Open Access Research article

Intergenic, gene terminal, and intragenic CpG islands in the human genome

Yulia A Medvedeva1*, Marina V Fridman1, Nina J Oparina2, Dmitry B Malko1, Ekaterina O Ermakova3, Ivan V Kulakovskiy1, Andreas Heinzel4 and Vsevolod J Makeev12

Author Affiliations

1 Research Institute for Genetics and Selection of Industrial Microorganisms, Genetika, 1st Dorozhny proezd, 1, Moscow, 117545, Russia

2 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str., 32, Moscow, 199991, Russia

3 Institute for Information Transmission Problems (The Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny per. 19, Moscow, 127994, Russia

4 Upper Austria University of Applied Sciences, Softwarepark 11, Hagenberg, 4232, Austria

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BMC Genomics 2010, 11:48  doi:10.1186/1471-2164-11-48

Published: 19 January 2010

Additional files

Additional file 1:

CAGE enriched non 5' CGI. Tables contain lists of genes with CAGE-enriched CGIs in 3' and intragenic regions separately.

Format: ZIP Size: 9KB Download file

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Additional file 2:

Gene elements. The archive contains row data used for statistical significance of gene elements and CGIs overlap. See Table 1 and Figure 1 in the manuscript.

Format: ZIP Size: 5.4MB Download file

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Additional file 3:

CGI classes. The archive contains classes of CGIs used for calculation of CAGE tag frequency.

Format: ZIP Size: 6MB Download file

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Additional file 4:

Monte Carlo Simulations. The archive contains Ruby scripts used to evaluate statistical significance of overlapping of gene segments and CGIs. Results of simulations with different "fixed" elements (see Methods) are also included.

Format: ZIP Size: 3.2MB Download file

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Additional file 5:

Comparative genomics. The archive contains row data and Perl scripts to perform substitution rates calculation.

Format: ZIP Size: 8.4MB Download file

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Additional file 6:

Sp1. This folder contains the data used for Sp1 binding sites prediction and detailed description of the procedure.

Format: ZIP Size: 406KB Download file

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