Abstract: Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.
Abstract: DNA microarrays allow the measurement of expression levels for a large number of genes, perhaps all genes of an organism, within a number of different experimental samples. It is very much important to extract biologically meaningful information from this huge amount of expression data to know the current state of the cell because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find association relationship between genes. Numerous association rule mining algorithms have been developed to analyze and associate this huge amount of gene expression data. This paper focuses on some of the popular association rule mining algorithms developed to analyze gene expression data.
Abstract: This paper gives a novel method for improving
classification performance for cancer classification with very few
microarray Gene expression data. The method employs classification
with individual gene ranking and gene subset ranking. For selection
and classification, the proposed method uses the same classifier. The
method is applied to three publicly available cancer gene expression
datasets from Lymphoma, Liver and Leukaemia datasets. Three
different classifiers namely Support vector machines-one against all
(SVM-OAA), K nearest neighbour (KNN) and Linear Discriminant
analysis (LDA) were tested and the results indicate the improvement
in performance of SVM-OAA classifier with satisfactory results on
all the three datasets when compared with the other two classifiers.
Abstract: The most common result of analysis of highthroughput
data in molecular biology represents a global list of
genes, ranked accordingly to a certain score. The score can be a
measure of differential expression. Recent work proposed a new
method for selecting a number of genes in a ranked gene list from
microarray gene expression data such that this set forms the
Optimally Functionally Enriched Network (OFTEN), formed by
known physical interactions between genes or their products. Here
we present calculation results of relative connectivity of genes from
META-OFTEN network and tentative biological interpretation of the
most reproducible signal. The relative connectivity and
inbetweenness values of genes from META-OFTEN network were
estimated.