Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei.
BACKGROUND: Functional annotation of trypanosomatid genomes has been a daunting task due to the low similarity of their genes with annotated genes of other organisms. Three recent studies have provided gene expression profiles in several different conditions and life stages for one of the main disea...
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ftdoajarticles:oai:doaj.org/article:eade6777eaa741428b9e71789048bdea 2023-05-15T15:08:16+02:00 Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. Hamed Shateri Najafabadi Reza Salavati 2010-01-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0000810 https://doaj.org/article/eade6777eaa741428b9e71789048bdea EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC2930875?pdf=render https://doaj.org/toc/1935-2735 1935-2735 doi:10.1371/journal.pntd.0000810 https://doaj.org/article/eade6777eaa741428b9e71789048bdea PLoS Neglected Tropical Diseases, Vol 4, Iss 8, p e1000920 (2010) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2010 ftdoajarticles https://doi.org/10.1371/journal.pntd.0000810 2022-12-31T16:26:08Z BACKGROUND: Functional annotation of trypanosomatid genomes has been a daunting task due to the low similarity of their genes with annotated genes of other organisms. Three recent studies have provided gene expression profiles in several different conditions and life stages for one of the main disease-causing trypanosomatids, Trypanosoma brucei. These data can be used to study the gene functions and regulatory mechanisms in this organism. METHODOLOGY/PRINCIPAL FINDINGS: Combining the data from three different microarray studies of T. brucei, we show that functional linkages among T. brucei genes can be identified based on gene coexpression, leading to a powerful approach for gene function prediction. These predictions can be further improved by considering the expression profiles of orthologous genes from other trypanosomatids. Furthermore, gene expression profiles can be used to discover potential regulatory elements within 3' untranslated regions. CONCLUSIONS/SIGNIFICANCE: These results suggest that although trypanosomatids do not regulate genes at transcription level, trypanosomatid genes with related functions are coregulated post-transcriptionally via modulation of mRNA stability, implying the presence of complex regulatory networks in these organisms. Our analysis highlights the demand for a thorough transcript profiling of T. brucei genome in parallel with other trypanosomatid genomes, which can provide a powerful means to improve their functional annotation. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLoS Neglected Tropical Diseases 4 8 e810 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Hamed Shateri Najafabadi Reza Salavati Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
BACKGROUND: Functional annotation of trypanosomatid genomes has been a daunting task due to the low similarity of their genes with annotated genes of other organisms. Three recent studies have provided gene expression profiles in several different conditions and life stages for one of the main disease-causing trypanosomatids, Trypanosoma brucei. These data can be used to study the gene functions and regulatory mechanisms in this organism. METHODOLOGY/PRINCIPAL FINDINGS: Combining the data from three different microarray studies of T. brucei, we show that functional linkages among T. brucei genes can be identified based on gene coexpression, leading to a powerful approach for gene function prediction. These predictions can be further improved by considering the expression profiles of orthologous genes from other trypanosomatids. Furthermore, gene expression profiles can be used to discover potential regulatory elements within 3' untranslated regions. CONCLUSIONS/SIGNIFICANCE: These results suggest that although trypanosomatids do not regulate genes at transcription level, trypanosomatid genes with related functions are coregulated post-transcriptionally via modulation of mRNA stability, implying the presence of complex regulatory networks in these organisms. Our analysis highlights the demand for a thorough transcript profiling of T. brucei genome in parallel with other trypanosomatid genomes, which can provide a powerful means to improve their functional annotation. |
format |
Article in Journal/Newspaper |
author |
Hamed Shateri Najafabadi Reza Salavati |
author_facet |
Hamed Shateri Najafabadi Reza Salavati |
author_sort |
Hamed Shateri Najafabadi |
title |
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
title_short |
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
title_full |
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
title_fullStr |
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
title_full_unstemmed |
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. |
title_sort |
functional genome annotation by combined analysis across microarray studies of trypanosoma brucei. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2010 |
url |
https://doi.org/10.1371/journal.pntd.0000810 https://doaj.org/article/eade6777eaa741428b9e71789048bdea |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 4, Iss 8, p e1000920 (2010) |
op_relation |
http://europepmc.org/articles/PMC2930875?pdf=render https://doaj.org/toc/1935-2735 1935-2735 doi:10.1371/journal.pntd.0000810 https://doaj.org/article/eade6777eaa741428b9e71789048bdea |
op_doi |
https://doi.org/10.1371/journal.pntd.0000810 |
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PLoS Neglected Tropical Diseases |
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4 |
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8 |
container_start_page |
e810 |
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1766339652992630784 |