This website contains supplementary material for:


T.R. Hvidsten, B. Wilczyński, A. Kryshtafovych, J. Tiuryn, J. Komorowski and K. Fidelis. Discovering regulatory binding site modules using rule-based learning. Genome Research 15: 856-66, 2005.



Discovering regulatory binding site modules using rule-based learning


Torgeir R. Hvidsten (1), Bartosz Wilczyński (2,3), Andriy Kryshtafovych (2),

Jerzy Tiuryn (4), Jan Komorowski (1) and Krzysztof Fidelis (2)


(1) The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden

(2) Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, CA, USA

(3) Institute of Mathematics of the Polish Academy of Sciences, Warsaw, Poland

(4) Faculty of Mathematics, Informatics, and Mechanics, Warsaw University, Poland


Corresponding authors:

Krzysztof Fidelis, Biology and Biotechnology Research Program,

Lawrence Livermore National Laboratory, 7000 East Ave., L-448, Livermore, CA, 94550, USA.



Rules and evaluation to binding data and Gene Ontology


The induced rules and their evaluation to binding data1 and Gene Ontology2 for six expression studies using known binding sites (file format):


  1. cell cycle3  (including putative motifs: cell cycle)
  2. sporulation4
  3. diauxic shift5
  4. heat and cold shock6
  5. pheromone7
  6. DNA-damaging agents8


Known binding sites were taken from the database of known and putative motifs published by Pilpel et al9.

Expression data was taken from ExpressDB10.


Selecting expression thresholds

Overlap between sequence motifs

Comparisons to other studies


Extended tables from the article


  1. Table 2 (extended with additional binding data11 and standard deviations for the random tests)
  2. Table 3 (extended with standard deviation for the random tests)
  3. Table 4 (extended to include all rules)
  4. Figure 4 (extended with graphs showing only significant edges)



1.         Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002;298(5594):799-804.

2.         Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25(1):25-29.

3.         Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998;2(1):65-73.

4.         Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science 1998;282(5389):699-705.

5.         DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997;278(5338):680-686.

6.         Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998;95(25):14863-14868.

7.         Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 2000;287(5454):873-880.

8.         Jelinsky SA, Estep P, Church GM, Samson LD. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 2000;20(21):8157-8167.

9.         Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001;29(2):153-159.

10.       Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Res 2000;10(4):431-445.

11.      Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature 2004;431(7004):99-104.