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.
Download
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)
clustex-0.32_eppstein
(extended with
non-simple k-shortest paths) [Latest Version]
1. The biggest responsive gene modules
Figure 2.
TNF responsive module (284
genes) [View & Download]
Figure 4. VEGF
responsive module (262
genes) [View & Download]
2. Reference responsive 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)
3. 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]
4. 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/~gujin/)
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