GeneTrail protocols

View GeneTrail computational protocol

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Associated diseases

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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 in pipelines

 (10)
2018
PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9

[…] 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 […]

2017
PMCID: 5431893
PMID: 28500316
DOI: 10.1038/s41598-017-01856-4

[…] because many canonical pathways are examined simultaneously, we used the method of benjamini-hochberg to correct for multiple testing., two other web-based bioinformatics tools (i.e., enrichnet and genetrail) for pathway analysis depend on popular public databases, such as the kyoto encyclopedia of genes and genomes (kegg), wiki pathways, and biocarta pathway. by using overrepresentation […]

2016
PMCID: 5117531
PMID: 27895807
DOI: 10.1186/s13148-016-0287-1

[…] targets. target networks were constructed using an offline version of mirtargetlink [] and visualized in cytoscape. mirna target pathway analysis has been carried out using genetrai2 []. for the genetrail2 analysis, all available categories were analyzed, the minimal category size was set to 4 and all p values were adjusted using benjamini-hochberg adjustment., we sequenced six brain, two […]

2016
PMCID: 5195898
PMID: 27869830
DOI: 10.1038/ng.3728

[…] h1975 and m1 or m2 was used to derive two independent gene lists. both lists were entered into david to generate two independent functional clustering lists with associated enrichment p-values. genetrail go analysis was performed using the same 1000 differentially expressed genes between parental h1975 and h1975 m1 or m2. genetrail go analysis was performed using the top 1500 differentially […]

2015
PMCID: 4628234
PMID: 26521232
DOI: 10.1186/s12974-015-0418-1

[…] mieaa (http://www.ccb.uni-saarland.de/mieaa_tool/) to further characterize the association of sets of mirnas with pathways, functional categories, diseases, tissues, or cell types. mieaa is based on genetrail [] and performs standard enrichment analyses like over-representation analysis or gene set enrichment analysis in the context of mirnas. this way, we identify significantly enriched mirna […]


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GeneTrail in publications

 (100)
PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9

[…] 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 […]

PMCID: 5908973
PMID: 29706885
DOI: 10.3389/fnagi.2018.00102

[…] v7.00) with a level of statistical significance set at p < 0.05., gene ontology (go) annotations and significantly altered pathways in kegg, reactome, and wikipathways were analyzed using genetrail2 (; rrid:scr_006250, v1.5; go, kegg, reactome retrieved 11/01/2016; wikipathways retrieved 18/02/2016) with the gene set enrichment analysis (gsea) method. gsea was performed using […]

PMCID: 5892948
PMID: 29634759
DOI: 10.1371/journal.pone.0193790

[…] density is shown in tables and , respectively., we investigated which pathways were altered by transcripts with significantly altered ribosome density using overrepresentation analysis (ora) with genetrail2 []. increased ribosome density was foremost associated with transcripts encoding proteins of mitochondria, mitochondrial and endoplasmic reticulum components (enrichment p<10−6), […]

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

[…] transcription, translation, mitochondrial function; fig. , supplementary table ). to determine whether cellular processes are significantly enriched, we used overrepresentation analysis (ora) with genetrail2 (fig. , supplementary table ). mitochondrion and mitochondrial respiration were highly enriched among the cellular component and biological process go-terms, respectively (53 hits). […]

PMCID: 5898914
PMID: 29561261
DOI: 10.7554/eLife.32332.045

[…] lack thereof). this resulted in 3458 human cnpc-enriched protein-coding genes present in at least two of the five gene sets (listed in , see also )., go term enrichment analysis was performed using genetrail2 (https://genetrail2.bioinf.uni-sb.de/) using the 3458 human cnpc-enriched protein-coding genes as input. we performed over-representation analysis as set-level statistic, using […]


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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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