Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: A hidden spatial-temporal Markov random field model for network-based
  analysis of time course gene expression data   Microarray time course (MTC) gene expression data are commonly collected to
study the dynamic nature of biological processes. One important problem is to
identify genes that show different expression profiles over time and pathways
that are perturbed during a given biological process. While methods are
available to identify the genes with differential expression levels over time,
there is a lack of methods that can incorporate the pathway information in
identifying the pathways being modified/activated during a biological process.
In this paper we develop a hidden spatial-temporal Markov random field
(hstMRF)-based method for identifying genes and subnetworks that are related to
biological processes, where the dependency of the differential expression
patterns of genes on the networks are modeled over time and over the network of
pathways. Simulation studies indicated that the method is quite effective in
identifying genes and modified subnetworks and has higher sensitivity than the
commonly used procedures that do not use the pathway structure or time
dependency information, with similar false discovery rates. Application to a
microarray gene expression study of systemic inflammation in humans identified
a core set of genes on the KEGG pathways that show clear differential
expression patterns over time. In addition, the method confirmed that the
TOLL-like signaling pathway plays an important role in immune response to
endotoxins.

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The categories of this paper are: cond-mat
29
The categories of this paper are: funct-an
25
The categories of this paper are: patt-sol
31
The categories of this paper are: ao-sci
36
The categories of this paper are: cmp-lg
34
The categories of this paper are: chem-ph
23
The categories of this paper are: solv-int
18
The categories of this paper are: econ
21
The categories of this paper are: adap-org
35
The categories of this paper are: mtrl-th
3
The categories of this paper are: physics
30
The categories of this paper are: q-alg
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The categories of this paper are: nlin
22
The categories of this paper are: chao-dyn
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The categories of this paper are: gr-qc
11
The categories of this paper are: hep-lat