Country/region
[
change
]
Terms of use
All of IBM
Home
Products
Services & solutions
Support & downloads
My account
IBM Research
Journals Home
Systems Journal
Journal of Research
and Development
Current Issue
Recent Issues
Papers in Progress
Search Journal Archives
Subscribe/Order
Description
Author's Guide
Staff
Contact Us
Related links
IBM Research: Computational Biology and Medical Informatics
IBM Research: Functional Genomics and Systems Biology
IBM Healthcare and Life Sciences
IBM Blue Gene
Systems Biology
Volume 50, Number 6, 2006
Table of contents:
HTML
PDF
This article:
HTML
PDF
Copyright info
Machine learning methods for transcription data integration - References
by D. T.
Holloway
,
M. A.
Kon
,
and C.
DeLisi
References
E. M. Conlon, X. S. Liu, J. D. Lieb, and J. S. Liu, “Integrating Regulatory Motif Discovery and Genome-Wide Expression Analysis,”
Proc. Natl. Acad. Sci.
100
, No. 6, 3339–3344 (2003).
S. Keles, M. J. van der Laan, and C. Vulpe, “Regulatory Motif Finding by Logic Regression,”
Bioinformatics
20
, No. 16, 2799–2811 (2004).
W. Wang, J. M. Cherry, D. Botstein, and H. Li, “A Systematic Approach to Reconstructing Transcription Networks in Saccharomyces scerevisiae,”
Proc. Natl. Acad. Sci.
99
, No. 26, 16893–16898 (2002).
H. Bussemaker, H. Li, and E. Siggia, “Regulatory Element Detection Using Correlation with Expression,”
Nature Genetics
27
, No. 2, 167–171 (2001).
K. Birnbaum, P. N. Benfey, and D. E. Shasha, “cis Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor/cis Element Relationships,”
Genome Res.
11
, No. 9, 1567–1573 (2001).
Z. Zhu, Y. Pilpel, and G. Church, “Computational Identification of Transcription Factor Binding Sites via a Transcription-Factor-Centric-Clustering (TFCC) Algorithm,”
J. Molec. Biol.
318
, No. 2, 71–81 (2002).
M. Pritsker, Y.-C. Liu, M. A. Beer, and S. Tavazoie, “Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation,”
Genome Res.
14
, No. 1, 99–108 (2004).
S. Elemento and S. Tavazoie, “Fast and Systematic Genome-Wide Discovery of Conserved Regulatory Elements Using a Non-Alignment Based Approach,”
Genome Biol.
6
, No. 2, R18 (2005).
M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. De Moor, E. Eskin, A. V. Favorov, M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu, “Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites,”
Nature Biotechnol.
23
, No. 1, 137–144 (2005).
G. D. Stormo, “DNA Binding Sites: Representation and Discovery,”
Bioinformatics
16
, No. 1, 16–23 (2000).
C. T. Workman and G. D. Stormo, “ANN-Spec: A Method for Discovering Transcription Factor Binding Sites with Improved Specificity,”
Proceedings of the Pacific Symposium on Biocomputing,
2000, pp. 467–478.
T. D. Schneider, G. D. Stormo, L. Gold, and A. Ehrenfeucht, “Information Content of Binding Sites on Nucleotide Sequences,”
J. Molec. Biol.
188
, No. 3, 415–431 (1986).
T. Schneider and R. Stephens, “Sequence Logos: A New Way to Display Consensus Sequences,”
Nucl. Acids Res.
18
, No. 20, 6097–6100 (1990).
M. C. Frith, M. C. Li, and Z. Weng, “Cluster-Buster: Finding Dense Clusters of Motifs in DNA Sequences,”
Nucl. Acids Res.
31
, No. 13, 3666–3668 (2003).
B. P. Berman, Y. Nibu, B. D. Pfeiffer, P. Tomancak, S. E. Celniker, M. Levine, G. M. Rubin, and M. B. Eisen, “Exploiting Transcription Factor Binding Site Clustering to Identify Cis-Regulatory Modules Involved in Pattern Formation in the Drosophila Genome,”
Proc. Natl. Acad. Sci.
