The recent advances in microarray technology enabled the measurement of gene expression levels of samples over a series of time points. Unlike the traditional 2D microarray data, such experiments generate 3D (gene-sample-time) microarray data, which require specialized methods for analysis. In this study, we propose a novel tensor factorization model for modeling 3D microarray data. The model a...

Current techniques for visualising large-scale microarray data are unable to present temporal features without reducing the number of elements being displayed. This paper introduces a technique that overcomes this problem by combining a novel display technique, which operates over a continuous temporal subset of the time series, with direct manipulation of the parameters defining the subset.

Predictive clustering is a general framework that unifies clustering and prediction. This paper investigates how to apply this framework to cluster time series data. The resulting system, Clus-TS, constructs predictive clustering trees (PCTs) that partition a given set of time series into homogeneous clusters. In addition, PCTs provide a symbolic description of the clusters. The paper considers...

Microarray time-series data provides us a possible means for identification of transcriptional regulation relationships among genes. Currently, the most widely used method in determining whether or not two genes have a potential regulatory relationship is to measure their expressional similarity using Pearson’s correlation coefficient. Although this traditional correlation method has been succe...

A data warehouse for the integrated storage and visualisation of genome and experimental transcriptome and proteome data of human-pathogenic fungi was established. It provides tools for uploading images and corresponding data from microarray experiments, two-dimensional (2D) gel experiments and mass spectrometry (MS) analyses. All data are cross-linked. A user can find out, on which gels in the...

MOTIVATION Many biological systems operate in a similar manner across a large number of species or conditions. Cross-species analysis of sequence and interaction data is often applied to determine the function of new genes. In contrast to these static measurements, microarrays measure the dynamic, condition-specific response of complex biological systems. The recent exponential growth in microa...

The emerging technology of DNA chips and microarrays makes it possible to simultaneously analyze the expression of many genes, such as the whole set of genes in the completely sequenced genome. We have been developing a system for network oriented analysis and visualization of such genome-scale gene expression data. It projects the time-series data of gene expression pro les on the functional r...

This paper presents work to support collaborative visualisation and data analysis in the microarray time-series explorer (MaTSE) software. We introduce a novel visualisation component called the ‘pattern browser’ which is used to support the annotation and adjustment of user queries. This includes an explanation of why this component is required and how it can be used with our online pattern re...