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Open Access Research article

Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster

Philge Philip12, Fredrik Pettersson3 and Per Stenberg12*

Author Affiliations

1 Deptartment of Molecular Biology, Umeå University, 901 87 Umeå, Sweden

2 Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden

3 UmBio, 907 19 Umeå, Sweden

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BMC Genomics 2012, 13:97  doi:10.1186/1471-2164-13-97

Published: 19 March 2012

Additional files

Additional file 1:

Gene feature AT-contents. AT contents of indicated gene features in Dm chromosomes. Table cells colored according to chromosome AT content (low - red to high - green).

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Additional file 2:

Sequence words from PCA models. Sorted lists of sequence words with corresponding loadings from all PCA multivariate models.

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Additional file 3:

Summary of fits for all multivariate models. Summary of fits for all multivariate models.

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Additional file 4:

PCA of individual gene features. Results of PCA of frequencies of sequence words within individual gene features in Dm chromosome arms. Chromosomes colour-coded, and gene features indicated by symbols as follows: green = X, magenta = 3R, brown = 2R, blue = 3L, yellow = 2L; ∇ = promoter, Δ = 5'UTR, □ = CDS, O = intron, + = 3'UTR, × = intergenic. (A), (B), (C), (D), (E) and (F) show 1st vs 2nd component score plots (R2cum = 0.473, 0.478, 0.759, 0.821, 0.565 and 0.791, respectively) of the AT-normalized 2-6 mer promoter, 5' UTR, coding sequence, intron, 3' UTR and intergenic sequence analyses, respectively.

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Additional file 5:

Correlation of gene-binding values from different data sets. Spearman correlations of gene-binding values for MOF, MSL-1 and MSL-3 proteins from different data sets. All correlations are significant (p < 0.05).

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Additional file 6:

Gene feature AT-contents grouped by MSL binding and expression status. AT contents of indicated gene features in expressed genes strongly and weakly bound by the MSL complex, and all expressed and unexpressed genes. Table cells colored according to the gene features' AT contents (low - red to high - green).

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Additional file 7:

Sequence words from OPLS-DA models. Sorted lists of sequence words with corresponding loadings from all OPLS-DA multivariate models.

Format: XLS Size: 2.2MB Download file

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Additional file 8:

Correlation between OPLS-DA models and AT-content as well as expression. Results from OPLS-DA models of frequencies of sequence words in features of expressed MSL strongly bound (green, O) vs MSL weakly bound genes (magenta, O) of chromosome X. (A), (B), (C) and (D): scatter plots of first component scores versus AT contents of promoters, coding sequences, introns and 3' UTRs, respectively. (E), (F), G) and (H): scatter plots of promoter, coding sequence, intron and 3' UTR first component scores versus gene expression levels, respectively.

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Additional file 9:

Heatmap summarizing our promoter and CDS results on chromosome X. A heatmap of expressed genes on chromosome X sorted with respect to average MSL enrichment. In the heatmap, presence of BEAF-32 within 500 bp of transcription start site (TSS) (column 2), promoter motif presence within 500 bp of TSS (column 3), OPLS-DA Y Prediction scores of three equally sized parts of CDS (columns 4-6) and high affinity site distance to genes (column 7) are shown.

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Additional file 10:

Insulator protein-TSS distances. Average distances from transcription start sites (TSS) of expressed MSL-bound (magenta) and - unbound (green) genes to BEAF-32, CP190, CTCF and SU(HW) binding sites.

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Additional file 11:

Plot of gene-binding values of MOF, MSL-1 and MSL-3 proteins. Enrichment of MOF, MSL-1 and MSL-3 within autosomal and X-linked genes in SL-2 cells (to the left and right, respectively) is shown by blue, red and green lines, respectively.

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Additional file 12:

Gene-binding values of MOF, MSL-1 and MSL-3 proteins. Gene-binding values for all genes in the genome.

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Additional file 13:

Expression of X-linked genes in control and in RNAi knockdown of msl-genes. Expression of X-linked genes in EGFP control (blue) and in RNAi knockdown of mof, msl-1 and msl-3 genes (red) in SL-2 cells, sorted by expression in EGFP controls. (A), (B) and (C): line plots of expression in EGFP control and mof RNAi, msl-1 RNAi and msl-3 RNAi cells, respectively. Expression levels in RNAi treated cells are shown as running averages for sets of 21 genes.

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Additional file 14:

Sequence word aligner algorithm. A flowchart for the iterative algorithm to identify complex motifs with significant predictive values for protein binding, based on the top sequence words obtained from OPLS-DA models designed to detect sequence differences between genes bound and not bound by the protein.

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