GeneTrail statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GeneTrail
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Tool usage distribution map

This map represents all the scientific publications referring to GeneTrail per scientific context
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Associated diseases

This word cloud represents GeneTrail usage per disease context
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Popular tool citations

chevron_left Gene set enrichment analysis miRNA enrichment chevron_right
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Protocols

GeneTrail specifications

Information


Unique identifier OMICS_02236
Name GeneTrail
Interface Web user interface, Application programming interface
Restrictions to use None
Input data GeneTrail is able to read various input file formats through which the user can provide measurement data or categories that should be analyzed. In general, GeneTrail2 will try to automatically detect type of the uploaded data. GeneTrail accepts the following simple, tab-delimited text files as inputs: identifier lists, score lists, and data matrices. More information: https://genetrail2.bioinf.uni-sb.de/help?topic=input_data
Computer skills Basic
Version 2.1.4
Stability Stable
Maintained Yes

Maintainer


  • person_outline Daniel Stöckel

Publications for GeneTrail

GeneTrail citations

 (44)
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A Novel S100A8/A9 Induced Fingerprint of Mesenchymal Stem Cells associated with Enhanced Wound Healing

2018
Sci Rep
PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9
call_split See protocol

[…] st and Venn diagram function in R-Studio employing differentially expressed pre-ranked genes which were associated with extracellular secretory function as classified using TopGO R-Studio package and GeneTrail2. The principle component analysis (PCA) based on regularized log transformed FPKM values with an adjusted p-value < 0.05. obtained from DEseq. 2 and was carried out using ggfortify and ggpl […]

library_books

Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line

2018
Sci Rep
PMCID: 5805679
PMID: 29422612
DOI: 10.1038/s41598-018-20518-7

[…] s (PCA). Additional visualizations were made using R packages ggplots, dheatmap and pheatmap. Overrepresentation Analysis (ORA) for GO-terms and pathways was performed on significant transcripts with GeneTrail2. […]

library_books

Micro ribonucleic acids and extracellular vesicles repertoire in the spent culture media is altered in women undergoing In Vitro Fertilization

2017
Sci Rep
PMCID: 5648749
PMID: 29051527
DOI: 10.1038/s41598-017-13683-8

[…] mented and published. For the analysis of miRNA sets, we used the microRNA enrichment analysis and annotation tool miEAA (available at http://www.ccb.uni-saarland.de/mieaa_tool/), which relies on the GeneTrail framework, (available at http://genetrail2.bioinf.uni-sb.de/). Effects of single miRNAs on pathways have been determined by the miRNA Pathway Dictionary (available at https://mpd.bioinf.uni- […]

library_books

Structure and functional impact of seed region variant in MIR 499 gene family in bronchial asthma

2017
PMCID: 5591547
PMID: 28886711
DOI: 10.1186/s12931-017-0648-0

[…] k []. Advanced gene set enrichment analysis was employed using the Gene Trail program with multiple testing correction via false discovery rate (FDR) estimation and significant level at 0.05 (https://genetrail2.bioinf.uni-sb.de/) []. In addition, mfold RNAfold (http://unafold.rna.albany.edu/?q=mfold) and KineFold web-servers (http://kinefold.curie.fr/) were conducted to predict the secondary struc […]

library_books

HSPs drive dichotomous T cell immune responses via DNA methylome remodelling in antigen presenting cells

2017
Nat Commun
PMCID: 5460028
PMID: 28561043
DOI: 10.1038/ncomms15648

[…] Genomatix Software GmbH). Distribution across TSS and CpG islands was determined using SeqMonk (Babraham Bioinformatics). Transcription factor binding analysis was performed using Genomatix software. Genetrail was used to test for gene ontology analysis using default parameters and Ensembl genes as background for enrichment. Results were corrected for multiple testing using Bonferroni adjustment. […]

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MicroRNAs Correlate with Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder in a Chinese Population

2017
PMCID: 5458669
PMID: 28550707
DOI: 10.12659/MSM.904642
call_split See protocol

[…] We used the miEAA (http://www.ccb.uni-saarland.de/mieaa_tool/) as a tool to characterize the association of the miRNAs with molecular pathways. MiEAA is based on GeneTrail [] and used for standard enrichment analyses, such as over-representation analysis or gene set enrichment analysis in the context of miRNAs. Adjusted p values <0.05 were considered significa […]


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GeneTrail institution(s)
Center for Bioinformatics, Saarland University, Saarbrücken, Germany; Center for Bioinformatics, Eberhard-Karls-University, Tübingen, Germany; Department of Human Genetics, Medical School, Saarland University, Homburg, Germany; Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany; Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany

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