Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: A new framework for identifying combinatorial regulation of
  transcription factors: a case study of the yeast cell cycle   By integrating heterogeneous functional genomic datasets, we have developed a
new framework for detecting combinatorial control of gene expression, which
includes estimating transcription factor activities using a singular value
decomposition method and reducing high-dimensional input gene space by
considering genomic properties of gene clusters. The prediction of cooperative
gene regulation is accomplished by either Gaussian Graphical Models or Pairwise
Mixed Graphical Models. The proposed framework was tested on yeast cell cycle
datasets: (1) 54 known yeast cell cycle genes with 9 cell cycle regulators and
(2) 676 putative yeast cell cycle genes with 9 cell cycle regulators. The new
framework gave promising results on inferring TF-TF and TF-gene interactions.
It also revealed several interesting mechanisms such as negatively correlated
protein-protein interactions and low affinity protein-DNA interactions that may
be important during the yeast cell cycle. The new framework may easily be
extended to study other higher eukaryotes.

25
The categories of this paper are: patt-sol
13
The categories of this paper are: quant-ph
36
The categories of this paper are: cmp-lg
7
The categories of this paper are: hep-th
5
The categories of this paper are: gr-qc
12
The categories of this paper are: nucl-th
19
The categories of this paper are: eess
21
The categories of this paper are: adap-org
30
The categories of this paper are: q-alg
4
The categories of this paper are: cond-mat
32
The categories of this paper are: atom-ph
28
The categories of this paper are: alg-geom
37
The categories of this paper are: supr-con
9
The categories of this paper are: nlin
29
The categories of this paper are: funct-an
1
The categories of this paper are: cs