99
, No. 2, 757–762 (2002).
D. Dinakarpandian, V. Raheja, S. Mehta, E. Schuetz, and P. Rogan, “Tandem Machine Learning for the Identification of Genes Regulated by Transcription Factors,”
BMC Bioinformatics
6
, No. 1, 204 (2005).
M. Rebeiz, N. L. Reeves, and J. W. Posakony, “SCORE: A Computational Approach to the Identification of Cis-Regulatory Modules and Target Genes in Whole-Genome Sequence Data,”
Proc. Natl. Acad. Sci.
99
, No. 15, 9888–9893 (2002).
V. Matys, O. V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B. Lewicki-Potapov, H. Saxel, A. E. Kel, and E. Wingender, “TRANSFAC
®
and Its Module TRANSCompel
®
Transcriptional Gene Regulation in Eukaryotes,”
Nucl. Acids Res.
34
, No. 1, D108–D110 (2006).
C. Lemer, E. Antezana, F. Couche, F. Fays, X. Santolaria, R. S. Janky, Y. Deville, J. Richelle, and S. J. Wodak, “The aMAZE LightBench: A Web Interface to a Relational Database of Cellular Processes,”
Nucl. Acids Res.
32
, D443–D448 (2004).
C. T. Harbison, D. B. Gordon, T. I. Lee, N. J. Rinaldi, K. D. Macisaac, T. W. Danford, N. M. Hannett, J.-B. Tagne, D. B. Reynolds, J. Yoo, E. G. Jennings, J. Zeitlinger, D. K. Pokholok, M. Kellis, P. A. Rolfe, K. T. Takusagawa, E. S. Lander, D. K. Gifford, E. Fraenkel, and R. A. Young, “Transcriptional Regulatory Code of a Eukaryotic Genome,”
Nature
431
, No. 7004, 99–104 (2004).
B. Ren, F. Robert, J. J. Wyrick, O. Aparicio, E. G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell, and R. A. Young, “Genome-Wide Location and Function of DNA Binding Proteins,”
Science
290
, No. 5500, 2306–2309 (2000).
J. Qian, J. Lin, N. M. Luscombe, H. Yu, and M. Gerstein, “Prediction of Regulatory Networks: Genome-Wide Identification of Transcription Factor Targets from Gene Expression Data,”
Bioinformatics
19
, No. 15, 1917–1926 (2003).
M. A. Beer and S. Tavazoie, “Predicting Gene Expression from Sequence,”
Cell
117
, No. 2, 185–198 (2004).
D. Holloway, M. Kon, and C. DeLisi, “Integrating Genomic Data to Predict Transcription Factor Binding,”
Proc. Workshop Genome Informatics
16
, No. 1, 83–94 (2005).
T. Jaakola, M. Diekhans, and D. Haussler, “Using the Fisher Kernel Method to Detect Remote Protein Homologies,”
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
, August 6–10, 1999, pp. 149–158.
S. Hua and Z. Sun, “A Novel Method of Protein Secondary Structure Prediction with High Segment Overlap Measure: Support Vector Machine Approach,”
J. Molec. Biol.
308
, No. 2, 397–407 (2001).
S. Hua and Z. Sun, “Support Vector Machine Approach for Protein Subcellular Localization Prediction,”
Bioinformatics
18
, No. 8, 721–728 (2001).
M. Wang, J. Yang, and K.-C. Chou, “Using String Kernel to Predict Signal Peptide Cleavage Site Based on Subsite Coupling Model,”
Amino Acids
28
, No. 4, 395–402 (2005).
T. S. Furey, N. Cristianini, N. Duffy, D. W. Bednarski, M. Schummer, and D. Haussler, “Support Vector Machine Classification and Validation of Cancer Tissue Samples Using Microarray Expression Data,”
Bioinformatics
16
, No. 10, 906–914 (2000).
