Figure 5
Network analysis in M. capitata of gene co-expression under heat stress. (a) Network topology of one WGCNA module (significantly enriched with up-regulated genes following 1 hr heat stress over 1 hr ambient control, p-value < 0.05, Fisher’s exact test, Methods). Each node represents a gene, and edges represent correlations between them. Major hubs (annotated nodes) are identified by the top 10% of degree and betweenness values in the network. Node size is directly correlated with degree (number of adjacent neighbors). Dark to light connections indicate high to low co-expression coefficients, respectively. Node color is correlated with the DESeq2 characterized heat 1 hr vs. ambient 1 hr contrast of significantly differentially expressed genes (i.e., gradient of dark red to light pink indicate highest to lowest over expression after 1 hr heat exposure; similarly, the gradient of dark blue to light blue indicates under expression). (b) Enlargement of the network region containing Tob1/Tob2 like transcription factor regulators. Dark to light red/blue nodes indicate high to low over/under expression, respectively, after 1 h of heat exposure. Legend for network hubs: 1. BTG/Tob- transcription factor regulators (K14443); 2. Metal regulated homodimeric repressors (IPR011991); 3. Zinc finger (Znf) domain participating in binding DNA, RNA, protein and/or lipid substrates (IPR013087); 4. Cysteine- serine-rich nuclear proteins (CSRNP) - transcription activator (K17494); 5. cAMP response element-binding protein (CREB)- transcription factor (K09050); 6. Rab30 (GTPases) regulators of intracellular membrane trafficking (K07917); 7. RAN- GTPase involved in nucleocytoplasmic transport of proteins and RNA through the nuclear pore complex (K07936); 8. Cytosolic phospholipase A2 (PLA2G4)- initiating lipid-based regulation of immune response, and other intracellular pathways (K16342). 9. Proteinase inhibitor I35 domain (IPR001820). All node annotations depicted in both (A and B) panels were generated by identifying significantly enriched (p-value < 0.05, Fisher’s exact test) KEGG orthologs (indicated by Kxxxxx) or InterPro domains (indicated by IPR0xxxxx).
