Selected examples of the detected SREs.

<p># Occ. is abbreviation for number of occurrences.</p

Interaction network of 103 QTLs for the number of panicles per plant.

<p>The circle shows the bin map and columns indicate position of the makers (ticks in million base pairs). The thickness of a link is proportional to the strength of the interaction effect. A short straight line indicates a main effect. Molecularly characterized genes related to yield are also labeled in the appropriate positions of the genome.</p

Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data

<p>Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.</p

Interaction network of seven QTLs for yield per plant.

<p>The circle shows the bin map and columns indicate position of the makers (ticks in million base pairs). The thickness of a link is proportional to the strength of the interaction effect. A short straight line indicates a main effect. Molecularly characterized genes related to yield are also labeled in the appropriate positions of the genome.</p

Estimated QTL effects from the full model for the number of grains per panicle.

<p><i>^a</i>add: additive effect; dom: dominance effect. If <i>i</i> equals <i>j</i>, then it is a main effect, otherwise, it is an interaction between locus <i>i</i> and locus <i>j</i>. Total number of effects is 5, all with a <i>p</i>-value ≤0.01.</p><p><i>^b</i>The estimated marker effect is denoted by and the standard deviation is denoted by .</p><p><i>^c</i><i>P</i>-value is obtained via <i>t</i>-test.</p><p><i>^d</i>Phenotypic variation explained.</p

Interaction network of nine QTLs for the number of grains per panicle.

<p>The circle shows the bin map and columns indicate position of the makers (ticks in million base pairs). The thickness of a link is proportional to the strength of the interaction effect. A short straight line indicates a main effect. Molecularly characterized genes related to yield are also labeled in the appropriate positions of the genome.</p

Estimated QTL effects from the main effect model for grain weight.

<p><i>^a</i>add: additive effect; dom: dominance effect. Total number of effects is 38, only 30 effects with a <i>p</i>-value ≤0.01 are listed in this table.</p><p><i>^b</i>The estimated marker effect is denoted by and the standard deviation is denoted by .</p><p><i>^c</i><i>P</i>-value is obtained via <i>t</i>-test.</p><p><i>^d</i>Phenotypic variation explained.</p

Estimated QTL effects from the main effect model for yield per plant.

<p><i>^a</i>add: additive effect; dom: dominance effect. Total number of effects is 4, all with a <i>p</i>-value ≤0.01.</p><p><i>^b</i>The estimated marker effect is denoted by and the standard deviation is denoted by .</p><p><i>^c</i><i>P</i>-value is obtained via <i>t</i>-test.</p><p><i>^d</i>Phenotypic variation explained.</p

Illustration of equation (12).

<p>Two possible SREs are considered in this example, one for SF1, and the other one for SF2. Four different conditions are shown. Binding of either SF can affect the probability of spliceosome assembly. The arrow connecting two SFs indicates the interaction between two SFs. The contribution to spliceosome assembly from SFs is represented by , and .</p

Interaction network of 52 QTLs for grain weight.

<p>The circle shows the bin map and columns indicate position of the makers (ticks in million base pairs). The thickness of a link is proportional to the strength of the interaction effect. A short straight line indicates a main effect. Molecularly characterized genes related to yield are also labeled in the appropriate positions of the genome.</p