Table 1:
Significant biological process gene ontology terms identified through DAVID pathway analysis of significant (p<0.05) proteins that were increased or decreased for VYS and EMB.
| Visceral Yolk Sac | ||
|---|---|---|
| Decreased | Increased | |
|
| ||
| 2 hr | Ribosome biogenesis | Short-term memory |
|
| ||
| Negative regulation of ATPase activity | ||
| 4 hr | Positive regulation of protein ubiquitination involved in ubiquitin-dependent | Cell migration |
| protein catabolic process | ||
|
| ||
| 6 hr | Cellular response to hydrogen peroxide | |
| Regulation of cell proliferation | ||
| - | Proteolysis | |
| DNA methylation | ||
| Negative regulation of canonical Wnt signaling | ||
| pathway | ||
|
| ||
| 8 hr | Regulation of centrosome duplication | - |
| Cellular response to interleukin-1 | ||
| NLS-bearing protein import into nucleus | ||
|
| ||
| 10 hr | Negative regulation of gene expression | |
| Transport | Thymus development | |
| Lipoprotein transport | Thyroid gland development | |
| Bone development | Regulation of cell proliferation | |
| Heart development | Transcription, DNA-templated | |
| Actin cytoskeleton organization | Positive regulation of cell migration | |
| Protein stabilization | ||
|
| ||
| Embryo | ||
|
| ||
| Wnt signaling pathway, planar cell polarity | ||
| 2 hr | - | pathway |
| Neural tube closure | ||
| Convergent extension involved in | ||
| organogenesis | ||
|
| ||
| 4 hr | Regulation of transcription, DNA-templated | Methylation |
| Cellular response to DNA damage stimulus | Ribosomal small subunit assembly | |
| Rac protein signal transduction | S-adenosylmethioninamine metabolic process | |
| Barbed-end actin filament capping | Translation | |
| Regulation of protein kinase C signaling | Cell-matrix adhesion | |
| Immune system process | Cellular response to amino acid stimulus | |
| Cellular response to transforming growth factor | ||
| beta stimulus | ||
|
| ||
| 6 hr | Bicellular tight junction assembly | |
| - | Myelin assembly | |
| Attachment of GPI anchor to protein | ||
|
| ||
| 8 hr | Response to amino acid | Ribosome biogenesis |
| DNA replication | rRNA processing | |
| Positive regulation of macroautophagy | Single organismal cell-cell adhesion | |
| DNA replication initiation | Ribosomal small subunit assembly | |
| Response to cadmium ion | Ventricular cardiac muscle cell action potential | |
| Post-translational protein acetylation | rRNA methylation | |
| Positive regulation of stress fiber assembly | ||
|
| ||
| 10 hr | Alpha-beta T cell differentiation | Metabolic Process |
| Negative regulation of endothelial cell | ||
| apoptotic process | ||
| Cell motility | ||
In addition to pathway analysis based on categorization of proteins into groups increased and decreased by VPA exposure, pre-ranked Gene Set Enrichment Analysis (GSEA) was also performed. In the EMB, GSEA identified 46 developmentally relevant pathways that were more enriched in proteins that increased in abundance following VPA exposure and seven pathways that were more enriched in decreased proteins (Supplemental Table 2). There was no enrichment of developmental pathways at 4 hr for increased proteins, or 6, 8, and 10 hr for decreased proteins.