8)
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SYK expression level distinguishes control from BRCA1 mutated lymphocytes

2018
PMCID: 5875411
PMID: 29618939
DOI: 10.2147/CMAR.S156359
call_split See protocol

[…] sed genes. Since FDR application was too stringent for this data set, genes with a P-value <0.001 were considered as differentially expressed. Gene set enrichment and pathway analysis were done using GeneAnalytics. […]

library_books

Regulation of insulin resistance and type II diabetes by hepatitis C virus infection: A driver function of circulating miRNAs

2018
J Cell Mol Med
PMCID: 5867149
PMID: 29411512
DOI: 10.1111/jcmm.13553

[…] receptor kinase phosphorylation (PTPN1), IGFBP4 and IGFBP5 cleavage (PAPPA), and TGF‐β signalling (PEG10). To further examine the extent of functional association of these genes with IR, we used the GeneAnalytics VarElect software (an integrated knowledge‐based software to analyse direct and indirect phenotypic linkage with genes) and identified several miR‐122 targets (SLC12A1, PTPN1 and PAPPA) […]

library_books

Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers

2018
PLoS Genet
PMCID: 5773092
PMID: 29346386
DOI: 10.1371/journal.pgen.1007135

[…] verrepresentation analysis was done using Innate-DB[] and using the Broad Institute’s molecular signatures database ‘investigate gene sets’ web tool[]. Kaplan-Meier analysis was done using the http://geneanalytics.duhs.duke.edu/Surv_sig.html tool. Samples were assigned to groups based on being above or below the median population value. […]

library_books

FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch

2018
eLife
PMCID: 5826274
PMID: 29360038
DOI: 10.7554/eLife.30649.056

[…] peech and language impairment.To attribute biological meaning to the modules, we calculated a module significance score for the resulting disease, gene ontology, and pathway annotations returned from GeneAnalytics () (See Materials and methods). The top five terms for the black song production module (negatively correlated to the amount of singing), the brown variability induction module (positive […]

call_split

Transcriptional and post translational changes in the brain of mice deficient in cholesterol removal mediated by cytochrome P450 46A1 (CYP46A1)

2017
PLoS One
PMCID: 5658173
PMID: 29073233
DOI: 10.1371/journal.pone.0187168
call_split See protocol

[…] validated using a second normalization step to the synthetic phosphopeptides added as internal standards. Differentially-abundant phosphorylated proteins in the Cyp46a1-/- brain were analyzed by the GeneAnalytics (LifeMap Sciences) software. […]

library_books

The genomic landscape of tuberous sclerosis complex

2017
Nat Commun
PMCID: 5481739
PMID: 28643795
DOI: 10.1038/ncomms15816

[…] s were imported into R for differential expression analysis via limma and counts per million (CPM) calculated and log2-transformed using voom followed by trimmed mean of M-values (TMM) normalization. GeneAnalytics (LifeMap Sciences; geneanalytics.genecards.org) was used for primary gene set enrichment analysis. A maximum of 300 gene symbols were used and up to 10 GO biological processes with mediu […]

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GeneAnalytics institution(s)
LifeMap Sciences Ltd., Tel Aviv, Israel; Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel; Institute of Oncology, Sheba Medical Center, Tel Hashomer, Israel; Surgical Department, Sourasky Medical Centre, Tel Aviv, Israel; LifeMap Sciences, Inc., Marshfield, MA, USA; Venividi Solutions LLC, Chinakville, MD, USA; Bonus BioGroup Ltd., Haifa, Israel
GeneAnalytics funding source(s)
This work was supported by LifeMap Sciences Inc. California (USA), the NHGRI grant U41HG003345, the Crown Human Genome Center and the Nella and Leon Benoziyo Center for Neurosciences at the Weizmann Institute of Sciences.

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