Figure 1.
Flowchart of microarray data ranking and analysis.
A) 450 E-dependent DEG list were identified by microarray in ovaries of ArKO vs WT as having ±2-fold change expression with p-value<0.05. B) The E-dependent DEG list was annotated using Gene Ontology and analysed for molecular function, cellular component and biological processeses. C) E-dependent DEG from the list were ranked based upon fold change of up/down regulation (Fold change); significance of the change (P-value); 5 major GeneGo biological processes genes: Hormonal processes, Reproductive processes, Sex determination and differentiation, Apoptosis and, Cellular processes. D) Genes that possess EREs. Genes identified from the list using these methods were compiled to form an E-dependent DEG with ERE Shortlist which was used for downstream analysis of gene networks and pathways affected by E using GeneGo pathway analysis. The E-dependent DEG list can be found in Table S1.
Table 1.
E-dependent DEG in ArKO ovary compared to WT ovary.
Figure 2.
Gene Ontology (GO) annotation E-dependent DEG list with Molecular Function, Cellular Component and Biological Processes categories.
A) Pie chart shows the distribution of the 388 E-dependent DEG that were matched to a Molecular Function using GO [6]. B) Pie chart shows the distribution of the 319 E-dependent DEG that were matched to a Cellular Component using GO [6]. C) Pie chart shows the distribution of the 302 E-dependent DEG that were matched to a Biological Processes using GO [6].
Table 2.
Twenty most up-regulated genes in the E-dependent DEG list.
Table 3.
Twenty most down-regulated genes in the E-dependent DEG list.
Table 4.
Twenty most significant differentially up-regulated genes in the E-dependent DEG list.
Table 5.
Twenty most significant differentially down-regulated genes in the E-dependent DEG list.
Figure 3.
Molecular network of identifying E-dependent DEG with ERE Shortlist genes in ArKO ovary.
Solid connecting lines represent a direct relationship between two molecules: activation marked as green solid line, inhibition marked as red solid line and unspecified marked as gray solid line. Thick cyan lines indicate the fragments of canonical pathways. Up-regulated genes are marked with red circles; down-regulated with blue circles. Genes with ERE are encircled. (Please refer to Figure S1 for detailed network object legend).
Figure 4.
Molecular network of identifying E-dependent DEG with ERE Shortlist genes in ArKO ovary.
Solid connecting lines represent a direct relationship between two molecules: activation marked as green solid line, inhibition marked as red solid line and unspecified marked as gray solid line. Thick cyan lines indicate the fragments of canonical pathways. Up-regulated genes are marked with red circles; down-regulated with blue circles. Genes with ERE are encircled. (Please refer to Figure S1 for detailed network object legend).
Figure 5.
Molecular network of identifying E-dependent DEG with ERE Shortlist genes in ArKO ovary.
Solid connecting lines represent a direct relationship between two molecules: activation marked as green solid line, inhibition marked as red solid line and unspecified marked as gray solid line. Thick cyan lines indicate the fragments of canonical pathways. Up-regulated genes are marked with red circles; down-regulated with blue circles. Genes with ERE are encircled. (Please refer to Figure S1 for detailed network object legend).
Figure 6.
Molecular network of identifying E-dependent DEG with ERE Shortlist genes in ArKO ovary.
Solid connecting lines represent a direct relationship between two molecules: activation marked as green solid line, inhibition marked as red solid line and unspecified marked as gray solid line. Thick cyan lines indicate the fragments of canonical pathways. Up-regulated genes are marked with red circles; down-regulated with blue circles. Genes with ERE are encircled. (Please refer to Figure S1 for detailed network object legend).
Figure 7.
Molecular network of identifying E-dependent DEG with ERE Shortlist genes in ArKO ovary.
Solid connecting lines represent a direct relationship between two molecules: activation marked as green solid line, inhibition marked as red solid line and unspecified marked as gray solid line. Thick cyan lines indicate the fragments of canonical pathways. Up-regulated genes are marked with red circles; down-regulated with blue circles. Genes with ERE are encircled. (Please refer to Figure S1 for detailed network object legend).
Table 6.
Top five gene networks identified by GeneGo Pathways Analysis using the E-dependent DEG Shortlist of 78 unique genes.