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®.
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
Find further instructions and explanations
here.
The data sources are as for Workflow 1.
Find further instructions and explanations
here.
The data sources are as for Workflow 1.
Mekonnen, Y. A., Gültas, M., Effa, K., Hanotte, O. and Schmitt, A. O. (2019) Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front. Genet. 10:1095. doi: 10.3389/fgene.2019.01095. 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 UK., Pukrop T. (2018) PI3K: A master regulator of brain metastasis-promoting macrophages/microglia. Glia. 66(11):2438-2455. doi: 10.1002/glia.23485. Epub 2018 Oct 25. 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. and Bukrinsky, M. (2018) Modified Ldl Particles Activate Inflammatory Pathways In Monocyte-Derived Macrophages: Transcriptome Analysis. Curr. Pharm. Des.,
11. doi: 10.2174/1381612824666180911120039.
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(8)
:e0201742. doi: 10.1371/journal.pone.0201742.
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(8):1103-1119. doi: 10.2217/epi-2018-0001. 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. doi: 10.1186/s12920-018-0330-5. Link
Triska, M., Solovyev, V., Baranova, A., Kel, A., Tatarinova, T.V. (2017) Nucleotide patterns aiding in prediction of eukaryotic promoters. PLoS One.
12(11):e0187243. doi: 10.1371/journal.pone.0187243. 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. doi: 10.1186/s13104-017-2447-6.
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(5):1211-1223. doi: 10.1038/mi.2016.125.
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. doi: 10.1016/j.ejps.2016.08.033.
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. doi: 10.1186/s12864-016-3352-4.
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. doi: 10.1016/j.euprot.2016.09.002.
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. doi: 10.18632/oncotarget.11804.
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. doi: 10.3389/fgene.2016.00042.
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. doi:10.18632/oncotarget.7698.
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. doi:10.1186/s12864-015-1312-z.
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. doi:10.3390/microarrays4020270.
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. doi:10.1038/cdd.2013.186
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