Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

Additional file 1:

Motif sites detected by PhyloCon in rice derived from MPSS. Table showes motif sites detected by PhyloCon in rice genes derived from MPSS. The position of sites shown in the third column indicates the distance to the start codon.

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Additional file 2:

Motif sites detected by PhyloCon in rice derived from YALE-1. Table showes motif sites detected by PhyloCon in rice genes derived from YALE-1. The position of sites shown in the third column indicates the distance to the start codon.

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Additional file 3:

Motif sites detected by PhyloCon in rice derived from YALE-2. Table showes motif sites detected by PhyloCon in rice genes derived from YALE-2. The position of sites shown in the third column indicates the distance to the start codon.

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Additional file 4:

Motif sites detected by PhyloCon in sorghum derived from MPSS. Table showes motif sites detected by PhyloCon in sorghum genes derived from MPSS. The position of sites shown in the third column indicates the distance to the start codon.

Format: XLS Size: 635KB Download file

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Additional file 5:

Motif sites detected by PhyloCon in sorghum derived from YALE-1. Table showes motif sites detected by PhyloCon in sorghum genes derived from YALE-1. The position of sites shown in the third column indicates the distance to the start codon.

Format: XLS Size: 616KB Download file

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Additional file 6:

Motif sites detected by PhyloCon in sorghum derived from YALE-2. Table showes motif sites detected by PhyloCon in sorghum genes derived from YALE-2. The position of sites shown in the third column indicates the distance to the start codon.

Format: XLS Size: 311KB Download file

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Additional file 7:

Long motifs detected by network-level conservation analysis. Table gives long motifs detected by network-level conservation analysis. The number of genes in rice and sorghum containing the respective motif in their upstream sequence are listed in the columns '#rice' and '#sorghum', respectively. Observed co-occurrences in syntenic pairs as well as the z-score are given.

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Additional file 8:

k-mer motifs detected by network-level conservation analysis. Table gives k-mer motifs detected by network-level conservation analysis. The number of genes in rice and sorghum containing the respective motif in their upstream sequence are listed in the columns '#rice' and '#sorghum', respectively. Observed co-occurrences in syntenic pairs as well as the z-score are given.

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Additional file 9:

Determination of significant and reliable expression levels in YALE-1. Significantly expressed probes have been determined according to [44]. Background expression is derived from all measurements of 58,404 oligonucleotide probes in 42 experiments. For each expression intensity, the percentage of measurements exceeding the respective expression level has been determined for two classes: (i) probes for which two or more replicates fell below the respective threshold and (ii) probes having higher intensities for 3 or more replicates. The x-axis depicts expression levels measured as the intensity of Cy5 dye, the y-axis the percentage of total measurements. For YALE-1, we found an expression intensity of 410 corresponding to the top 5% of all measurements.

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Additional file 10:

Background distribution for MPSS expression data. Pearson correlations have been calculated for each gene versus all other genes. The correlation matrix has been used as background distribution for genome-wide expression similarities. The 99%-quantile has been numerically determined as significance level for co-expression of a gene pair. As an example, additional file 2 shows the background distribution for the MPSS expression data. X-axis depicts Pearson Correlation Coefficients, y-axis the number of gene pairs. The line marks the obtained 99%-quantile for MPSS at r = 0.79.

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