Download Analysis of Microarray Data: A Network-Based Approach by Frank Emmert-Streib, Matthias Dehmer PDF

By Frank Emmert-Streib, Matthias Dehmer

ISBN-10: 3527318224

ISBN-13: 9783527318223

This ebook is the 1st to target the appliance of mathematical networks for interpreting microarray facts. this technique is going well past the normal clustering tools normally used.

From the contents:

  • Understanding and Preprocessing Microarray information
  • Clustering of Microarray info
  • Reconstruction of the Yeast mobilephone Cycle through Partial Correlations of upper Order
  • Bilayer Verification set of rules
  • Probabilistic Boolean Networks as versions for Gene rules
  • Estimating Transcriptional Regulatory Networks by way of a Bayesian community
  • Analysis of healing Compound results
  • Statistical tools for Inference of Genetic Networks and Regulatory Modules
  • Identification of Genetic Networks by way of Structural Equations
  • Predicting practical Modules utilizing Microarray and Protein interplay facts
  • Integrating effects from Literature Mining and Microarray Experiments to deduce Gene Networks

The booklet is for either, scientists utilizing the method in addition to these constructing new research recommendations.

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Extra info for Analysis of Microarray Data: A Network-Based Approach

Example text

In early work, Affymetrix performed a careful examination of characteristics required for the design of probes from which hybridization signals could be used to determine relative expression level of a gene from a complex sample. An array consisting of 16 000 probes was used to examine the expression of just 12 genes [14]. By making hundreds of probes per gene and then examining the characteristics of the probes that most accurately reported the expression level of the gene, a set of heuristic probe design criteria was derived.

Although PCR products serve as effective array reagents, because they are easy to produce and they stick well to glass without advanced chemistry, they can also be a source of error and variability. For instance, early attempts to create yeast genome microarrays representing more than 6000 yeast genes involved weeks and months of effort to perform 6000 PCR reactions with a typical success rate of 85%. The resulting library represented a collection of printable DNA fragments at various concentrations and of varying purity.

2000) A cultivated taste for yeast. Genome Biology, 1 (1), 1031– 1034. M. (1994) Molecular computation of solutions to combinatorial problems. Science, 266 (5187), 1021– 1024. Amos, M. (2005) Theoretical and Experimental DNA Computation, Springer. Gillespie, D. and Spiegelman, S. (1965) A quantitative assay for DNA–RNA hybrids with DNA immobilized on a membrane. Journal of Molecular Biology, 12 (3), 829–842. J. R. (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzylmethyl-paper and hybridization with DNA probes.

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