geneXplain-platform

geneXplain platform

The comprehensive bioinformatics platform, also available as Java API

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The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch.

 

Own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses.
GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.

User Interface of the genexplain platform

The start page provides an easy access to a number of application areas.

Key features

Integrated databases and analysis tools

The platform provides an integrated view on several databases and analysis tools, public domain as well as commercial ones. They can be combined in a highly flexible way to design customized analyses.

Ready-made workflows for an easy start

A rapidly growing number of proven workflows facilitates a quick and easy access to the platform and its complex analysis functions. Input forms are simple and user-friendly. Workflows can be easily customized to specific needs. Experienced users can create their own workflows.

Fully integrated upstream analysis

The platform provides a fully integrated upstream analysis, which combines state-of-the-art analysis of regulatory genome regions with sophisticated pathway analyses.

Knowledge-based data analysis

The platform uses a number of renowned high-quality databases for the data analysis. TRANSFAC® and TRANSPATH® are expert-curated databases. GeneWays is generated by an NLP-based text-mining approach, providing a helpful complement for manually curated data. Well-known public-domain databases like Reactome and HumanCyc are integrated and applied as well.

JavaScript and R scripts

User-specific scripts in JavaScript and in R can be added directly into the platform, and immediately executed. They can be combined with pre-existing analyses, and can be part of the workflows.

NGS data analysis

NGS data analysis is supported by the platform. ChIP-seq data sets containing in vivo transcription factor binding sites or methylation results can be analyzed with the help of ready-made workflows. Galaxy tools are integrated, supporting RNA-seq data analysis, and many functions more.

Simulation engine inside

The platform contains a simulation engine that executes differential equation systems and visualizes the results. Parameter optimization, parameter fitting (based on expression data), and hierarchical modeling are supported.

Group project work including chat function

Share your data and results with other members of the project. Discuss what you are doing while working together on a dataset.

Insights

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RNA-seq – from raw reads to full integrated, advanced gene analysis of your experimental data

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Transcription factors – deep view on binding sites and corresponding factors/enhancers

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Networks – upstream analysis to discover novel master regulators and underlying mechanisms

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NGS – gene expression profiling, detection of genetics changes and molecular analysis

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Drug targets – best pipeline to find therapeutic targets

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Pathways – identify major players and inferred activity in canonical pathways or reconstructed networks

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ChIP-seq – peak calling, classify and analyze target genes

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SNPs – focus on gain or loss of protein functions

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Gene Ontology – map, reduce and visualize GO terms

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Single Sequences – work with mouse, human and rat genome builds

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miRNA – target identification, enrichment and more

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Cluster – create your own gene or protein cluster

New applications

Out now !
New workflows
  • Fully automatic pipelines for paired RNA-seq libraries
  • New workflows for analyzing multiple BAM files
  • Estimate DEGs from raw RNA-seq data, counts or normalized transcriptomic data
  • Support of new species Zebrafish and Arabidopsis
  • Investigate tissue- or cell-line specific miRNA promoter regions with TRANSFAC®
  • Identifying miRNA binding sites in tissue-specific genes with HumanPSD™
  • New pipeline to analyze SNPs with TRANSFAC® and TRANSPATH® at once
New and updated databases
  • Ensembl Arabidopsis thaliana (TAIR10)
  • Ensembl Danio rerio (GRCz11)
  • TRANSFAC® 2022.1
  • TRANSPATH® 2022.1
  • HumanPSD™ 2022.1
New tools
  • Support of Affymetrix miRNA-4.1 microarray chip & Agilent miRNA microarray chips
  • Enable multiple miRNA ID support and conversion handling
  • TRANSFAC® MATCH™ for tracks
  • Convert table to VCF track
  • Filter VCF by genotype
View full feature list
Download full feature list

Videos

Find below a compilation of our introductory and tutorial videos.
In English Language
This video is a general introduction to the geneXplain® platform. (3:21 min)

 

In Chinese Language
This video is a general introduction to the geneXplain® platform; it introduces you to different workflows. (1:38 min)
It shows you how to register a free platform account and to login. The audio-visual also introduces you to the look and feel of the geneXplain® platform interface. (4:11 min)
This video demonstrates how to upload raw data from an experiment to the geneXplain® platform for further analysis. (2:46 min)
In this video microarray data is used as an example to show you how to further analyze data from high-throughput experiments on the geneXplain® platform. (6:45 min)

Current platform release

geneXplain® platform major 7.0 release

Download full new features list

New and updated databases:

  • Ensembl Arabidopsis thaliana (TAIR10)
  • Ensembl Danio rerio (GRCz11)
  • HumanPSD™ is updated to version 2022.1
  • TRANSFAC® is updated to version 2022.1
  • TRANSPATH® is updated to version 2022.1

New workflows:

  • Fully automatic pipelines for paired RNA-seq libraries
  • New workflows for analyzing multiple BAM files
  • Estimate DEGs from raw RNA-seq data, counts or normalized transcriptomic data
  • Support of new species Zebrafish and Arabidopsis
  • Investigate tissue- or cell-line specific miRNA promoter regions with TRANSFAC®
  • Identifying miRNA binding sites in tissue-specific genes with HumanPSD™
  • New pipeline to analyze SNPs with TRANSFAC® and TRANSPATH® at once

