ClustEx:
identification of responsive gene modules by network-based gene clustering
and extending [2012/05/03 Updated, v0.32]
Citation: Jin Gu, Yang Chen, Shao Li, Yanda Li. Identification of
responsive gene modules by network-based gene clustering and extending:
application to inflammation and angiogenesis. BMC Systems Biology 2010,
4:47. [Full Text]
Applications:
[1] Analyze the "regulation of cell cycle" gene
module of TNF treatment. Yang Chen*, Jin Gu*, Dan Li, Shao Li.
Time-course network analysis reveals TNF-alpha can promote G1/S transition
of cell cycle in vascular endothelial cells. Bioinformatics 2012, 28(1):1-4.
[2] Identify the gene modules associated with
different cellular processes of vascular endothelial cells. Jin Gu#,
Shao Li#. Towards integrative annotating the cell-type specific gene
functional and signaling map in vascular endothelial cells. Molecular
BioSystems 2012, 8(8):2041-2049.
Package Download
clustex-0.32_eppstein
(extended with non-simple k-shortest paths)
clustex-0.31_eppstein
(extended with non-simple k-shortest paths)
clustex-0.31_KSP (extended
with simple k-shortest paths)
clustex-0.1 (original package)
The source data and results for the
BMC Systems Biology paper
The biggest responsive gene modules
Figure 2. TNF responsive
module (284 genes)
[View & Download]
Figure 4. VEGF responsive module (262
genes) [View & Download]
Reference gene sets (only include the genes
both in Affy U133Plus2/U133A platform and HPRD release 7)
TNFLitRef (376 genes, retrieved 998 abstracts from PubMed, processed by
Agilent Literature Cytoscape plug-in)
TNFNetPathRef (184 genes, NetPath database TNF/NF-kB signaling pathway)
TNFPathDBRef (63 genes, BioCarta/PID/Reactome related pathways)
VEGFLitRef (342 genes, retrieved 871 abstracts from PubMed, processed by
Agilent Literature Cytoscape plug-in)
VEGFPathDBRef (109 genes, BioCarta/PID/KEGG related pathways)
dChip processed signal files
(log-transformed)
TNF (GSE9055, TNF 10ng/ml, HUVEC, 0~8h, 25
time points, Affy Human U133Plus2.0 & HPRD7)
[Download]
VEGF (GSE10778, VEGF 100ng/ml, HUVEC,
0~6h, 5 time points, Affy Human U133A & HPRD7)
[Download]
Fold changes (log-transformed: 1 = 2 fold
change) & expression correlations
TNF
Fold_changes
Expression_correlations
VEGF
Fold_changes
Expression_correlations
Any problem please contact Jin Gu
(wellgoo at gmail dot com)
Personal site (http://bioinfo.au.tsinghua.edu.cn/member/jgu/)
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