BioInformatics

The bioinformatics group analyzes genetic, epigenetic, transcriptomic and proteomic data from basic research and clinical trials and develops necessary software and databases.

Group Leader: Dr Wei

Bioinformatics Facility

The bioinformatics group analyzes genomic (i.e., SNP, promoter and CpG-island microarrays and next generation sequencing), transcriptomic (i.e., Affymetrix expression and exon microarrays, RNA-seq) and proteomic (i.e., ELISA and MALDI-TOF MS) data from basic research and clinical trials and develops necessary software and databases. It advises researchers on experimental design and does both low level and high level analyses.

Low level analyses involve data quality assessment, background subtraction and normalization. High level analyses involve the identification of abnormal genomic regions and differentially expressed genes and proteins and the classification of patient samples using supervised and unsupervised analyses, such as ANOVA, multiple regression, hierarchical clustering, principle component analysis, logistic regression, partial least square analysis and neural network. The results are presented according to the requirements of individual research projects.

The facility also provides advice on gene ontology analysis, promoter analysis and building gene interaction networks.
Commercial software, such as Expression Console, Genotyping Console, Affymetrix Power tools, IGB, MatLab and PLS_Toolbox, and academic software, such as Bioconductor, SAM, dChip, PAINT, CisGenome, CytoScape and SNVMix is used. In addition, new computer programs are developed using several programming languages such as R, VBA, MatLab and C#.

The bioinformatics facility uses a combination of locally installed and public databases. It is involved in several aspects of cancer research, for example, (i) the identification of human genes whose expression are significantly changed following some treatment such as EBV virus infection, irradiation, demethylation or addition of CD40 ligand, or (ii) genes that are up or down regulated at different stages of tumour development, and (iii) the diagnosis and prognosis of cancers according to ELISA and mass spectrum data of blood and urine samples.

 

Selected papers...

 

Automated Pub Med Search for Dr. Wenbin Wei

Lim, K. P., et al. (2011). "Fibroblast gene expression profile reflects the stage of tumour progression in oral squamous cell carcinoma." J Pathol 223: 459-469.

Lu, X.,et al. (2011). "Therapeutic targeting the loss of the birt-hogg-dube suppressor gene." Mol Cancer Ther 10(1): 80-9.

Murray, P. G., et al. (2010). "Epigenetic Silencing of a Proapoptotic Cell Adhesion Molecule, the Immunoglobulin Superfamily Member IGSF4, by Promoter CpG Methylation Protects Hodgkin Lymphoma Cells from Apoptosis." Am J Pathol 177: 1480-1490.

Caldwell, G. M., et al. (2010). "Wnt signalling in adenomas of familial adenomatous polyposis patients." Br J Cancer 103(6): 910-7.

Ward, D. G.,et al. (2010). "Detection of pancreatic adenocarcinoma using circulating fragments of fibrinogen." Eur J Gastroenterol Hepatol 22(11): 1358-63.

Wei, W.,et al. (2010). "10 Years of SELDI: What Have We Learnt?" Current Proteomics 7 (1): 15-25.

Birgersdotter, A.,et al. (2010). "Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas." Am J Clin Pathol 133(2): 271-80.

Birgersdotter, A., et al. (2009). "Inflammation and tissue repair markers distinguish the nodular sclerosis and mixed cellularity subtypes of classical Hodgkin's lymphoma." Br J Cancer 101(8): 1393-401.

Rathinam, S., et al. (2009). "Confounding Effects of Benign Lung Diseases on Nonsmall Cell Lung Cancer Serum Biomarker Discovery." Clin Proteom 5(3-4): 148-155.

Shah, K. M., et al. (2009). "The EBV-encoded latent membrane proteins, LMP2A and LMP2B, limit the actions of interferon by targeting interferon receptors for degradation." Oncogene. 28: 3903–3914.

Mohri, Y., et al. (2009). "Identification of macrophage migration inhibitory factor and human neutrophil peptides 1-3 as potential biomarkers for gastric cancer." Br J Cancer 101(2): 295-302.

Yap, L. F., et al. (2009). "Upregulation of Eps8 in oral squamous cell carcinoma promotes cell migration and invasion through integrin-dependent Rac1 activation." Oncogene 28(27): 2524-34.

Rogers, L. J., et al. (2009). "Chemoradiation in advanced vulval carcinoma." Int J Gynecol Cancer 19(4): 745-51.

Chidrawar, S., et al. (2009). "Cytomegalovirus-seropositivity has a profound influence on the magnitude of major lymphoid subsets within healthy individuals." Clin Exp Immunol 155(3): 423-32.

Bose, S., et al. (2009). "The ATM tumour suppressor gene is down-regulated in EBV-associated nasopharyngeal carcinoma. " J Pathol, 217, 345-52.