P. Pavlidis and W. S. Noble, “Gene Functional Classification from Heterogeneous Data,”
RECOMB Conference Proceedings,
2001, pp. 249–255.
A. Zien, G. Ratsch, S. Mika, B. Scholkopf, T. Lengauer, and K.-R. Muller, “Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites,”
Bioinformatics
16
, No. 9, 799–807 (2000).
G. Lanckriet, N. Cristianini, M. Jordan, and W. S. Noble, “A Statistical Framework for Genomic Data Fusion,”
Bioinformatics
20
, No. 16, 2626–2635 (2004).
B. Scholkopf and A. J. Smola,
Learning with Kernels
, MIT Press, Cambridge, MA, 2002.
P.-N. Tan, M. Steinbach, and V. Kumar,
Introduction to Data Mining
, Addison-Wesley Publishing Co., Boston, MA, 2005.
D. Holloway, M. Kon, and C. DeLisi, “Machine Learning and Data Combination for Regulatory Pathway Prediction,”
Synthetic & Syst. Biol.
(2006), submitted.
T. I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J.-B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, and R. A. Young, “Transcriptional Regulatory Networks in Saccharomyces cerevisiae,”
Science
298
, No. 5594, 799–804 (2002).
P. Hodges, A. McKee, B. Davis, W. Payne, and J. Garrels, “The Yeast Proteome Database (YPD): A Model for the Organization and Presentation of Genome-Wide Functional Data,”
Nucl. Acids Res.
27
, No. 1, 69–73 (1999).
R. Young, “Transcriptional Regulatory Network”; see
http://staffa.wi.mit.edu/cgi-bin/young_public/navframe.cgi?s=17&f=evidence
.
M. Kellis et al., “Yeast Comparative Genomics”; see
http://www.broad.mit.edu/annotation/fungi/comp_yeasts/
(2003).
J. van Helden, “Regulatory Sequence Analysis Tools,”
Nucl. Acids Res.
31
, No. 13, 3593–3596 (2003).
E. Birney, T. D. Andrews, P. Bevan, M. Caccamo, Y. Chen, L. Clarke, G. Coates, J. Cuff, V. Curwen, T. Cutts, T. Down, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H.-R. Hotz, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, K. C. Woodwark, G. Cameron, R. Durbin, A. Cox, T. Hubbard, and M. Clamp, “An Overview of Ensembl,”
Genome Res.
14
, No. 5, 925–928 (2004).
R. L. Tatusov and D. J. Lipman, “National Center for Biotechnology Information, NCBI Toolkit”; see
http://www.ncbi.nlm.nih.gov/
.
A. Smit, R. Hubley, and P. Green, “Repeatmasker Open 3.0”; see
http://repeatmasker.org
.
S. Aerts, G. Thijs, B. Coessens, M. Staes, Y. Moreau, and B. De Moor, “Toucan: Deciphering the Cis-Regulatory Logic of Coregulated Genes,”
Nucl. Acids Res.
31
, No. 6, 1753–1764 (2003).
C. Harbison, E. Fraenkel, and R. Young, “Matrices for Motifs”; see
http://jura.wi.mit.edu/fraenkel/download/release_v24/final_set/Final_InTableS2_v24.motifs
.
E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Graf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. P. Hubbard, “Ensembl 2006,”
Nucl. Acids Res.
34
, No. 1, D556–D561 (2006).
