cDNA Microarray Technology as a Tool for Better Understanding 
of Progress of Malignant Diseases

D 2005

cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases

KOUTNÁ, Irena, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK et. al.

Basic information

Original name

cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases

Name in Czech

cDNA microarray technologie jako nástroj k lepšímu pochopení progrese maligních onemocnění

Authors

KOUTNÁ, Irena (203 Czech Republic), Eva JANSOVÁ (203 Czech Republic), Petr KRONTORÁD (203 Czech Republic), Zbyněk SVOBODA (203 Czech Republic), Michal KOZUBEK (203 Czech Republic, guarantor) and Stanislav KOZUBEK (203 Czech Republic)

Edition

Prague, Czech Republic, Prague Post Genome Technology Workshop, p. 69-72, 4 pp. 2005

Publisher

Czech Pattern Recognition Society

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

Genetics and molecular biology

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14330/05:00013836

Organization unit

Faculty of Informatics

ISBN

80-01-03239-6

Keywords in English

microarray

Abstract

ORIG CZ

V originále

Array technologies have made it straightforward to monitor the expression pattern of thousands of genes simultaneously. We develop new tools, not only for the analysis of gene expression, but also for better diagnostics of various types of malignances in our laboratory. The development of better diagnostic techniques requires different approach in the evaluation of obtained microarray data. The first step of microarray data processing is precise image analysis of the data obtained using scanner. The software developed in our laboratory was used. The grid was fully-automatically set up for each image and the alignment to the array of spots was checked. This software also contains normalisation methods. We learned the differences in agnostics of various types of malignances and therefore our results represent new possibilities how to validate microarray data. Human 19,008 cDNA microarrays were used to analyze gene expression profiles of 18 patients with colorectal cancer against normal colon epithelium.The transcriptome maps (TM) (Caron et al., 2001; Versteeg et al., 2003) obtained were analyzed in order to prove positional relationships between the regulated genes suggesting the influence of chromatin remodeling effects. We identified 195 prominent genes with significantly altered expression in colon cancer. A comparison of TMs showed chromosome regions with conserved changes of gene expression typical of colorectal cancer in general and patient-specific variable regions. This study proved the existence of chromosome gene clusters in which regulated genes are located in close molecular neighborhood and that belong to the conserved TM component. Comparison of TMs is suggested as a tool facilitating detailed and illustrative diagnostics and treatment planning for individual patients. Large scale expression analysis of differentiation processes of HL-60 cells into monocytes and granulocytes and K562 cells into megakaryocytes by high-density cDNA microarrays containing 19,000 genes and EST sequences was used to study the differences among various types of differentiation and the kinetics of the processes. Based on the time dependence of the level of gene expression, genes were divided into 10 groups of regulated genes (GRGs). Intersections of GRGs from three types of differentiation showed that there are subsets of genes regulated in two pathways by either the same or quite different ways. Using visualization software developed in our laboratory, the regulated genes were mapped to chromosomes. The mapping showed that genes related to differentiation are mostly localized in regions with increased gene expression where they form clusters. Changes of cluster expression profiles along chromosomes revealed, in some cases, alternating kinetics in which up-regulated genes are followed by down regulated ones and vice versa. Epigenetic mechanisms have been suggested to control this type of gene regulation. Our results demonstrate that there are not only regions of increased or decreased levels of gene expression but, in fact, in some chromosome regions we can find clustering of genes related to specific cell rocesses. The results of position clustering of genes during various types of differentiation constitute big potential in diagnostics of leukemia where we can find several combinations of changes in gene expression which lead to cessation of normal differentiation of stem cells.

In Czech

cDNA microarray technologie jako nástroj k lepšímu pochopení progrese maligních onemocnění

Links

MSM0021622419, plan (intention)

Name: Vysoce paralelní a distribuované výpočetní systémy

Investor: Ministry of Education, Youth and Sports of the CR, Highly Parallel and Distributed Computing Systems

Citovat

KOUTNÁ, Irena, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK and Stanislav KOZUBEK. cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases. In Prague Post Genome Technology Workshop. Prague, Czech Republic: Czech Pattern Recognition Society, 2005, p. 69-72. ISBN 80-01-03239-6.

