GeneAnalytics protocols

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Associated diseases

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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 in pipeline

2016
PMCID: 4850677
PMID: 27130208
DOI: 10.1186/s13104-016-2038-y

[…] corrected p values of <0.05 were identified. lists of upregulated and downregulated genes in icm and te were also separately analyzed for overrepresentation of genes in superpaths using geneanalytics (https://ga.genecards.org). superpaths are a collection of 1073 unified pathways generated from multiple pathway sources using nearest neighbor graphing and hierarchical clustering []. […]


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GeneAnalytics in publications

 (21)
PMCID: 5875411
PMID: 29618939
DOI: 10.2147/CMAR.S156359

[…] 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., total rna was extracted from primary lymphocyte cells using a direct-zol™ rna miniprep kit (zymo research), according to the protocol recommended by the manufacturer. complementary […]

PMCID: 5834609
PMID: 29500447
DOI: 10.1038/s41598-018-21860-6

[…] (p < 0.00061 per individual t-test based on tukey–kramer’s post hoc correction, fig. ). genes that were up- or downregulated by at least five-fold (fig. , green marks) were further analyzed using geneanalytics to score and classify matching biological processes, tissue and organ systems (fig. ). the results indicated that in all cases, the biological process involved relate to ecm […]

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

[…] 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., we would like to thank dr. robert cardiff and aatish […]

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

[…] 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 […]

PMCID: 5773952
PMID: 29168353
DOI: 10.1002/cam4.1256

[…] “synovial,” “arthritis,” “rheumatoid,” “joint,” “pain,” “sensitization,” and “nociception.” this was done via an ‘undirected’ review of all publications citing each gene, which was accessed via geneanalytics genecards’ “publications” section for each gene of interest ., we next determined the presence of any linkage disequilibrium (ld) among the 70 most discriminatory snps, […]


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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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