Showing papers on "Gene expression profiling published in 1998"

Cluster analysis and display of genome-wide expression patterns

Abstract: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is de- scribed that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be inter- preted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly charac- terized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.

Gene Expression Profiling of Alveolar Rhabdomyosarcoma with cDNA Microarrays

Abstract: Several forms of human sarcoma, lymphoma, and leukemia are characterized by somatically acquired chromosome translocations that result in fusion genes that encode chimeric transcription factors with oncogenic properties. We have used cDNA microarrays containing 1238 cDNAs to investigate the gene expression profile of a group of seven alveolar rhabdomyosarcoma (ARMS) cell lines characterized by the presence of the PAX3-FKHR fusion gene. Using the method of multidimensional scaling to represent the relationships among the cell lines in two-dimensional Euclidean space, we determined that ARMS cells show a consistent pattern of gene expression, which allows the cells to be clustered together. By searching across the seven ARMS cell lines, we found that 37 of 1238 genes were most consistently expressed in ARMS relative to a reference cell line. Only three of these genes have been previously reported to be expressed in ARMS. Among these 37 were genes related to both primary (PAX3-FKHR) and secondary (CDK4) genetic alterations in ARMS. These results in ARMS demonstrate the potential of cDNA microarray technology to elucidate tumor-specific gene expression profiles in human cancers.

High throughput analysis of differential gene expression.

Abstract: Elucidation of the changes in gene expression associated with biological processes is a central problem in biology. Advances in molecular and computational biology have led to the development of powerful, high-thoughput methods for the analysis of differential gene expression. These tools have opened up new opportunities in disciplines ranging from cell and developmental biology to drug development and pharmacogenomics. In this review, the attributes of five commonly used differential gene expression methods are discussed: expressed sequence tag (EST) sequencing, cDNA microarray hybridization, subtractive cloning, differential display, and serial analysis of gene expression (SAGE). The application of EST sequencing and microarray hybridization is illustrated by the discovery of novel genes associated with osteoblast differentiation. The application of subtractive cloning is presented as a tool to identify genes regulated in vivo by the transcription factor pax-6. These and other examples illustrate the power of genomics for discovering novel genes that are important in biology and which also represent new targets for drug development. The central theme of the review is that each of the approaches to identifying differentially expressed genes is useful, and that the experimental context and subsequent evaluation of differentially expressed genes are the critical features that determine success. J. Cell. Biochem. Suppls. 30/31:286-296, 1998. © 1998 Wiley-Liss, Inc.

Mining the gene expression matrix: inferring gene relationships from large scale gene expression data

Abstract: In order to infer the logical principles underlying biological development and phenotypic change, it is necessary to determine large-scale temporal gene expression patters. To quote Eric Lander, “The mRNA levels sensitively reflect the state of the cell, perhaps uniquely defining cell types, stages, and responses. To decipher the logic of gene regulation, we should aim to be able to monitor the expression level of all genes simultaneously…” (Lander, 1996). One method for accomplishing this involves the use of reverse transcription polymerase chain reaction (RT-PCR) to assay the expression levels of large numbers of genes in a tissue at different time points during development, with a standard protocol. The relative amounts of mRNA produced at these time points provide a gene expression time series for each gene.

Expression profiling of single cells using 3 prime end amplification (TPEA) PCR

Abstract: The ability to relate the physiological status of individual cells to the complement of genes they express is limited by current methodological approaches for performing these analyses. We report here the development of a robust and reproducible method for amplifying 34 sequences of mRNA derived from single cells and demonstrate that the amplified cDNA, derived from individual human lymphoblastoma cells, can be used for the expression profiling of up to 40 different genes per cell. In addition, we show that 3 prime end amplification (TPEA) PCR can be used to enable the detection of both high and low abundance mRNA species in samples harvested from live neurons in rat brain slices. This procedure will facilitate the study of complex tissue function at the cellular level.

Comparative gene expression profiling by oligonucleotide fingerprinting

Abstract: The use of hybridisation of synthetic oligonucleotides to cDNAs under high stringency to characterise gene sequences has been demonstrated by a number of groups. We have used two cDNA libraries of 9 and 12 day mouse embryos (24 133 and 34 783 clones respectively) in a pilot study to characterise expressed genes by hybridisation with 110 hybridisation probes. We have identified 33 369 clusters of cDNA clones, that ranged in representation from 1 to 487 copies (0.7%). 737 were assigned to known rodent genes, and a further 13 845 showed significant homologies. A total of 404 clusters were identified as significantly differentially represented (P < 0.01) between the two cDNA libraries. This study demonstrates the utility of the fingerprinting approach for the generation of comparative gene expression profiles through the analysis of cDNAs derived from different biological materials.

