Fig 1.
Comparison of overall gene expression between the three treatment groups.
Mammary gland samples belong to wild-type dams (WT), Tryptophan hydroxylase (Tph1) deficient dams (serotonin deficient; KO), and Tph1 deficient dams injected daily with 5-hydroxytryptophan (RC). (A) The bar graph shows the number of genes upregulated in each group for each of the three pairwise comparisons. The numbers represent the total number of differentially expressed genes (DEG) at 5% FDR (and at 1% FDR in parenthesis). (B) The Venn diagram shows the overlap between genes that showed significant differential expression at 5% FDR in each of the three pairwise comparisons.
Table 1.
Functional characterization of the 62 most significant genes (FDR ≤ 0.01 and fold change ≥ 2) detected simultaneously in the mouse mammary gland on day 10 of lactation between WT vs. KO dams and WT vs. RC dams.
Table 2.
Functional characterization of the 97 most significant genes (FDR ≤ 0.01 and fold change ≥ 2) detected in the mouse mammary gland on day 10 of lactation between WT vs. KO dams.
These are functional terms that were detected exclusively in this specific comparison.
Table 3.
Functional characterization of the 204 most significant genes (FDR ≤ 0.01 and fold change ≥ 2) detected in the mouse mammary gland on day 10 of lactation between WT vs. RC dams.
These are functional terms that were detected exclusively in this specific comparison.
Fig 2.
List of Gene Ontology (GO) biological process terms that were significantly enriched (FDR ≤ 0.01) with differentially expressed genes (DEG) detected simultaneously in both pairwise comparisons involving the wild-type (WT) mammary glands on day 10 of lactation: WT vs. Knock-out (A) and WT vs. Rescue (B).
The graph shows the term name, the total number of genes within each term, and the number of genes up-regulated (green) and down-regulated (yellow) in the knock-out or rescue compared to the WT. Knock-out = Tryptophan hydroxylase (Tph1) deficient mice; Rescue = Tph1 knock-out + 100 mg/kg daily injections of 5-hydroxytryptophan.
Fig 3.
List of Gene Ontology (GO) terms that were significantly enriched (FDR ≤ 0.01) with differentially expressed genes (DEG) detected between wild-type (WT) vs. Knock-out mammary glands on day 10 of lactation.
The graph shows the term name, the total number of genes within each term, and the number of genes up-regulated (green) and down-regulated (yellow) in the knock-out compared to the wild-type. Knock-out = Tryptophan hydroxylase (Tph1) deficient mice.
Fig 4.
List of Gene Ontology (GO) terms that were significantly enriched (FDR ≤ 0.01) with differentially expressed genes (DEG) detected between wild-type (WT) vs. Rescue mammary gland on day 10 of lactation.
The graph shows the term name, the total number of genes within each term, and the number of genes up-regulated (green) and down-regulated (yellow) in the Rescue compared to the wild-type. Rescue = Tryptophan hydroxylase (Tph1) knock-out + 100 mg/kg daily injections of 5-hydroxytryptophan.
Table 4.
Medical Subject Headings (MeSH) terms that were significantly enriched (FDR ≤ 0.01) with differentially expressed genes detected in the mammary gland on day 10 of lactation for the following pairwise comparisons: WT vs. KO and WT vs. RC.
Fig 5.
Validation of overall gene expression.
Fold changes of four differentially expressed genes measured by RNA-Seq (blue) versus qRT-PCR (orange). Genes period circadian clock 2 (Per2), a novel transcript unit [Chr5:30,208,00730,212,059] (NTU), and G protein-coupled receptor 113 (Gpr113) were statistically upregulated in the mammary gland of RC dams while gene GLIS family zinc finger 3 (Glis3) was statistically upregulated in the mammary gland of WT dams.