@inproceedings{573507,
   author = {Koutná, Irena and Jansová, Eva and Krontorád, Petr and Svoboda, Zbyněk and Kozubek, Michal and Kozubek, Stanislav},
   address = {Prague, Czech Republic},
   booktitle = {Prague Post Genome Technology Workshop},
   keywords = {microarray},
   language = {eng},
   location = {Prague, Czech Republic},
   isbn = {80-01-03239-6},
   pages = {69-72},
   publisher = {Czech Pattern Recognition Society},
   title = {cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases},
   year = {2005}
}

TY  - JOUR
ID  - 573507
AU  - Koutná, Irena - Jansová, Eva - Krontorád, Petr - Svoboda, Zbyněk - Kozubek, Michal - Kozubek, Stanislav
PY  - 2005
TI  - cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases
PB  - Czech Pattern Recognition Society
CY  - Prague, Czech Republic
SN  - 8001032396
KW  - microarray
N2  - Array technologies have made it straightforward to monitor the expression pattern of thousands of genes simultaneously. We develop new tools, not only for the analysis of gene expression, but also for better diagnostics of various types of malignances in our laboratory. The development of better diagnostic techniques requires different approach in the evaluation of obtained microarray data. The first step of microarray data processing is precise image analysis of the data obtained using scanner. The software developed in our laboratory was used. The grid was fully-automatically set up for each image and the alignment to the array of spots was checked. This software also contains normalisation methods. We learned the differences in agnostics of various types of malignances and therefore our results represent new possibilities how to validate microarray data. Human 19,008 cDNA microarrays were used to analyze gene expression profiles of 18 patients with colorectal cancer against normal colon epithelium.The transcriptome maps (TM) (Caron et al., 2001; Versteeg et al., 2003) obtained were analyzed in order to prove positional relationships between the regulated genes suggesting the influence of chromatin remodeling effects. We identified 195 prominent genes with significantly altered expression in colon cancer. A comparison of TMs showed chromosome regions with conserved changes of gene expression typical of colorectal cancer in general and patient-specific variable regions. This study proved the existence of chromosome gene clusters in which regulated genes are located in close molecular neighborhood and that belong to the conserved TM component. Comparison of TMs is suggested as a tool facilitating detailed and illustrative diagnostics and treatment planning for individual patients. Large scale expression analysis of differentiation processes of HL-60 cells into monocytes and granulocytes and K562 cells into megakaryocytes by high-density cDNA microarrays containing 19,000 genes and EST sequences was used to study the differences among various types of differentiation and the kinetics of the processes. Based on the time dependence of the level of gene expression, genes were divided into 10 groups of regulated genes (GRGs). Intersections of GRGs from three types of differentiation showed that there are subsets of genes regulated in two pathways by either the same or quite different ways. Using visualization software developed in our laboratory, the regulated genes were mapped to chromosomes. The mapping showed that genes related to differentiation are mostly localized in regions with increased gene expression where they form clusters. Changes of cluster expression profiles along chromosomes revealed, in some cases, alternating kinetics in which up-regulated genes are followed by down regulated ones and vice versa. Epigenetic mechanisms have been suggested to control this type of gene regulation. Our results demonstrate that there are not only regions of increased or decreased levels of gene expression but, in fact, in some chromosome regions we can find clustering of genes related to specific cell rocesses. The results of position clustering of genes during various types of differentiation constitute big potential in diagnostics of leukemia where we can find several combinations of changes in gene expression which lead to cessation of normal differentiation of stem cells.
ER  -

KOUTNÁ, Irena, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK and Stanislav KOZUBEK. cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases. In \textit{Prague Post Genome Technology Workshop}. Prague, Czech Republic: Czech Pattern Recognition Society, 2005, p.~69-72. ISBN~80-01-03239-6.

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