Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions

doi:10.1186/1471-2105-8-174

BMC Bioinformatics

Volume 8

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Research article

Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions

Davide Corà¹ , Ferdinando Di Cunto² , Michele Caselle¹ and Paolo Provero¹^,2

¹Dept of Theoretical Physics, University of Turin and INFN, Turin, Italy

²Molecular Biotechnology Center and Dept. of Genetics, Biology and Biochemistry, University of Turin, Italy

author email corresponding author email

BMC Bioinformatics 2007, 8:174doi:10.1186/1471-2105-8-174


Published:	24 May 2007

Additional files

Additional file 1:

List of 7-mers displaying conserved overrepresentation in 3' UTR regions. For each oligo we report the numbers m, N and n as defined in the Methods section and the significance of the overrepresentation expressed as – log₁₀of the P-value (before Bonferroni correction). We also list for each oligo the n human genes with a mouse ortholog in the corresponding mouse set, listing the Ensembl id, gene symbol, Entrez gene id and description.

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Additional file 2:

7-mers displaying strand asymmetry in human 3' UTR regions. For each oligo we report the z-value as defined in the text

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Additional file 3:

7-mers displaying strand asymmetry in mouse 3' UTRs. As in additional file 2.

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Additional file 4:

7-mers displaying conserved overrepresentation in 3' UTRs: validation with the seed regions of known miRNAs. For each oligo we report the known human miRNAs with seed region (defined as described in the text) matching the oligo.

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Additional file 5:

7-mers displaying strand asymmetry in human 3' UTRs: validation with seed regions of known miRNAs. As in additional file 4.

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Additional file 8:

List of 6-mers displaying conserved overrepresentation in 3' UTRs. As in additional file 1.

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Additional file 9:

List of 6-mers displaying strand asymmetry in human 3' UTRs. As in additional file 2.

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Additional file 10:

List of 5-mers displaying conserved overrepresentation in 3' UTRs. As in additional file 1.

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Additional file 11:

List of 5-mers displaying conserved overrepresentation in human 3' UTRs. As in additional file 2.

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Additional file 6:

7-mers displaying conserved overrepresentation in 3' UTRs: validation with seed regions of putative miRNAs. As in additional file 4.

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Additional file 7:

7-mers displaying strand asymmetry in human 3' UTRs: validation with seed regions of putative miRNAs. As in additional file 4.

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Additional file 12:

Length distribution of 3' UTRs of the genes conserved overrepresented 7-mers. 3' UTR length of genes appearing in at least one of 465 sets selected by conserved overrepresentation (red) compared to all genes in our dataset (green).

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Additional file 13:

Length distribution of 3' UTRs of the genes conserved instances of the 7-mers selected with the method of Ref [21]. The genes represented in red have at least one conserved instance of one of the 465 hightest-ranking 7-mers identified using the method introduced in [21]. The length distribution of their 3' UTRs is compared to the length distribution of all the genes in the dataset (green).

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