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C-GATE - catalogue of genes affected by transposable elements

BACKGROUND: Functional regulatory sequences are present in many transposable element (TE) copies, resulting in TEs being frequently exapted by host genes. Today, many examples of TEs impacting host gene expression can be found in the literature and we believe a new catalogue of such exaptations woul...

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Detalles Bibliográficos
Autores principales: Rebollo, Rita, Farivar, Sharareh, Mager, Dixie L
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472293/
https://www.ncbi.nlm.nih.gov/pubmed/22621612
http://dx.doi.org/10.1186/1759-8753-3-9
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author Rebollo, Rita
Farivar, Sharareh
Mager, Dixie L
author_facet Rebollo, Rita
Farivar, Sharareh
Mager, Dixie L
author_sort Rebollo, Rita
collection PubMed
description BACKGROUND: Functional regulatory sequences are present in many transposable element (TE) copies, resulting in TEs being frequently exapted by host genes. Today, many examples of TEs impacting host gene expression can be found in the literature and we believe a new catalogue of such exaptations would be useful for the field. FINDINGS: We have established the catalogue of genes affected by transposable elements (C-GATE), which can be found at https://sites.google.com/site/tecatalog/. To date, it holds 221 cases of biologically verified TE exaptations and more than 10,000 in silico TE-gene partnerships. C-GATE is interactive and allows users to include missed or new TE exaptation data. C-GATE provides a graphic representation of the entire library, which may be used for future statistical analysis of TE impact on host gene expression. CONCLUSIONS: We hope C-GATE will be valuable for the TE community but also for others who have realized the role that TEs may have in their research.
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spelling pubmed-34722932012-10-17 C-GATE - catalogue of genes affected by transposable elements Rebollo, Rita Farivar, Sharareh Mager, Dixie L Mob DNA Short Report BACKGROUND: Functional regulatory sequences are present in many transposable element (TE) copies, resulting in TEs being frequently exapted by host genes. Today, many examples of TEs impacting host gene expression can be found in the literature and we believe a new catalogue of such exaptations would be useful for the field. FINDINGS: We have established the catalogue of genes affected by transposable elements (C-GATE), which can be found at https://sites.google.com/site/tecatalog/. To date, it holds 221 cases of biologically verified TE exaptations and more than 10,000 in silico TE-gene partnerships. C-GATE is interactive and allows users to include missed or new TE exaptation data. C-GATE provides a graphic representation of the entire library, which may be used for future statistical analysis of TE impact on host gene expression. CONCLUSIONS: We hope C-GATE will be valuable for the TE community but also for others who have realized the role that TEs may have in their research. BioMed Central 2012-05-23 /pmc/articles/PMC3472293/ /pubmed/22621612 http://dx.doi.org/10.1186/1759-8753-3-9 Text en Copyright ©2012 Rebollo et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Rebollo, Rita
Farivar, Sharareh
Mager, Dixie L
C-GATE - catalogue of genes affected by transposable elements
title C-GATE - catalogue of genes affected by transposable elements
title_full C-GATE - catalogue of genes affected by transposable elements
title_fullStr C-GATE - catalogue of genes affected by transposable elements
title_full_unstemmed C-GATE - catalogue of genes affected by transposable elements
title_short C-GATE - catalogue of genes affected by transposable elements
title_sort c-gate - catalogue of genes affected by transposable elements
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472293/
https://www.ncbi.nlm.nih.gov/pubmed/22621612
http://dx.doi.org/10.1186/1759-8753-3-9
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