Abstract
In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling techniques, a central component of functional genomics studies. Historically, Northern blots were the de facto standard for determining RNA transcript levels. However, driven by the demand for analysis of large sets of genes in parallel, high-throughput methods, such as microarrays, dominate modern profiling efforts. To facilitate assessment of these methods, in comparison to Northern blots, we created a database of published Northern results obtained with a standardized commercial multiple tissue blot (dbMTN). In order to demonstrate the utility of the dbMTN collection for technology comparison, we also generated expression profiles for genes across a set of human tissues, using multiple profiling techniques. No method produced profiles that were strongly correlated with the Northern blot data. The highest correlations to the Northern blot data were determined with microarrays for the subset of genes observed to be specifically expressed in a single tissue in the Northern analyses. The database and expression profiling data are available via the project website (http://www.cisreg.ca). We believe that emphasis on multitechnique validation of expression profiles is justified, as the correlation results between platforms are not encouraging on the whole. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531-6912/suppmat
| Original language | English |
|---|---|
| Pages (from-to) | 584-595 |
| Number of pages | 12 |
| Journal | Comparative and Functional Genomics |
| Volume | 5 |
| Issue number | 8 |
| DOIs | |
| State | Published - Dec 1 2004 |
| Externally published | Yes |
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Keywords
- Database
- Gene expression
- Genomics
- Microarray
- Northern
ASJC Scopus subject areas
- Applied Microbiology and Biotechnology
- Biotechnology
- Genetics(clinical)
Cite this
Exploring the foundation of genomics : A Northern blot reference set for the comparative analysis of transcript profiling technologies. / Kemmer, Danielle; Faxén, Margareta; Hodges, Emily; Lim, Jonathan; Herzog, Elena; Ljungström, Elsebrit; Lundmark, Anders; Olsen, Mary K.; Podowski, Raf; Sonnhammer, Erik L L; Nilsson, Peter; Reimers, Mark; Lenhard, Boris; Roberds, Steven L.; Wahlestedt, Claes R; Höög, Christer; Agarwal, Pankaj; Wasserman, Wyeth W.
In: Comparative and Functional Genomics, Vol. 5, No. 8, 01.12.2004, p. 584-595.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Exploring the foundation of genomics
T2 - A Northern blot reference set for the comparative analysis of transcript profiling technologies
AU - Kemmer, Danielle
AU - Faxén, Margareta
AU - Hodges, Emily
AU - Lim, Jonathan
AU - Herzog, Elena
AU - Ljungström, Elsebrit
AU - Lundmark, Anders
AU - Olsen, Mary K.
AU - Podowski, Raf
AU - Sonnhammer, Erik L L
AU - Nilsson, Peter
AU - Reimers, Mark
AU - Lenhard, Boris
AU - Roberds, Steven L.
AU - Wahlestedt, Claes R
AU - Höög, Christer
AU - Agarwal, Pankaj
AU - Wasserman, Wyeth W.
PY - 2004/12/1
Y1 - 2004/12/1
N2 - In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling techniques, a central component of functional genomics studies. Historically, Northern blots were the de facto standard for determining RNA transcript levels. However, driven by the demand for analysis of large sets of genes in parallel, high-throughput methods, such as microarrays, dominate modern profiling efforts. To facilitate assessment of these methods, in comparison to Northern blots, we created a database of published Northern results obtained with a standardized commercial multiple tissue blot (dbMTN). In order to demonstrate the utility of the dbMTN collection for technology comparison, we also generated expression profiles for genes across a set of human tissues, using multiple profiling techniques. No method produced profiles that were strongly correlated with the Northern blot data. The highest correlations to the Northern blot data were determined with microarrays for the subset of genes observed to be specifically expressed in a single tissue in the Northern analyses. The database and expression profiling data are available via the project website (http://www.cisreg.ca). We believe that emphasis on multitechnique validation of expression profiles is justified, as the correlation results between platforms are not encouraging on the whole. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531-6912/suppmat
AB - In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling techniques, a central component of functional genomics studies. Historically, Northern blots were the de facto standard for determining RNA transcript levels. However, driven by the demand for analysis of large sets of genes in parallel, high-throughput methods, such as microarrays, dominate modern profiling efforts. To facilitate assessment of these methods, in comparison to Northern blots, we created a database of published Northern results obtained with a standardized commercial multiple tissue blot (dbMTN). In order to demonstrate the utility of the dbMTN collection for technology comparison, we also generated expression profiles for genes across a set of human tissues, using multiple profiling techniques. No method produced profiles that were strongly correlated with the Northern blot data. The highest correlations to the Northern blot data were determined with microarrays for the subset of genes observed to be specifically expressed in a single tissue in the Northern analyses. The database and expression profiling data are available via the project website (http://www.cisreg.ca). We believe that emphasis on multitechnique validation of expression profiles is justified, as the correlation results between platforms are not encouraging on the whole. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531-6912/suppmat
KW - Database
KW - Gene expression
KW - Genomics
KW - Microarray
KW - Northern
UR - http://www.scopus.com/inward/record.url?scp=20144381449&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=20144381449&partnerID=8YFLogxK
U2 - 10.1002/cfg.443
DO - 10.1002/cfg.443
M3 - Article
C2 - 18629180
AN - SCOPUS:20144381449
VL - 5
SP - 584
EP - 595
JO - Comparative and Functional Genomics
JF - Comparative and Functional Genomics
SN - 1531-6912
IS - 8
ER -