Gene expression profile of the intima and media of experimentally induced cerebral aneurysms in rats by laser-microdissection and microarray techniques.

Abstract: Cerebral aneurysm is a common disease with a high prevalence and can cause a catastrophic subarachnoid hemorrhage. To elucidate the molecular mechanism of the formation and progression of cerebral aneurysms, gene expression profiling was performed in experimentally induced rat cerebral aneurysms. The intima and media of cerebral arterial walls in rats with or without aneurysm induction were dissected respectively by a laser-microdissection technique. Changes in gene expression in the intima and media of aneurysmal walls were analyzed using Agilent Rat Oligo Microarrays, followed by a specific pathway analysis using GeneSpring software. Of the 41,012 genes examined, 633 were differentially expressed between a normal cerebral artery and a cerebral aneurysm in the intima, with 395 showing increased expression and 238 showing decreased expression. In the media, 1344 were differentially expressed, with 928 showing increased expression and 416 showing decreased expression. Specific pathway analysis revealed that increased gene expression was associated with proteinase, reactive oxygen species, growth factor, chemokine, complement, adhesion molecule and apoptosis in both the intima and the media of aneurysmal walls. Some genes showed an opposite expression pattern between the intima and the media indicating a different role between endothelial cells and vascular smooth muscle cells in cerebral aneurysm formation and progression. These data suggest that cerebral aneurysmal formation and progression are closely related to vascular inflammation, degeneration of extracellular matrix and apoptosis.

A method for analyzing the qualitative and quantitative aspects of gene expression: A transcriptional profile revealed for HeLa cells

Abstract: A number of strategies have been devised by which differentially expressed genes in different cell types or tissues can be identified We here report an efficient method to analyze the qualitative and quantitative aspects of transcripts and to construct an extensive gene expression profile in any kind of cell or tissue of interest This method enables us to analyze the composition of mRNA species, reflecting gene activities, by measuring the frequency of appearance of concatamerized 17mer cDNA mini-fragments, which are proportional to the abundance of mRNA As compared with a related method previously described by others, we can analyze approximately 3-4 bp longer cDNA fragments derived from amounts of total RNA as small as 1 microg Using this technique we examined 10 100 cDNA mini-fragments from HeLa cells and constructed a gene expression profile consisting of 3665 genes This method should thus provide an overall indication of gene activities and a rational means for monitoring gene fluctuation in different cells or tissues at different stages of development, in normal and disease states

Toxicogenomics screening of small molecules using high-density, nanocapillary real-time PCR.

Abstract: Compounds which induce toxicity through similar mechanisms lead to characteristic gene expression patterns. The concept that structurally similar compounds may have similar biological profiles, the so-called generalized neighborhood behavior, is less obvious to be demonstrated. We screened 625 compounds from a fully combinatorial library for their gene expression profiles in vitro over a selected toxicity panel of 56 genes. We used the novel nanocapillary, quantitative real-time PCR OpenArray technology that is coupling outstanding analytical performance with the medium-throughput ideal for such a sample-per-feature ratio. Applying a hybrid clustering on the gene expression data, correlation was analyzed between molecular scaffold and biological fingerprint. Structurally highly dissimilar, but similarly hepatotoxic compounds show similar fingerprint on our toxicity panel, however compounds of the same scaffold and of unknown biological effect do not always share similar fingerprints. Out of 12 different scaffolds, 4 families show non-correlating, uniform distribution among clusters whilst 8 families show neighborhood behavior of varying strength. Structurally not similar compounds may have highly similar biological activity, on the other hand, compounds of the same scaffold family do not all share the same biological effects based on toxicology related gene expression fingerprint.

Cell Type-Specific mRNA Amplification and Expression Profiling from Breast Tumor Sections

Abstract: : The evolution of solid tumors involves acquisition of genetic abnormalities, which result in changes in both the set of genes expressed and the relative levels of gene expression. However, the increasing number of candidate genes whose expression needs to be evaluated for prognostic, diagnostic, therapeutic, or research purposes will require obtaining material from numerous tissue sections. Therefore this proposal is motivated by the need for more effective use of clinical specimens, and will address the problem of obtaining sufficient and cell type specific mRNA from clinical breast tumor specimens. This will entail adapting/developing procedures to amplify with fidelity the mRNA repertoire expressed in small numbers of normal, pre-cancerous and malignant breast epithelia. To this end, in this project period, we have concentrated effort on establishing and validating microarray-based assays for measuring gene expression levels and have demonstrated the capability to isolate and amplify mRNA from cultured cells. Realization of these objectives will allow, in the future, development of a resource, consisting of amplified mRNA populations from individual cells from normal and tumor material, that can be used for evaluation of the prognostic, diagnostic and/or therapeutic importance of genes expressed in breast cancer.