This figure shows the edges (grey) of the Multinet, which correspond to interactions between genes.

<p>Only the interactions of genes that are involved in more than one network are shown for clarity. (A) Nodes corresponding to LoF-tolerant and essential genes are shown in blue and red respectively. Size of the nodes is scaled based on the degree centrality of the gene in Multinet. Essential genes tend to be bigger and in the center while LoF-tolerant genes tend to be smaller and on the periphery. (B) Nodes corresponding to LoF-tolerant and essential genes are shown in orange and green respectively. Size of the nodes is scaled based on the number of networks the gene is involved in. Essential genes tend to be involved in more networks and hence are bigger while LoF-tolerant genes are smaller. Most LoF-tolerant genes are not involved in any network and are not present in the Multinet.</p

Distributions of various network and evolutionary properties for the four gene categories: LoF-tolerant (blue); neutral (cyan); with known disease-causing mutations (pink) and essential (red).

<p>Spearman correlation coefficients (C) between the corresponding property values of all genes with the gene significance scores are shown at the top right of each boxplot. Corresponding pvalues (P) are also shown.</p

Structural Interaction Network (SIN).

<p>(A) Schematic of SIN construction shown by combining three-dimensional protein structural information from ipfam with PPI network. Nodes in resulting SIN are shown in red with color intensity indicating the number of interaction interfaces used by the protein. Closer look is provided for four nodes in SIN. While the surface of proteins is generally shown by circular lines, an interface is depicted using a straight line. Rectangle 1 shows a protein using one interaction interface to interact with one protein; rectangle 2 shows a protein with two simultaneously possible interactions and consequently two interaction interfaces; rectangle 3 shows a protein with three mutually exclusive and one simultaneously possible interactions resulting in two interaction interfaces; rectangle 4 shows four simultaneously possible interactions resulting in four interfaces. (B) Distributions of accessible surface areas of missense SNPs (cyan) and disease-causing missense SNVs (pink).</p

Prediction of functional indispensability scores.

<p>(A) ROC curve resulting from cross-validation of the logistic regression model to distinguish LoF-tolerant and essential genes. Participation of (B) LoF-tolerant and (C) essential genes in various networks. Rows correspond to gene names while columns correspond to networks. Presence of a gene in a network is shown by red while its absence is shown by yellow. (D) Distribution of predicted functional indispensability scores for five gene categories: LoF-tolerant (blue); neutral (cyan); identified in GWA studies (light blue); with known disease-causing mutations (pink) and essential (red).</p

Summary of the RNA-seq based assembly, functional annotation and coding sequences (CDs) from the foot transcriptomes of <i>P</i>. <i>viridis</i>.

<p>Summary of the RNA-seq based assembly, functional annotation and coding sequences (CDs) from the foot transcriptomes of <i>P</i>. <i>viridis</i>.</p

Validation of byssus protein coding genes by qRT-PCR. β-actin was used as an internal control and each value represents average of 3 separate biological replicates.

<p>Real-time PCR validates the byssus protein coding genes (A) between the Cd_50 and Control and (B) between the Cd_100 and Control (48-h).</p

High accumulation of Cd in the <i>P</i>. <i>viridis</i> byssus.

<p>High accumulation of Cd in the <i>P</i>. <i>viridis</i> byssus.</p

DEG number for Cd_50 vs Control and Cd_100 vs Control.

<p>(A) Up-regulated gene numbers at the three time points; (B) Down-regulated gene numbers at the three time points; (C) Heatmap representation of cluster analysis for the expression patterns of over 9,000 DEGs between the control and different concentrations of Cd stimulation (48-h treatment). The RPKM change patterns of the two concentration of Cd stimulation (Cd_50 and Cd_100) were shown to be clustered together.</p

Annotation of unigenes from the <i>P</i>. <i>viridis</i> foot transcriptomes.

<p>Venn diagrams of annotated unigenes (A) and Nr species distribution of unigenes (B) are useful for assessment of the transcriptome assemblies.</p

Function classification of DEGs in the <i>P</i>. <i>viridis</i> transcriptomes (48-h treatment).

<p>(A) KEGG metabolic pathway annotation of DEGs; (B) Histogram presentations of the COG classification.</p