Article Figures & Data
- Figure 1
Volcano plot. Differentially expressed (DE) proteins are represented in terms of their measured significance of the change (y-axis) and the expression change (x-axis). Dotted lines represent the thresholds used to select the DE genes: 0.6 for expression change and 0.05 for p value. The upregulated proteins (positive log fold change) are shown in red, whereas the downregulated genes are blue. Insignificant proteins are shown in black.
- Figure 2
(A) Broad perspective of protein:protein interaction showing clusters of highly connected subnetworks of interconnected proteins. (B) Zoomed perspective of protein:protein interaction showing central suite of largest network. The higher the number of connections, the closer to the center The gene will be drawn. Blue indicates a downregulated differentially expressed (DE) protein, and red indicates an upregulated DE protein. A, activation; B, binding; C, catalysis; R, reaction.
- Figure 3
Enrichment map from gene set enrichment analysis) illustrating networks of significantly enriched gene sets from proteomic analysis. Node size represents the number of genes in the gene set; edge thickness is proportional to the overlap between gene sets; red represents upregulation with valproic acid treatment.
- Figure 4
Cellular networks affected by VPA treatment. Enriched gene sets based on differentially expressed proteins and subsequent enrichment analysis mapped into common clusters. Nodes represent pathways and edges represent overlapping genes. Increasing node size represents increased number of proteins contributing to that pathway. Increasing edge thickness represents increased overlap between pathways. Node darkness corresponds to decreasing p value according to legend in bottom right. VPA, valproic acid.
- Table 1
Gene ontology (GO) biologic processes significantly enriched after valproic acid treatment
GO term # proteins (DE/all) P value Low-density lipoprotein particle clearance 6/9 0.002 ATP hydrolysis coupled cation transmembrane transport 9/19 0.003 SRP-dependent cotranslational protein targeting to membrane 10/24 0.005 Viral transcription 10/24 0.005 Ephrin receptor signaling pathway 7/15 0.009 Membrane organization 31/112 0.01 Regulation of hormone secretion 9/3 0.012 G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 9/17 0.018 Response to insulin 11/33 0.021 Generation of precursor metabolites and energy 30/110 0.026 Nuclear-transcribed mRNA catabolic process 10/30 0.028 Mitochondrion organization 20/75 0.03 Retrograde vesicle-mediated transport, Golgi to Endoplasmic Reticulum (ER) 5/11 0.031 Regulation of neurotransmitter transport 10/19 0.033 Regulation of nucleotide metabolic process 6/15 0.036 Gluconeogenesis 7/19 0.037 Antigen processing and presentation 7/19 0.037 Dendrite morphogenesis 7/19 0.037 Monovalent inorganic cation transport 16/58 0.038 Cellular response to hormone stimulus 19/64 0.04 Metal ion transport 20/77 0.04 ATP metabolic process 19/73 0.044 Regulation of dendrite development 5/12 0.046 Regulation of peptidyl-tyrosine phosphorylation 6/16 0.049 Tricarboxylic acid cycle 7/20 0.049 # proteins are the number of proteins differentially expressed in this proteomic data set out of the total number of proteins that contribute to that GO term.
P value represents the corrected p value after Elim pruning.
- Table 2
Gene ontology (GO) molecular functions significantly enriched after valproic acid treatment
GO term # proteins (DE/all) P value GTP binding 18/51 0.002 GTPase activity 14/38 0.003 Structural constituent of ribosome 9/20 0.004 Clathrin adaptor activity 4/5 0.004 Ionotropic glutamate receptor binding 3/3 0.005 Organic anion transmembrane transporter activity 6/12 0.01 Active transmembrane transport activity 11/27 0.02 Drug transmembrane transporter activity 4/7 0.021 Hexosyl transferase activity 4/7 0.021 6-phosphofructokinase activity 2/2 0.031 Malate dehydrogenase activity 2/2 0.031 Calcium-transporting ATPase activity 2/2 0.031 Voltage-gated anion channel activity 2/2 0.031 Oxaloacetate decarboxylase activity 2/2 0.031 Porin activity 2/2 0.031 G protein-coupled serotonin receptor binding 2/2 0.031 Angiostatin binding 2/2 0.031 Alpha-glucosidase activity 2/2 0.031 Purine ribonucleotide binding 47/178 0.033 Isocitrate dehydrogenase activity 3/5 0.042 GTP-dependent protein binding 3/5 0.042 Potassium ion binding 3/5 0.042 # proteins are the number of proteins differentially expressed in this proteomic data set out of the total number of proteins that contribute to that GO term. P value represents the corrected p value after Elim pruning.
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