Open Access Highly Accessed Research article

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters

Paul Gagniuc1* and Constantin Ionescu-Tirgoviste2

Author Affiliations

1 Institute of Genetics, University of Bucharest, Bucharest 060101, Romania

2 National Institute of Diabetes, Nutrition and Metabolic Diseases “N.C. Paulescu”, Bucharest, Romania

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BMC Genomics 2012, 13:512  doi:10.1186/1471-2164-13-512

Published: 28 September 2012

Additional files

Additional file 1:

Promotor sequences. A complete set of 20,586 gene promoters from The Eukaryotic Promoter Database (6,649 gene promoters - Oryza sativa, 1,922 gene promoters - Drosophila Melanogaster and 8,512 gene promoters - Homo sapiens) and PlantProm Database (3,503 gene promoters - Arabidopsis thaliana).

Format: RAR Size: 3.6MB Download file

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Additional file 2:

Organism-specific data. Comparative analysis undertaken for 20,586 promoters from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiens and Oryza sativa.

Format: XLS Size: 115KB Download file

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Additional file 3:

PromKappa and PromNN. PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis and PromNN (Promoter analysis by Neural Network) software program used for sorting promoter patterns.

Format: RAR Size: 4.4MB Download file

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Additional file 4:

Tissue-specific data. Promoter analysis in Homo sapiens, based on tissuespecific gene expression profiles.

Format: XLS Size: 435KB Download file

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Additional file 5:

Observations for HOX genes. Comparative analysis of HOX gene promoter patterns.

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Additional file 6:

Observed and expected frequencies. Analysis involving expected and observed promoter frequencies based on Organism-specific and Tissue-specific data.

Format: XLS Size: 25KB Download file

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Additional file 7:

Distribution in other species. A secondary distribution of gene promoters in Bos taurus, Gallus gallus, Mus musculus, Rattus norvegicus, Xenopus laevis and Zea mays.

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Additional file 8:

DET1 promoter pattern. Shows a simulation which highlights the promoter sequence resistance to random mutations.

Format: DOC Size: 146KB Download file

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Additional file 9:

Promoter pattern animation. Animation showing several hundred promoter patterns in succession and ordered according to their class.

Format: WMV Size: 6.5MB Download file

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Additional file 10:

List of tissue-specific genes. List of 6,534 tissue-specific gene names from TiGER database (gene names were sorted and redundancy was removed).

Format: RAR Size: 27KB Download file

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Additional file 11:

Tissue-specific promoter patterns. The complete set of 2,369 image-based promoter patterns used for tissue-specific analysis.

Format: RAR Size: 15.1MB Download file

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Additional file 12:

Organism-specific promoter patterns. The complete set of 20,597 image-based promoter patterns used for a comparative analysis of the four species taken into consideration.

Format: RAR Size: 6.3MB Download file

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Additional file 13:

Gene promoters used for neural network training. List of 918 image-based promoter patterns used for PromNN training.

Format: RAR Size: 6.3MB Download file

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