Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Kilpinen, Sami K Ojala, Kalle A Kallioniemi, Olli P England BioData mining BioData Min. 2011 Mar 31;4:5. eng BACKGROUND: Gene expression microarray...
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/162845 2023-08-20T04:09:36+02:00 Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Kilpinen, S. K. Ojala, K. A. Kallioniemi, Olli Institute for Molecular Medicine Finland 2016-05-25T12:06:01Z 1 application/pdf http://hdl.handle.net/10138/162845 eng eng https://doi.org/10.1186/1756-0381-4-5 BioData mining 1756-0381 Kilpinen , S K , Ojala , K A & Kallioniemi , O 2011 , ' Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data ' , BioData mining , vol. 4 , pp. 5 . https://doi.org/10.1186/1756-0381-4-5 PURE: 21154729 PURE UUID: f7a1cfb4-420d-4824-9d46-38c8eebfab9f RIS: urn:43AEF3ED3E50550D179D567001AA5D2E WOS: 000208761200005 Scopus: 79953226313 http://hdl.handle.net/10138/162845 cc_by openAccess info:eu-repo/semantics/openAccess 3111 Biomedicine Article publishedVersion 2016 ftunivhelsihelda https://doi.org/10.1186/1756-0381-4-5 2023-07-28T06:34:16Z Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Kilpinen, Sami K Ojala, Kalle A Kallioniemi, Olli P England BioData mining BioData Min. 2011 Mar 31;4:5. eng BACKGROUND: Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual test samples is not as developed as e.g. in the field of nucleotide sequence comparisons. We have created a rapid and powerful approach for the alignment of microarray gene expression profiles (AGEP) from test samples with those contained in a large annotated public reference database and demonstrate here how this can facilitate interpretation of microarray data from individual samples. METHODS: AGEP is based on the calculation of kernel density distributions for the levels of expression of each gene in each reference tissue type and provides a quantitation of the similarity between the test sample and the reference tissue types as well as the identity of the typical and atypical genes in each comparison. As a reference database, we used 1654 samples from 44 normal tissues (extracted from the Genesapiens database). RESULTS: Using leave-one-out validation, AGEP correctly defined the tissue of origin for 1521 (93.6%) of all the 1654 samples in the original database. Independent validation of 195 external normal tissue samples resulted in 87% accuracy for the exact tissue type and 97% accuracy with related tissue types. AGEP analysis of 10 Duchenne muscular dystrophy (DMD) samples provided quantitative description of the key pathogenetic events, such as the extent of inflammation, in individual samples and pinpointed tissue-specific genes whose expression changed (SAMD4A) in DMD. AGEP analysis of microarray data from adipocytic differentiation of mesenchymal stem cells and from normal myeloid cell types and leukemias provided quantitative ... Article in Journal/Newspaper sami Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto Kalle ENVELOPE(14.340,14.340,68.187,68.187) Kallioniemi ENVELOPE(23.770,23.770,67.008,67.008) Ojala ENVELOPE(25.417,25.417,66.833,66.833) Olli ENVELOPE(23.683,23.683,67.950,67.950) BioData Mining 4 1 |
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Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto |
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ftunivhelsihelda |
language |
English |
topic |
3111 Biomedicine |
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3111 Biomedicine Kilpinen, S. K. Ojala, K. A. Kallioniemi, Olli Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
topic_facet |
3111 Biomedicine |
description |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Kilpinen, Sami K Ojala, Kalle A Kallioniemi, Olli P England BioData mining BioData Min. 2011 Mar 31;4:5. eng BACKGROUND: Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual test samples is not as developed as e.g. in the field of nucleotide sequence comparisons. We have created a rapid and powerful approach for the alignment of microarray gene expression profiles (AGEP) from test samples with those contained in a large annotated public reference database and demonstrate here how this can facilitate interpretation of microarray data from individual samples. METHODS: AGEP is based on the calculation of kernel density distributions for the levels of expression of each gene in each reference tissue type and provides a quantitation of the similarity between the test sample and the reference tissue types as well as the identity of the typical and atypical genes in each comparison. As a reference database, we used 1654 samples from 44 normal tissues (extracted from the Genesapiens database). RESULTS: Using leave-one-out validation, AGEP correctly defined the tissue of origin for 1521 (93.6%) of all the 1654 samples in the original database. Independent validation of 195 external normal tissue samples resulted in 87% accuracy for the exact tissue type and 97% accuracy with related tissue types. AGEP analysis of 10 Duchenne muscular dystrophy (DMD) samples provided quantitative description of the key pathogenetic events, such as the extent of inflammation, in individual samples and pinpointed tissue-specific genes whose expression changed (SAMD4A) in DMD. AGEP analysis of microarray data from adipocytic differentiation of mesenchymal stem cells and from normal myeloid cell types and leukemias provided quantitative ... |
author2 |
Institute for Molecular Medicine Finland |
format |
Article in Journal/Newspaper |
author |
Kilpinen, S. K. Ojala, K. A. Kallioniemi, Olli |
author_facet |
Kilpinen, S. K. Ojala, K. A. Kallioniemi, Olli |
author_sort |
Kilpinen, S. K. |
title |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
title_short |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
title_full |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
title_fullStr |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
title_full_unstemmed |
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data |
title_sort |
alignment of gene expression profiles from test samples against a reference database: new method for context-specific interpretation of microarray data |
publishDate |
2016 |
url |
http://hdl.handle.net/10138/162845 |
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ENVELOPE(14.340,14.340,68.187,68.187) ENVELOPE(23.770,23.770,67.008,67.008) ENVELOPE(25.417,25.417,66.833,66.833) ENVELOPE(23.683,23.683,67.950,67.950) |
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Kalle Kallioniemi Ojala Olli |
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Kalle Kallioniemi Ojala Olli |
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sami |
genre_facet |
sami |
op_relation |
https://doi.org/10.1186/1756-0381-4-5 BioData mining 1756-0381 Kilpinen , S K , Ojala , K A & Kallioniemi , O 2011 , ' Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data ' , BioData mining , vol. 4 , pp. 5 . https://doi.org/10.1186/1756-0381-4-5 PURE: 21154729 PURE UUID: f7a1cfb4-420d-4824-9d46-38c8eebfab9f RIS: urn:43AEF3ED3E50550D179D567001AA5D2E WOS: 000208761200005 Scopus: 79953226313 http://hdl.handle.net/10138/162845 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1186/1756-0381-4-5 |
container_title |
BioData Mining |
container_volume |
4 |
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1 |
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1774723026537938944 |