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C-GATE - catalogue of genes affected by transposable elements.

Rebollo R, Farivar S, Mager DL - Mob DNA (2012)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada. rrebollo@bccrc.ca.

ABSTRACT

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.

No MeSH data available.


Graphic representation of C-GATE at time of publication. (A) C-GATE general graphs. Pie charts depicting the proportion of TE types (LTR, LINE, SINE, DNA), their regulatory effects on host genes and a bar chart showing species concerned for all examples found in the general C-GATE (biologically confirmed cases). (B) Graphs per TE type present in the C-GATE. Pie charts of regulatory impact of TEs on host genes, separated by TE types. The legend is the same as panel A, regulatory elements. (C)Homo sapiens exapted TEs. Graphic representation of all TE types and their regulatory effects in the human genome. The first pie chart also depicts the proportion of TEs present in the human genome (100% is equal to all TE types in the genome) based on the published sequenced genome [20]. In order to view the updated graphs, please go to the C-GATE website http://sites.google.com/site/tecatalog/. C-GATE: catalogue of genes affected by transposable elements; TE: transposable elements.
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Figure 1: Graphic representation of C-GATE at time of publication. (A) C-GATE general graphs. Pie charts depicting the proportion of TE types (LTR, LINE, SINE, DNA), their regulatory effects on host genes and a bar chart showing species concerned for all examples found in the general C-GATE (biologically confirmed cases). (B) Graphs per TE type present in the C-GATE. Pie charts of regulatory impact of TEs on host genes, separated by TE types. The legend is the same as panel A, regulatory elements. (C)Homo sapiens exapted TEs. Graphic representation of all TE types and their regulatory effects in the human genome. The first pie chart also depicts the proportion of TEs present in the human genome (100% is equal to all TE types in the genome) based on the published sequenced genome [20]. In order to view the updated graphs, please go to the C-GATE website http://sites.google.com/site/tecatalog/. C-GATE: catalogue of genes affected by transposable elements; TE: transposable elements.

Mentions: C-GATE is formatted as shown in Table 1, and each user can either upload an example through an online form or multiple examples by downloading a table and submitting it in the C-GATE forum. A ‘comment’ section allows for more descriptive information regarding the publication, facilitating user comprehension of each case hosted within the catalogue. The website also holds graphic visualization of the general C-GATE data-set that is automatically updated with every new entry uploaded (Figure 1). Such graphic representations might be useful in the future to access exaptation frequency between TEs. Today, the catalogue shows a biased representation of human and mouse examples, which we hope will decrease with usage. For instance, almost 4,000 human genes are present in both C-GATE and pC-GATE. At the time of publication C-GATE, although incomplete, holds 221 cases previously described in the literature and our pC-GATE harbors more than 10,000 examples. We reinforce the notion that C-GATE is not complete and many already published TE exaptation examples are still to be included and we hope users will participate in this task. We want this database to help researchers obtain information on particular TE sequences or determine if their gene of interest is controlled by a TE copy. We invite researchers to discuss the catalogue on the forum present in C-GATE and we also expect many new examples of exapted TEs to be inserted by the users in the near future.


C-GATE - catalogue of genes affected by transposable elements.

Rebollo R, Farivar S, Mager DL - Mob DNA (2012)

Graphic representation of C-GATE at time of publication. (A) C-GATE general graphs. Pie charts depicting the proportion of TE types (LTR, LINE, SINE, DNA), their regulatory effects on host genes and a bar chart showing species concerned for all examples found in the general C-GATE (biologically confirmed cases). (B) Graphs per TE type present in the C-GATE. Pie charts of regulatory impact of TEs on host genes, separated by TE types. The legend is the same as panel A, regulatory elements. (C)Homo sapiens exapted TEs. Graphic representation of all TE types and their regulatory effects in the human genome. The first pie chart also depicts the proportion of TEs present in the human genome (100% is equal to all TE types in the genome) based on the published sequenced genome [20]. In order to view the updated graphs, please go to the C-GATE website http://sites.google.com/site/tecatalog/. C-GATE: catalogue of genes affected by transposable elements; TE: transposable elements.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472293&req=5

Figure 1: Graphic representation of C-GATE at time of publication. (A) C-GATE general graphs. Pie charts depicting the proportion of TE types (LTR, LINE, SINE, DNA), their regulatory effects on host genes and a bar chart showing species concerned for all examples found in the general C-GATE (biologically confirmed cases). (B) Graphs per TE type present in the C-GATE. Pie charts of regulatory impact of TEs on host genes, separated by TE types. The legend is the same as panel A, regulatory elements. (C)Homo sapiens exapted TEs. Graphic representation of all TE types and their regulatory effects in the human genome. The first pie chart also depicts the proportion of TEs present in the human genome (100% is equal to all TE types in the genome) based on the published sequenced genome [20]. In order to view the updated graphs, please go to the C-GATE website http://sites.google.com/site/tecatalog/. C-GATE: catalogue of genes affected by transposable elements; TE: transposable elements.
Mentions: C-GATE is formatted as shown in Table 1, and each user can either upload an example through an online form or multiple examples by downloading a table and submitting it in the C-GATE forum. A ‘comment’ section allows for more descriptive information regarding the publication, facilitating user comprehension of each case hosted within the catalogue. The website also holds graphic visualization of the general C-GATE data-set that is automatically updated with every new entry uploaded (Figure 1). Such graphic representations might be useful in the future to access exaptation frequency between TEs. Today, the catalogue shows a biased representation of human and mouse examples, which we hope will decrease with usage. For instance, almost 4,000 human genes are present in both C-GATE and pC-GATE. At the time of publication C-GATE, although incomplete, holds 221 cases previously described in the literature and our pC-GATE harbors more than 10,000 examples. We reinforce the notion that C-GATE is not complete and many already published TE exaptation examples are still to be included and we hope users will participate in this task. We want this database to help researchers obtain information on particular TE sequences or determine if their gene of interest is controlled by a TE copy. We invite researchers to discuss the catalogue on the forum present in C-GATE and we also expect many new examples of exapted TEs to be inserted by the users in the near future.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada. rrebollo@bccrc.ca.

ABSTRACT

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.

No MeSH data available.