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Resource:A statistical framework for genomic data fusion

Name: Resource:A statistical framework for genomic data fusion
Description: A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins.

The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data.

Matlab code to center a kernel matrix and Matlab code for normalization are available.
Parent Organization: University of Washington; Washington; USA
Resource Type(s): Data set, Source code
Resource: Resource
URL: http://noble.gs.washington.edu/proj/sdp-svm/
Id: nlx_149420
PMID: PMID 15130933
Keywords: kernel matrix, random, gene expression, BLAST, Smith-Waterman, Pfam HMM, Hydrophobicity FFT, Linear interaction, diffusion kernel, protein, membrane, Ribosomal
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Facts about Resource:A statistical framework for genomic data fusionRDF feed
CurationStatusCurated  +
DefiningCitationhttp://noble.gs.washington.edu/proj/sdp-svm/  +
DefinitionA statistical framework for genomic data f A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins.

The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data.

Matlab code to center a kernel matrix and Matlab code for normalization are available.
tlab code for normalization are available.
Has default formThis property is a special property in this wiki.Resource  +
Has roleData set  +, and Source code  +
Idnlx_149420  +
Is part ofUniversity of Washington; Washington; USA  +
KeywordsKernel matrix  +, Random  +, Gene expression  +, BLAST  +, Smith-Waterman  +, Pfam HMM  +, Hydrophobicity FFT  +, Linear interaction  +, Diffusion kernel  +, Protein  +, Membrane  +, and Ribosomal  +
LabelResource:A statistical framework for genomic data fusion  +
ModifiedDate31 July 2012  +
PMID15130933  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +