REGGAE: a novel approach for the identification of key transcriptional regulators.

REGGAE: a novel approach for the identification of key transcriptional regulators. Kehl, T., Schneider, L., Kattler, K., Stöckel, D., Wegert, J., Gerstner, N., Ludwig, N., Distler, U., Schick, M., Keller, U., Tenzer, S., Gessler, M., Walter, J., Keller, A., Graf, N., Meese, E., & Lenhof, H. Bioinformatics (Oxford, England), May, 2018.
doi abstract bibtex

Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Here, we present REGGAE (REGulator-Gene Association Enrichment), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms. REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de. tkehl@bioinf.uni-sb.de. Supplementary data are available at Bioinformatics online.

@Article{Kehl2018,
  author       = {Kehl, Tim and Schneider, Lara and Kattler, Kathrin and Stöckel, Daniel and Wegert, Jenny and Gerstner, Nico and Ludwig, Nicole and Distler, Ute and Schick, Markus and Keller, Ulrich and Tenzer, Stefan and Gessler, Manfred and Walter, Jörn and Keller, Andreas and Graf, Norbert and Meese, Eckart and Lenhof, Hans-Peter},
  title        = {REGGAE: a novel approach for the identification of key transcriptional regulators.},
  journal      = {Bioinformatics (Oxford, England)},
  year         = {2018},
  month        = may,
  issn         = {1367-4811},
  abstract     = {Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Here, we present REGGAE (REGulator-Gene Association Enrichment), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms. REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de. tkehl@bioinf.uni-sb.de. Supplementary data are available at Bioinformatics online.},
  country      = {England},
  doi          = {10.1093/bioinformatics/bty372},
  issn-linking = {1367-4803},
  nlm-id       = {9808944},
  owner        = {NLM},
  pii          = {4993882},
  pmid         = {29741575},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-05-09},
}

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