ClustEx: identification of responsive gene modules by network-based gene clustering and extending [2012/05/03 Updated, v0.32]


[NEW!] ClustEx 2.0

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/)