Embryonic stem cells (ESC) are capable of differentiating into cells and tissues of all three germ layers, but difficulties in predicting and controlling ESC differentiation limit the development of potential therapeutic applications in regenerative medicine from such cells. Various systematic methods have been used to decode the complex signaling pathways and gene regulatory networks (GRNs) that govern the ESC differentiation, by measuring the expression profiles after perturbing key transcription factors (TFs) [1] and protein–protein interactions (PPI) [2]. Though computational methods have been applied to model the complex dynamics underlying ESC differentiation [3], a systematic method to integrate available large-scale omics data for ESC differentiation and predict the key genes that drive lineage specific differentiation is still lacking.

We developed a novel regression-based network inference method by integrating temporal expression profiles from ESC differentiation, PPI data, and available knowledge regarding...

References

References
1.
Nishiyama
,
A.
,
Xin
,
L.
,
Sharov
,
A. A.
,
Thomas
,
M.
,
Mowrer
,
G.
,
Meyers
,
E.
,
Piao
,
Y.
,
Mehta
,
S.
,
Yee
,
S.
,
Nakatake
,
Y.
,
Stagg
,
C.
,
Sharova
,
L.
,
Correa-Cerro
,
L. S.
,
Bassey
,
U.
,
Hoang
,
H.
,
Kim
,
E.
,
Tapnio
,
R.
,
Qian
,
Y.
,
Dudekula
,
D.
,
Zalzman
,
M.
,
Li
,
M.
,
Falco
,
G.
,
Yang
,
H.-T.
,
Lee
,
S.-L.
,
Monti
,
M.
,
Stanghellini
,
I.
,
Islam
,
M. N.
,
Nagaraja
,
R.
,
Goldberg
,
I.
,
Wang
,
W.
,
Longo
,
D. L.
,
Schlessinger
,
D.
, and
Ko
,
M. S. H.
,
2009
, “
Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors
,”
Cell Stem Cell
,
5
(
4
), pp.
420
433
.10.1016/j.stem.2009.07.012
2.
Yousefi
,
M.
,
Hajihoseini
,
V.
,
Jung
,
W.
,
Hosseinpour
,
B.
,
Rassouli
,
H.
,
Lee
,
B.
,
Baharvand
,
H.
,
Lee
,
K.
, and
Salekdeh
,
G. H.
,
2012
, “
Embryonic Stem Cell Interactomics: The Beginning of a Long Road to Biological Function
,”
Stem Cell Rev.
,
8
(
4
), pp.
1138
1154
.10.1007/s12015-012-9400-9
3.
Zhang
,
J.
,
Li
,
L.
,
Peng
,
L.
,
Sun
,
Y.
, and
Li
,
J.
,
2013
, “
An Efficient Weighted Graph Strategy to Identify Differentiation Associated Genes in Embryonic Stem Cells
,”
PLoS One
,
8
(
4
), p.
e62716
.10.1371/journal.pone.0062716
4.
Schäfer
,
J.
, and
Strimmer
,
K.
,
2005
, “
An Empirical Bayes Approach to Inferring Large-Scale Gene Association Networks
,”
Bioinformatics
,
21
(
6
), pp.
754
764
.10.1093/bioinformatics/bti062
5.
Huang
,
T.
,
Liu
,
L.
,
Qian
,
Z.
,
Tu
,
K.
,
Li
,
Y.
, and
Xie
,
L.
,
2010
, “
Using GeneReg to Construct Time Delay Gene Regulatory Networks
,”
BMC Res. Notes
,
3
(
1
), pp.
142
151
.10.1186/1756-0500-3-142
6.
Zoppoli
,
P.
,
Morganella
,
S.
, and
Ceccarelli
,
M.
,
2010
, “
TimeDelay-ARACNE: Reverse Engineering of Gene Networks From Time-Course Data by an Information Theoretic Approach
,”
BMC Bioinf.
,
11
, pp.
154
168
.10.1186/1471-2105-11-154
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