Analysis of Whole-Genome Tiling Microarrays

Using whole genome tiling arrays allows us to study the plasticity of the Arabidopsis transcriptome under numerous conditions. The aspects monitored include expression measurements of known genes; detection of transcription factor binding sites; identification of new, previously uncharacterized genes and alternative splicing events; assessing differential expression of known and new genes under abiotic stresses as well as for a number of mutants in proteins required for mRNA capping, splicing, and biogenesis of small RNAs.

People specializing in this area

Group Leader

Gunnar Rätsch, Ph.D.

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Graduate Students

Jonas Behr

I have been working on methods to efficiently incorporate transcriptome measurements like tiling array data and RNA-Seq data into our gene finding system mGene. Results show substantial improvements in prediction accuracy of protein coding genes compared to ab-initio gene finding methods.

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Alumnae and Alumni

Johannes Eichner

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Georg Zeller, Ph.D.

I have been developing methods for normalization and segmentation of tiling array data with the aims to i) reduce probe sequence effects on hybridization intensity and ii) in comparison to existing methods more accurately segment transcribed exons out of the intergenic/intronic background.

The normalization and segmentation methods have been applied to 11 Arabidopsis tissues and developmental stages aiming to identify new transcripts. Moreover, based on tiling arrays we globally assessed transcriptome changes upon abiotic stress treatment identifying several hundred new, stress-induced transcripts.

A further subproject is aimed at the identification of alternative splicing events, primarily intron retention events, from tiling array data. We approach this task as a two-step classification problem: First, a classifier is trained to discriminate between exons and introns. Subsequently, introns with a large inclusion probability in some tissue are identified as bona fide candidates for alternative splicing by a second classifier.

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Publications

• Eichner, J, Zeller, G, Laubinger, S, and Rätsch, G (2011).
  Detection of Alternative Splicing in Arabidopsis thaliana from Whole-Genome Tiling Arrays with Support Vector Machines
  BMC Bioinformatics, 12(55).
  Supplementary website http://www.biomedcentral.com/1471-2105/12/55

• Laubinger, S, Zeller, G, Henz, SR, Buechel, S, Sachsenberg, T, Wang, J, Rätsch, G, and Weigel, D (2010).
  Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome
  PNAS.
  Supplementary website http://www.pnas.org/content/early/2010/09/21/1012891107
  Printable file

• Zeller, G, Henz, SR, Widmer, CK, Sachsenberg, T, Rätsch, G, Weigel, D, and Laubinger, S (2009).
  Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays
  Plant Journal, 58(6):1068-1082.
  Supplementary website http://www.weigelworld.org/resources/microarray/at-tax
  Printable file

• Naouar, N, Vandepoele, K, Lammens, T, Casneuf, T, Zeller, G, van Hummelen, P, Weigel, D, Rätsch, G, Inzé, D, Kuiper, M, De Veylder, L, and Vuylsteke, M (2009).
  Quantitative RNA expression analysis with Affymetrix Tiling 1.0R Arrays identifies new E2F target genes
  Plant Journal, 57(1):184-194.
  Printable file

• Zeller, G (2009).
  Machine Learning Algorithms for the Analysis of Data from Whole-Genome Tiling Microarrays
  PhD thesis, Universitaet Tuebingen.
  Supplementary website http://nbn-resolving.de/urn:nbn:de:bsz:21-opus-47351
  Printable file

• Plantegenet, S, Weber, J, Goldstein, DR, Zeller, G, Nussbaumer, C, Thomas, J, Weigel, D, Harshmann, K, and Hardtke, CS (2009).
  Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance
  Molecular Systems Biology, 5:Article 242.
  Printable file

• Zeller, G, Henz, S, Laubinger, S, Weigel, D, and Rätsch, G (2008).
  Transcript Normalization and Segmentation of Tiling Array Data
  In: Pacific Symposium on Biocomputing, vol. 13, pp. 527-538, Stanford, World Scientific.
  Supplementary website http://www.fml.tuebingen.mpg.de/raetsch/projects/PSBTiling
  Printable file

• Laubinger, S, Zeller, G, Henz, S, Sachsenberger, T, Widmer, C, Naouar, N, Vuylsteke, M, Schölkopf, B, Rätsch, G, and Weigel, D (2008).
  At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
  Genome Biology, 9:R112.
  Supplementary website http://www.weigelworld.org/resources/microarray/at-tax
  Printable file

• Laubinger, S, Sachsenberg, T, Zeller, G, Busch, W, Lohmann, J, Rätsch, G, and Weigel, D (2008).
  Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
  PNAS, 105(25):8795-8800.
  Printable file

• Behr, J (2008).
  Improving Gene Finding Accuracy with Tiling Array and RNA-Seq Data
  Diplom Thesis, Jonas Behr.

• Zeller, G (2005).
  Resequencing Data of 20 Arabidopsis Ecotypes
  Diplomarbeit, Universität Tübingen.
  Printable file