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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

Alexis Vandenbon1*, Yutaro Kumagai23, Shizuo Akira23 and Daron M Standley1*

Author Affiliations

1 Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan

2 Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan

3 Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan

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BMC Genomics 2012, 13(Suppl 7):S11  doi:10.1186/1471-2164-13-S7-S11

Published: 13 December 2012

Additional files

Additional file 1:

Figure S1 - (PPT, Powerpoint file) Workflow of our framework for the detection of co-occurring motifs. The analysis of genome-wide tendencies starts with a set of TFBSs, predicted in promoter sequences and a set of PWMs. For each pair of motifs, FR values are calculated, and used for further analysis of genome-wide tendencies. The analysis of co-occurrences in sets of co-regulated genes similarly starts with the prediction of TFBSs. Using these, significantly over-represented TFBSs are detected, and for each motif the tendency to co-occur with each of the over-represented motifs is analysed. The significance of the co-occurrences is evaluated using a random sampling approach, sampling sequences from the genomic set of promoters.

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Additional file 2:

Supporting text - (DOC, Word file) On the asymmetry of the Frequency Ration measure.

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Additional file 3:

Figure S2 - (PPT, Powerpoint file) Genome-wide tendencies of Frequency Ratios in human promoter sequences. (A) Histogram of FR values for all PWM pairs in the genomic set of human promoter sequences. (B,C,D) Plots of GC content differences as measure of PWM-to-PWM dissimilarity (Y-axis) versus FR values (X-axis, same as in A), for all promoters (B), CpGhigh promoters (C), and CpGlow promoters (D).

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Additional file 4:

Figure S3 - (PPT, Powerpoint file) Tendencies of Frequency Ratio in semi-artificial and completely artificial sequences. Plot of GC content differences as measure of PWM-to-PWM dissimilarity (Y-axis) versus FR values (X-axis) in semi-artificial sequences (A), and completely artificial sequences (B), semi-artificial CpGhigh sequences (C), and semi-artificial CpGlow sequences (D).

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Additional file 5:

Figure S4 - (PPT, Powerpoint file) Genome-wide tendencies of Frequency Ratios for 200 randomly selected 7-mers in human and mouse promoter sequences. Plots of GC content differences (Y-axis) versus FR values (X-axis) are shown for all human promoters (A), all mouse promoters (B), human CpGhigh promoters (C), mouse CpGhigh promoters (D), human CpGlow promoters (E), and mouse CpGlow promoters (F).

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Additional file 6:

Figure S5 - (PPT, Powerpoint file) Heatmap representation of the average expression values for each of the 44 clusters obtained from the GNF GeneAtlas mouse data.

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Additional file 7:

Table S1 - (XLS, Excel Spreadsheet) Summary of main tissues for the 44 clusters obtained from the GNF GeneAtlas data.

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Additional file 8:

Table S2 - (XLS, Excel Spreadsheet) Summary of over-represented PWM motifs in tissue-specific sets of mouse promoters (GNF GeneAtlas data and Amit et al. data)

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Additional file 9:

Figure S6 - (PPT, Powerpoint file) Histogram of the PWM-to-PWM GC content differences of co-occurring motifs predicted by three approaches. Co-occurrences predicted by the FR measure are least affected by PWM-to-PWM GC content differences. The distribution of GC content differences of predicted co-occurring pairs of PWMs is shown 1) for the 1294 PWMs found to be significantly co-occurring with an over-represented motif according to FR values ("co-occurring motifs, FR"), 2) for the PWMs found to be co-occurring with an over-represented motif according to Pocc ("co-occurring motifs, Pocc"), and 3) for the PWMs found to be co-occurring with an over-represented motif according to the approach of Sudarsanam et al. ("co-occurring motifs, Sudarsanam"). For the latter two approaches the 1294 pairs with the most significant co-occurrence were used.

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Additional file 10:

Figure S7 - (PPT, Powerpoint file) Heatmap representation of clusters of TLR-stimulated DC gene expression data referred to in the main text.

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Additional file 11:

Table S3 - (XLS, Excel Spreadsheet) Summary for the co-occurrences in tissue-specific sets of mouse promoters (GNF GeneAtlas data and Amit et al. data).

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