New tools:

  • Support of Affymetrix miRNA-4.1 microarray chip & Agilent miRNA microarray chips
  • Enable multiple miRNA ID support and conversion handling
  • TRANSFAC® MATCH™ for tracks
  • Convert table to VCF track
  • Filter VCF by genotype

     

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      Demo Workflows

      Here, we list workflows that were used to prove the capabilities of the geneXplain platform, for instance in the cited publications. The links given direct you straight into the platform without requiring any registration.
      Using these demo workflows, you will be able to reproduce the published results and to learn more about the platform’s look and feel. To work with your own data, however, registration is required. Additional licensing is necessary for certain third-party products such as TRANSFAC® or TRANSPATH®.
      Workflows 1-3 are from our recent publication Koschmann et al., Microarrays 4, 270-286.
      1. Workflow “Identify enriched motifs in promoters“,
      applied to datasets of naphthalene-treated mouse liver and lung tissue.
      Find further instructions and explanations here.
      Origin of datasets:
      GEO GSE18858 and GSE17933
      Thomas, R.S., et al. (2011) Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment. Toxicol. Sci. 120, 194-205. PMID: 21097997
      Thomas, R.S., et al. (2009) Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.Toxicol. Sci. 112, 311-321. PMID: 19776212
      2. Workflow “Find master regulators in the TRANSPATH® network“,
      applied to datasets of naphthalene-treated mouse liver and lung tissue.
      Find further instructions and explanations here.
      The data sources are as for Workflow 1.
      3. Workflow “Enriched upstream analysis with TRANSFAC® and TRANSPATH® network“,
      applied to datasets of naphthalene-treated mouse liver and lung tissue.
      Find further instructions and explanations here.
      The data sources are as for Workflow 1.

      Workflow management

      Sequential launching of particular analysis modules can be saved as a graphically represented workflow. Modules are shown as purple rectangles, and outputs of each step serve as inputs into the next analysis step. A workflow that is specific for a given data set can be easily constructed by drag and drop of the required analysis modules. In addition, Java scripts and R scripts can be added directly within the platform, for more specific requirements of the analysis.
      The picture shows a small workflow for the gene set enrichment analysis (GSEA) of using four different ontologies: Gene Ontology (GO) Biological Process, GO Cellular Compartment, GO Molecular Function, and Reactome's functional assignments (see on the right side). The larger light blue boxes are analysis functions (program modules, "Bricks"). Green boxes stand for input files, especially user-defined inputs. Yellow boxes represent automatic delivery or output files. A workflow can be intuitively designs by simple drag-and-drop of the constituents and graphically connecting them.

      Workflow management in the geneXplain platform. (Click image to see the complete picture).

      See demo workflows for a collection of executable workflows: no registration required!

      Videos

      Intro video of the geneXplain platform.

      Information downloads

      Publications

      Benjamin, S.J., Hawley, K.L., Vera-Licona, P., La Vake, C.J., Cervantes, J.L., Ruan, Y., Radolf, J.D., Salazar, J.C. (2021) Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation. BMC Immunol. 22, 32 Link

      Meier, T., Timm, M., Montani, M., Wilkens, L. (2021) Gene networks and transcriptional regulators associated with liver cancer development and progression. BMC Med. Genomics 14, 41. Link

      Ural, B.B., Yeung, S.T., Damani-Yokota, P., Devlin, J.C., de Vries, M., Vera-Licona, P., Samji, T., Sawai, C.M., Jang, G., Perez, O.A., Pham, Q., Maher, L., Loke, P., Dittmann, M., Reizis, B., Khanna, K.M. (2020) Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties. Sci. Immunol. 5, eaax8756. Link

      Mekonnen, Y.A., Gültas, M., Effa, K., Hanotte, O., Schmitt, A.O. (2019) Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front. Genet. 10, 1095. Link

      Blazquez, R., Wlochowitz, D., Wolff, A., Seitz, S., Wachter, A., Perera-Bel, J., Bleckmann, A., Beißbarth, T., Salinas, G., Riemenschneider, M.J., Proescholdt, M., Evert, M., Utpatel, K., Siam, L., Schatlo, B., Balkenhol, M., Stadelmann, C., Schildhaus, H.U., Korf, U., Reinz, E., Wiemann, S., Vollmer, E., Schulz, M., Ritter, U., Hanisch, U.K., Pukrop, T. (2018) PI3K: A master regulator of brain metastasis-promoting macrophages/microglia. Glia 66, 2438-2455. Link

      Orekhov, A.N., Oishi, Y., Nikiforov, N.G., Zhelankin, A.V., Dubrovsky, L., Sobenin, I.A., Kel, A., Stelmashenko, D., Makeev, V.J., Foxx, K., Jin, X., Kruth, H.S. Bukrinsky, M. (2018) Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. Curr. Pharm. Des. 24, 3143-3151. Link

