Supplementary Material for: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen and Reinhold Schäfer: Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS Content (9 Figures, 3 Tables, 1 Text, 1 List of References) Supplementary Figures S1: Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. S2: Impact of transcription factor knock-down on the KRAS pathway-mediated mRNA expression profile S3: RNA expression of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS- transformed RAS-ROSE cells S4: Effects of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA knock-down in RAS-ROSE cells on the activity of cytoplasmic signaling downstream of RAS S5: Effect of Fosl1 overepxression and Otx1 knockdown on Fosl1mRNA and phospho-Erk. S6: Effects on growth characteristics of RAS-ROSE cells after silencing Fosl1, Hmga2, Klf6, JunB S7: Effects on growth characteristics of RAS-ROSE cells after silencing Otx1, Gfi1, RelA S8: Effects on distribution of cell cycle phases in KRAS-transformed RAS-ROSE cells after silencing of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA S9: Effect of perturbation strength and noise on algorithm performance. Supplementary Tables S1: Rules for finding transcription factor-related patterns in genome-wide expression data (related to Fig. 3B and C). S2: Known interaction (related to Fig. 4) S3: Quantification of the network. Supplementary Texts Generation of artificial data sets Supplementary References Supplementary Fig. 1 Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. Western Blot analysis of nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1 and RelA in RAS-ROSE cells 48 h after transfections with scrambled siRNAduplex (Sc), transfection reagents only (Mock) and two independent transcription factor specific siRNAs (1, 2). ß-tubulin control (*). 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