A prognostic model for the combined analysis of gene expression profiling in hepatocellular carcinoma.
Journal Title: Bioinformation - Year 2008, Vol 2, Issue 9
Abstract
Microarray techniques using cDNA array and comparative genomic hybridization (CGH) have been developed for several discovery applications. They are frequently applied for the prediction and diagnosis of cancer in recent years. Many studies have shown that integrating genomic data from different sources may increase the reliability of gene expression analysis results in understanding cancer progression. Therefore, developing a good prognostic model dealing simultaneously with different types of dataset is important. The challenge with these types of data is high background noise. We describe an analytical two-stage framework with a multi-parallel data analysis method named wavelet-based generalized singular value decomposition and shaving method (WGSVD-shaving). This method is proposed for de-noising and dimension-reduction during early stage prognosis modeling. We also applied a supervised gene clustering technique with penalized logistic regression with Cox-model on an integrated data. We show the accuracy of the method using a simulated dataset with a case study on Hepatocelluar Carcinoma (HCC) cDNA and CGH data. The method shows improved results from GSVD-shaving and has application in the discovery of candidate genes associated with cancer.
Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma.
Previous studies have been conducted in gene expression profiling to identify groups of genes that characterize the colorectal carcinoma disease. Despite the success of previous attempts to identify groups of genes in th...
Modeling of pyruvate decarboxylases from ethanol producing bacteria.
Pyruvate decarboxylase (PDC) is a key enzyme in homoethanol fermentation process, which decarboxylates 2-keto acid pyruvate into acetaldehyde and carbon dioxide. PDC enzymes from potential ethanol-producing bacteria such...
BrainSnail: a dynamic information display system for the sciences.
Scientific reference management has become crucial in rapidly expanding fields of biology. Many of the reference management systems currently employed are reference centric and not object/process focused. BrainSnail is a...
Binding site prediction of galanin peptide using evolutionary trace method.
Galanin is a neuropeptide with aminoacid length ranging from 29 to 31 is widely distributed in central and peripheral nervous system. Galanin controls various psychological processes such as sensation of pain, learning,...
In silico Construction of phosphomannose isomerase (PMI) transformation vectors and evaluation of the effectiveness of vectors in tobacco (Nicotiana tabacum L.)
Phosphomannose isomerase (pmi) gene isolated from Escherichia coli allows transgenic plants carrying it to convert mannose-6-phosphate (from mannose), a carbon source that could not be naturally utilized by plants into f...