J. E. Galagan, S. E. Calvo, K. A. Borkovich, E. U. Selker, N. D. Read, D. Jaffe, W. FitzHugh, L.-J. Ma, S. Smirnov, S. Purcell, B. Rehman, T. Elkins, R. Engels, S. Wang, C. B. Nielsen, J. Butler, M. Endrizzi, D. Qui, P. Ianakiev, D. Bell-Pedersen, M. A. Nelson, M. Werner-Washburne, C. P. Selitrennikoff, J. A. Kinsey, E. L. Braun, A. Zelter, U. Schulte, G. O. Kothe, G. Jedd, W. Mewes, C. Staben, E. Marcotte, D. Greenberg, A. Roy, K. Foley, J. Naylor, N. Stange-Thomann, R. Barrett, S. Gnerre, M. Kamal, M. Kamvysselis, E. Mauceli, C. Bielke, S. Rudd, D. Frishman, S. Krystofova, C. Rasmussen, R. L. Metzenberg, D. D. Perkins, S. Kroken, C. Cogoni, G. Macino, D. Catcheside, W. Li, R. J. Pratt, S. A. Osmani, C. P. C. DeSouza, L. Glass, M. J. Orbach, J. A. Berglund, R. Voelker, O. Yarden, M. Plamann, S. Seiler, J. Dunlap, A. Radford, R. Aramayo, D. O. Natvig, L. A. Alex, G. Mannhaupt, D. J. Ebbole, M. Freitag, I. Paulsen, M. S. Sachs, E. S. Lander, C. Nusbaum, and B. Birren, “The Genome Sequence of the Filamentous Fungus
Neurospora crassa
,”
Nature
422
, No. 6934, 859–868 (2003).
R. Dean, “Fungal Genomics Laboratory at North Carolina State University, Broad Institute of MIT and Harvard”; see
http://www.fungalgenomics.ncsu.edu
and
http://www.broad.mit.edu
.
P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston, “Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting,”
Science
301
, No. 5629, 71–76 (2003).
M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander, “Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements,”
Nature
423
, No. 6037, 241–254 (2003).
A. Halees, D. Leyfer, and Z. Weng, “Promoser: A Larger-Scale Mammalian Promoter and Transcription Start Site Identification Service,”
Nucl. Acids Res.
31
, No. 13, 3554–3559 (2003).
P. Pavlidis, I. Wapinski, and W. S. Noble, “Support Vector Machine Classification on the Web,”
Bioinformatics
20
, No. 4, 586–587 (2004).
J. Ihmels, S. Bergman, and N. Barkai, “Naama Barkai Group”; see
http://barkai-serv.weizmann.ac.il/GroupPage/
.
The Mathworks, “MATLAB: MATrix LABoratory”; see
http://www.mathworks.com/
.
J. Weston, A. Elisseeff, G. Bakir, and F. Sinz, “SPIDER: Object Oriented Machine Learning Library”; see
http://www.kyb.tuebingen.mpg.de/bs/people/spider/
.
J. C. Platt, “Probabilistic Outputs for Support Vector Machines and Comparisons to Regularized Likelihood Methods,” in
Advances in Large Margin Classifiers
, P. Bartlett, B. Schölkopf, D. Schuurmans, and A. Smola, Eds., MIT Press, Cambridge, MA, 2000.
N. Simonis, S. J. Wodak, G. N. Cohen, and J. van Helden, “Combining Pattern Discovery and Discriminant Analysis to Predict Gene Co-Regulation,”
Bioinformatics
20
, No. 15, 2370–2379 (2004).
F. Gao, B. Foat, and H. Bussemaker, “Defining Transcriptional Networks Through Integrative Modeling of mRNA Expression and Transcription Factor Binding Data,”
BMC Bioinformatics
5
, No.1, 31 (2004).
D. Goodsell and R. Dickerson, “Bending and Curvature Calculations in B-DNA,”
Nucl. Acids Res.
22
, No. 24, 5497–5503 (1994).
S. Parker, J. Greenbaum, G. Benson, and T. D. Tullius, “Structure-Based DNA Sequence Alignment,” poster presented at the 5th International Workshop in Bioinformatics and Systems Biology, Berlin, Germany, August 2005.
B. Balasubramanian, W. K. Pogozelski, and T. D. Tullius, “DNA Strand Breaking by the Hydroxyl Radical Is Governed by the Accessible Surface Areas of the Hydrogen Atoms of the DNA Backbone,”
Proc. Natl. Acad. Sci.
95
, No. 17, 9738–9743 (1998).
About IBM
Privacy
Contact