A link between multiple high throughput technology datasets

Elmar Bucher, Pekka Kohonen, Vidal Fey, John Mpindi, Henri Sara, Tommi Pisto, Henrik Edgren, Sami Kilpinen, Kalle Ojala, Pekka Tiikkainen, Paula Vainio, Kristiina Iljin, Niko Sahlberg, Juha K. Rantala, Rami Mäkelä, Petri Saviranta, Merja Perälä, Matthias Nees, Saija Haapa-Paananen, Olli Kallioniemi

Research output: Contribution to conferenceConference articleScientific

Abstract

Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.
Original languageEnglish
Publication statusPublished - 2008
MoE publication typeNot Eligible
Event9th International Conference on Systems Biology, ICSB2008 - Göteborg, Sweden
Duration: 22 Aug 200828 Aug 2008

Conference

Conference9th International Conference on Systems Biology, ICSB2008
Abbreviated titleICSB2008
CountrySweden
CityGöteborg
Period22/08/0828/08/08

Fingerprint

Technology
MicroRNAs
Endpoint Determination
Protein Array Analysis
Gene Dosage
Small Interfering RNA
Libraries
Neoplasms
Databases
Gene Expression
Cell Line
Antibodies
Genes
Datasets

Keywords

  • high througput screening technology
  • database design
  • database management system
  • R
  • MySQL

Cite this

Bucher, E., Kohonen, P., Fey, V., Mpindi, J., Sara, H., Pisto, T., ... Kallioniemi, O. (2008). A link between multiple high throughput technology datasets. Paper presented at 9th International Conference on Systems Biology, ICSB2008, Göteborg, Sweden.
Bucher, Elmar ; Kohonen, Pekka ; Fey, Vidal ; Mpindi, John ; Sara, Henri ; Pisto, Tommi ; Edgren, Henrik ; Kilpinen, Sami ; Ojala, Kalle ; Tiikkainen, Pekka ; Vainio, Paula ; Iljin, Kristiina ; Sahlberg, Niko ; Rantala, Juha K. ; Mäkelä, Rami ; Saviranta, Petri ; Perälä, Merja ; Nees, Matthias ; Haapa-Paananen, Saija ; Kallioniemi, Olli. / A link between multiple high throughput technology datasets. Paper presented at 9th International Conference on Systems Biology, ICSB2008, Göteborg, Sweden.
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title = "A link between multiple high throughput technology datasets",
abstract = "Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.",
keywords = "high througput screening technology, database design, database management system, R, MySQL",
author = "Elmar Bucher and Pekka Kohonen and Vidal Fey and John Mpindi and Henri Sara and Tommi Pisto and Henrik Edgren and Sami Kilpinen and Kalle Ojala and Pekka Tiikkainen and Paula Vainio and Kristiina Iljin and Niko Sahlberg and Rantala, {Juha K.} and Rami M{\"a}kel{\"a} and Petri Saviranta and Merja Per{\"a}l{\"a} and Matthias Nees and Saija Haapa-Paananen and Olli Kallioniemi",
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language = "English",
note = "9th International Conference on Systems Biology, ICSB2008, ICSB2008 ; Conference date: 22-08-2008 Through 28-08-2008",

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Bucher, E, Kohonen, P, Fey, V, Mpindi, J, Sara, H, Pisto, T, Edgren, H, Kilpinen, S, Ojala, K, Tiikkainen, P, Vainio, P, Iljin, K, Sahlberg, N, Rantala, JK, Mäkelä, R, Saviranta, P, Perälä, M, Nees, M, Haapa-Paananen, S & Kallioniemi, O 2008, 'A link between multiple high throughput technology datasets' Paper presented at 9th International Conference on Systems Biology, ICSB2008, Göteborg, Sweden, 22/08/08 - 28/08/08, .

A link between multiple high throughput technology datasets. / Bucher, Elmar; Kohonen, Pekka; Fey, Vidal; Mpindi, John; Sara, Henri; Pisto, Tommi; Edgren, Henrik; Kilpinen, Sami; Ojala, Kalle; Tiikkainen, Pekka; Vainio, Paula; Iljin, Kristiina; Sahlberg, Niko; Rantala, Juha K.; Mäkelä, Rami; Saviranta, Petri; Perälä, Merja; Nees, Matthias; Haapa-Paananen, Saija; Kallioniemi, Olli.

2008. Paper presented at 9th International Conference on Systems Biology, ICSB2008, Göteborg, Sweden.

Research output: Contribution to conferenceConference articleScientific

TY - CONF

T1 - A link between multiple high throughput technology datasets

AU - Bucher, Elmar

AU - Kohonen, Pekka

AU - Fey, Vidal

AU - Mpindi, John

AU - Sara, Henri

AU - Pisto, Tommi

AU - Edgren, Henrik

AU - Kilpinen, Sami

AU - Ojala, Kalle

AU - Tiikkainen, Pekka

AU - Vainio, Paula

AU - Iljin, Kristiina

AU - Sahlberg, Niko

AU - Rantala, Juha K.

AU - Mäkelä, Rami

AU - Saviranta, Petri

AU - Perälä, Merja

AU - Nees, Matthias

AU - Haapa-Paananen, Saija

AU - Kallioniemi, Olli

PY - 2008

Y1 - 2008

N2 - Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.

AB - Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.

KW - high througput screening technology

KW - database design

KW - database management system

KW - R

KW - MySQL

M3 - Conference article

ER -

Bucher E, Kohonen P, Fey V, Mpindi J, Sara H, Pisto T et al. A link between multiple high throughput technology datasets. 2008. Paper presented at 9th International Conference on Systems Biology, ICSB2008, Göteborg, Sweden.