GeneTrail 3.2

How to cite

All of our tools are highly intertwined and can be called within each other in order to provide the possibility to use the same data in several analyses or combine and compare the results. Please make sure to cite all used features with the corresponding publications. In the following table you can see which feature belongs to which server.

Publications

Web services

ClinOmicsTrail^bc

Lara Schneider, Tim Kehl, Kristina Thedinga, Nadja Liddy Grammes, Christina Backes, Christopher Mohr, Benjamin Schubert, Kerstin Lenhof, Nico Gerstner, Andreas Daniel Hartkopf, Markus Wallwiener, Oliver Kohlbacher, Andreas Keller, Eckart Meese, Norbert Graf, Hans-Peter Lenhof ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification Bioinformatics 2019 doi: 10.1093/bioinformatics/btz302 BibTeX

@article{10.1093/bioinformatics/btz302,
    author = {Schneider, Lara and Kehl, Tim and Thedinga, Kristina and Grammes, Nadja Liddy and Backes, Christina and Mohr, Christopher and Schubert, Benjamin and Lenhof, Kerstin and Gerstner, Nico and Hartkopf, Andreas Daniel and Wallwiener, Markus and Kohlbacher, Oliver and Keller, Andreas and Meese, Eckart and Graf, Norbert and Lenhof, Hans-Peter},
    title = "{ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification}",
    journal = {Bioinformatics},
    year = {2019},
    month = {04},
    abstract = "{Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process.Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results.ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de.Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz302},
    url = {https://doi.org/10.1093/bioinformatics/btz302},
    note = {btz302},
    eprint = {http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz302/28698194/btz302.pdf},
}

DrugTargetInspector

Lara Schneider, Daniel Stöckel, Tim Kehl, Andreas Gerasch, Nicole Ludwig, Petra Leidinger, Hanno Huwer, Stefan Tenzer, Oliver Kohlbacher, Andreas Hildebrandt, Michael Kaufmann, Manfred Gessler, Andreas Keller, Eckart Meese, Norbert Graf, and Hans-Peter Lenhof DrugTargetInspector: An assistance tool for patient treatment stratification International Journal of Cancer 2015 doi: 10.1002/ijc.29897 BibTeX

@article{schneider2015drugtargetinspector,
  title={DrugTargetInspector: An assistance tool for patient treatment stratification},
  author={Schneider, Lara and St{\"o}ckel, Daniel and Kehl, Tim and Gerasch, Andreas and Ludwig, Nicole and Leidinger, Petra and Huwer, Hanno and Tenzer, Stefan and Kohlbacher, Oliver and Hildebrandt, Andreas and Kaufmann, Michael and Gessler, Manfred and Keller, Andreas and Meese, Eckart and Graf, Norbert and Lenhof, Hans-Peter},
  journal={International Journal of Cancer},
  year={2015},
  doi={10.1002/ijc.29897},
  publisher={Wiley Online Library}
}

GeneTrail

Backes, Christina and Keller, Andreas and Kuentzer, Jan and Kneissl, Benny and Comtesse, Nicole and Elnakady, Yasser A and M{\"u}ller, Rolf and Meese, Eckart and Lenhof, Hans-Peter GeneTrail—advanced gene set enrichment analysis Nucleic acids research 2007 doi: 10.1093/nar/gkm323 BibTeX

@article{backes2007genetrail,
  title={GeneTrail—advanced gene set enrichment analysis},
  author={Backes, Christina and Keller, Andreas and Kuentzer, Jan and Kneissl, Benny and Comtesse, Nicole and Elnakady, Yasser A and M{\"u}ller, Rolf and Meese, Eckart and Lenhof, Hans-Peter},
  journal={Nucleic acids research},
  volume={35},
  number={suppl\_2},
  pages={W186--W192},
  year={2007},
  publisher={Oxford University Press}
}

GeneTrail 2

Daniel Stöckel, Tim Kehl, Patrick Trampert, Lara Schneider, Christina Backes, Nicole Ludwig, Andreas Gerasch, Michael Kaufmann, Manfred Gessler, Norbert Graf, Eckart Meese, Andreas Keller, Hans-Peter Lenhof Multi-omics Enrichment Analysis using the GeneTrail2 Web Service Bioinformatics 2016 doi: 10.1093/bioinformatics/btv770 BibTeX

