Zuguang Gu's Website

DATABASES

InterMitoBase is an integrated platform providing high quality protein-protein interaction (PPI) data in human mitochondrion and useful tools to analysis PPI network.

Currently there are 490 proteins locating in mitochondrion and 2323 proteins outside mitochondrion that exist in the mitochondrial PPI network. There are totally 5883 non-redundant interactions in the database. Among them, 1640 interactions are new that have not been coverd in other PPI databases such as HPRD, BioGrid, DIP and IntAct.

TiMoD

Tissue Specific Transcriptional Regulatory Network Motif Database

The network contains transcription factors, microRNAs and genes. The network was constructed from target predicted interactions for each tissue. Motif is basic mode of interactions. Currently the database provide motifs containing three nodes. Interactions in the motifs have been manually curated.

SOFTWARES

CePa

CePa is a useful tool to find significant pathways from pathway structure information. The motivation of the software is that the traditional over-representation analysis (ORA) methods find significant pathways without the topological information. The tool also emphasizes that multiple choices to look for important nodes in network is necessary.

SiGPAT

SiGPAT is a useful tool based on gene set analysis for microarray data. It can find significant expression patterns of gene sets by pri-defined biological knowledge. To be unique to other tools, SiGPAT assignes two statistics for each gene sets and classifies expression patterns of gene sets form two dimension distribution of set-level statistics. The tool was evaluated with better performance than current tools such as GSEA and SAM-GS

SGS

The methodology is based on the view that genes being more differentially expressed play more important roles in the gene expression profile. Therefore, a weighted distribution of gene expression is included to calculate the extent of up-regulation and down-regulation of the gene set. Two kinds of cutoffs are introduced to determine the gene sets which are both biological reasonable and statistical significant. Our method can effectively decrease the false positive predictions caused by the large size of gene set. To suit the analysis of microarray data with various experimental designs, including few repeats or multiple conditions, three models were proposed in SGS.

cDNA microarray analysis platform

We developed a cDNA microarray data analysis platform providing a lot of tools for microarray data analysis including seven modules which include data import, visualization, preparation of data, finding differentially expressed genes, cluster, gene set analysis and transcriptional regulation analysis. Users are independent from others and so are the sets of data. The platform makes the microarray data as the center and the gene list as the key through it.