Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Integration of Differential Gene-combination Search and Gene Set
  Enrichment Analysis: A General Approach   Gene Set Enrichment Analysis (GSEA) and its variations aim to discover
collections of genes that show moderate but coordinated differences in
expression. However, such techniques may be ineffective if many individual
genes in a phenotype-related gene set have weak discriminative power. A
potential solution is to search for combinations of genes that are highly
differentiating even when individual genes are not. Although such techniques
have been developed, these approaches have not been used with GSEA to any
significant degree because of the large number of potential gene combinations
and the heterogeneity of measures that assess the differentiation provided by
gene groups of different sizes.
  To integrate the search for differentiating gene combinations and GSEA, we
propose a general framework with two key components: (A) a procedure that
reduces the number of scores to be handled by GSEA to the number of genes by
summarizing the scores of the gene combinations involving a particular gene in
a single score, and (B) a procedure to integrate the heterogeneous scores from
combinations of different sizes and from different gene combination measures by
mapping the scores to p-values. Experiments on four gene expression data sets
demonstrate that the integration of GSEA and gene combination search can
enhance the power of traditional GSEA by discovering gene sets that include
genes with weak individual differentiation but strong joint discriminative
power. Also, gene sets discovered by the integrative framework share several
common biological processes and improve the consistency of the results among
three lung cancer data sets.

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The categories of this paper are: math-ph
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The categories of this paper are: quant-ph
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The categories of this paper are: ao-sci
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The categories of this paper are: atom-ph
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The categories of this paper are: adap-org
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The categories of this paper are: hep-ph
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The categories of this paper are: supr-con
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The categories of this paper are: plasm-ph
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The categories of this paper are: funct-an
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The categories of this paper are: physics
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The categories of this paper are: cond-mat
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The categories of this paper are: nlin
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The categories of this paper are: stat
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The categories of this paper are: hep-th
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The categories of this paper are: nucl-th
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The categories of this paper are: mtrl-th