      Kalozoumi, G., Kel-Margoulis, O., Vafiadaki, E., Greenberg, D., Bernard, H., Soreq, H., Depaulis, A., Sanoudou, D. (2018) Glial responses during epileptogenesis in Mus musculus point to potential therapeutic targets. PLoS One 13, e0201742. Link

      Smetanina, M.A., Kel, A.E., Sevost’ianova, K.S., Maiborodin, I.V., Shevela, A.I., Zolotukhin, I.A., Stegmaier, P., Filipenko, M.L. (2018) DNA methylation and gene expression profiling reveal MFAP5 as a regulatory driver of extracellular matrix remodeling in varicose vein disease. Epigenomics 10, 1103-1119. Link

      Boyarskikh, U., Pintus, S., Mandrik, N., Stelmashenko, D., Kiselev, I., Evshin, I., Sharipov, R., Stegmaier, P., Kolpakov, F., Filipenko, M., Kel, A. (2018) Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. BMC Med. Genomics 11(Suppl 1), 12. Link

      Triska, M., Solovyev, V., Baranova, A., Kel, A., Tatarinova, T.V. (2017) Nucleotide patterns aiding in prediction of eukaryotic promoters. PLoS One 12, e0187243. Link

      Niehof, M., Hildebrandt, T., Danov, O., Arndt, K., Koschmann, J., Dahlmann, F., Hansen, T. and Sewald, K. (2017) RNA isolation from precision-cut lung slices (PCLS) from different species. BMC Res. Notes 10, 121. Link

      Mandić, A.D., Bennek, E., Verdier, J., Zhang, K., Roubrocks, S., Davis, R.J., Denecke, B., Gassler, N., Streetz, K., Kel, A., Hornef, M., Cubero, F. J., Trautwein, C. and Sellge, G. (2017) c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine. Mucosal Immunol. 10, 1211-1223. Link

      Pietrzyńska, M., Zembrzuska, J., Tomczak, R., Mikołajczyk, J., Rusińska-Roszak, D., Voelkel, A., Buchwald, T., Jampílek, J., Lukáč, M., Devínsky, F. (2016) Experimental and in silico investigations of organic phosphates and phosphonates sorption on polymer-ceramic monolithic materials and hydroxyapatite. Eur. J. Pharm. Sci. 93, 295-303. Link

      Kural, K.C., Tandon, N., Skoblov, M., Kel-Margoulis, O.V. and Baranova, A.V. (2016) Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence. BMC Genomics 17(Suppl 14), 1030. Link

      Kel, A.E., Stegmaier, P., Valeev, T., Koschmann, J., Poroikov, V., Kel-Margoulis, O.V. and Wingender, E. (2016) Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EuPA Open Proteomics 13, 1-13. Link

      Ciribilli, Y., Singh, P., Inga, A., Borlak, J. (2016) c-Myc targeted regulators of cell metabolism in a transgenic mouse model of papillary lung adenocarcinoma. Oncotarget 7, 65514-65539. Link

      Wlochowitz, D., Haubrock, M., Arackal, J., Bleckmann, A., Wolff, A., Beißbarth, T., Wingender, E., Gültas, M. (2016) Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front. Genet. 7, 42. Link

      Lee, E.H., Oh, J.H., Selvaraj, S., Park, S.M., Choi, M.S., Spanel, R., Yoon, S. and Borlak, J. (2016) Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice. Oncotarget 7, 14983-15017. Link

      Borlak, J., Singh, P. and Gazzana, G. (2015) Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events. BMC Genomics 16, 124. Link

      Koschmann, J., Bhar, A., Stegmaier,P., Kel, A. E. and Wingender, E. (2015) “Upstream Analysis”: An integrated promoter-pathway analysis approach to causal interpretation of microarray data. Microarrays 4, 270-286. Link

      Shi, Y., Nikulenkov, F., Zawacka-Pankau, J., Li, H., Gabdoulline, R., Xu, J., Eriksson, S., Hedström, E., Issaeva, N., Kel, A., Arnér, E.S., Selivanova, G. (2014) ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis. Cell Death Differ. 21, 612-623. Link

      Schlereth, K., Heyl, C., Krampitz, A.M., Mernberger, M., Finkernagel, F., Scharfe, M., Jarek, M., Leich, E., Rosenwald, A., Stiewe, T. (2013) Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53’s Tumor Suppressor Functions. PLoS Genet. 9, e1003726. PubMed

      Nikulenkov, F., Spinnler, C., Li, H., Tonelli, C., Shi, Y., Turunen, M., Kivioja, T., Ignatiev, I., Kel, A., Taipale, J., Selivanova, G. (2012) Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ. 19, 1992-2002. PubMed

      Zawacka-Pankau, J., Grinkevich, V.V., Hunten, S., Nikulenkov, F., Gluch, A., Li, H., Enge, M., Kel, A., Selivanova, G. (2011) Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. J. Biol. Chem. 286, 41600-41615. PubMed

      Kel, A., Kolpakov, F., Poroikov, V., Selivanova, G. (2011) GeneXplain — Identification of Causal Biomarkers and Drug Targets in Personalized Cancer Pathways. J. Biomol. Tech. 22(Suppl), S16. PubMed
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