@article{stoeckel2016genetrail2,
  title={Multi-omics Enrichment Analysis using the GeneTrail2 Web Service},
  author={St{\"o}ckel, Daniel and Kehl, Tim and Trampert, Patrick and Schneider, Lara and Backes, Christina and Ludwig, Nicole and Gerasch, Andreas and Kaufmann, Michael and Gessler, Manfred and Graf, Norbert and Meese, Eckart and Keller, Andreas and Lenhof, Hans-Peter},
  journal={Bioinformatics},
  year={2016},
  doi={10.1093/bioinformatics/btv770},
  publisher={Oxford University Press}
}

GeneTrail 3

Nico Gerstner, Tim Kehl, Kerstin Lenhof, Anne Müller, Carolin Mayer, Lea Eckhart, Nadja Liddy Grammes, Caroline Diener, Martin Hart, Oliver Hahn, Jörn Walter, Tony Wyss-Coray, Eckart Meese, Andreas Keller, Hans-Peter Lenhof GeneTrail 3: advanced high-throughput enrichment analysis Nucleic Acids Research 2020 doi: 10.1093/nar/gkaa306 BibTeX

@article{gerstner2020genetrail,
  title={GeneTrail 3: advanced high-throughput enrichment analysis},
  author={Gerstner, Nico and Kehl, Tim and Lenhof, Kerstin and M{\"u}ller, Anne and Mayer, Carolin and Eckhart, Lea and Grammes, Nadja Liddy and Diener, Caroline and Hart, Martin and Hahn, Oliver and others},
  journal={Nucleic Acids Research},
  year={2020}
}

NetworkTrail

Daniel Stöckel, Oliver Müller, Tim Kehl, Andreas Gerasch, Christina Backes, Alexander Rurainski, Andreas Keller, Michael Kaufmann, and Hans-Peter Lenhof NetworkTrail — a web service for identifying and visualizing deregulated subnetworks Bioinformatics 2013 doi: 10.1093/bioinformatics/btt204 BibTeX

@article{stockel2013networktrail,
  title={NetworkTrail — a web service for identifying and visualizing deregulated subnetworks},
  author={St{\"o}ckel, Daniel and M{\"u}ller, Oliver and Kehl, Tim and Gerasch, Andreas and Backes, Christina and Rurainski, Alexander and Keller, Andreas and Kaufmann, Michael and Lenhof, Hans-Peter},
  journal={Bioinformatics},
  volume={29},
  number={13},
  pages={1702--1703},
  year={2013},
  doi={10.1093/bioinformatics/btt204},
  publisher={Oxford University Press}
}

RegulatorTrail

Tim Kehl, Lara Schneider, Florian Schmidt, Daniel Stöckel, Nico Gerstner, Christina Backes, Eckart Meese, Andreas Keller, Marcel Schulz, and Hans-Peter Lenhof RegulatorTrail — a web service for the identification of key regulators Nucleic Acid Research 2017 doi: 10.1093/nar/gkx350

Databases

miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database

Tim Kehl, Fabian Kern, Christina Backes, Tobias Fehlmann, Daniel Stöckel, Eckart Meese, Hans-Peter Lenhof, Andreas Keller. Tim Kehl, Fabian Kern, Christina Backes, Tobias Fehlmann, Daniel Stöckel, Eckart Meese, Hans-Peter Lenhof, Andreas Keller Nucleic Acids Research. 2019. 10.1093/nar/gkz1022 BibTeX

@article{10.1093/nar/gkz1022,
    author = {Kehl, Tim and Kern, Fabian and Backes, Christina and Fehlmann, Tobias and Stöckel, Daniel and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
    title = "{miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database}",
    journal = {Nucleic Acids Research},
    year = {2019},
    month = {11},
    abstract = "{Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkz1022},
    url = {https://doi.org/10.1093/nar/gkz1022},
    note = {gkz1022},
    eprint = {http://oup.prod.sis.lan/nar/advance-article-pdf/doi/10.1093/nar/gkz1022/30437520/gkz1022.pdf},
}

miRPathDB: a new dictionary on microRNAs and target pathways

Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckard Meese, Hans-Peter Lenhof, Andreas Keller. miRPathDB: a new dictionary on microRNAs and target pathways. Nucleic Acids Research. 2016. 10.1093/nar/gkw926 BibTeX

@article{stoeckel2016genetrail2,
  title={miRPathDB: a new dictionary on microRNAs and target pathways},
  author={Backes, Christina and Kehl, Tim and St{\"o}ckel, Daniel and Fehlmann, Tobias and Schneider, Lara and Meese, Eckard and Lenhof, Hans-Peter and Keller, Andreas},
  journal={Nucleic Acids Research},
  year={2016},
  doi={10.1093/nar/gkw926},
  publisher={Oxford University Press}
}