Figure 1.
Development-associated changes in tissue expression patterns and the biological functions of the four dynamic types of liver genes.
(A) The four dynamic types of liver genes with differentially expressed mRNA during E11.5, E14.5, E15.5, and 3 dpp. All the 1,428 differentially expressed genes exhibited mRNA changes between any two developmental stages that exceeded 2 fold. (B) Hierarchical clustering of biological functions for the four dynamic types. The biological functions are annotated by PANTHER. The ratio of each function in a type is expressed relative to its median ratio across all the four types and is depicted according to a color scale shown at the bottom. Red and green indicate the ratio of each function above and below the median, respectively. The magnitude of deviation from the median is represented by the color saturation. (C) Tissue expression patterns of the four dynamic types, shown for both the transcriptome and proteome. The three axes represent the ratio of the tissue-enriched genes in liver, hematopoietic tissue, and embryonic tissue. Gene tissue distribution information was annotated by GeneAtlas.
Figure 2.
Pathway analysis of the dynamic types.
(A) Type A network, developed by Ingenuity Pathway Analysis (www.ingenuity.com), integrating the transcriptome (green) and proteome (red). When a gene is shared by both transcriptome and proteome, we choose its data of proteome. The biological functions of the network are indicated with rectangles and ellipses. (B) Type C (green) and type D (red) pathways of blood coagulation and complement cascades. Pathways shared by both types are shown as half red and green (A symbol in the pathways represents a group of genes but not only one gene. Different Type C or D gene presents at the same symbol.).
Figure 3.
Cluster analysis showing mRNA and protein abundance for genes differentially expressed in mouse liver at E11.5, E14.5, E15.5, and 3 dpp.
All the 2,593 differentially expressed mRNAs (left panel) and 187 differentially expressed proteins (right panel) changed more than 2-fold between any two developmental stages, as analyzed by Cluster 3.0 and TreeView. The expression level of each mRNA or protein at a development stage is shown relative to its median abundance across all the developmental stages and is depicted according to the color scale. Red and green indicate expression levels above and below the median, respectively. The magnitude of deviation from the median is indicated by color saturation.
Figure 4.
Up-regulation of blood coagulation and complement cascades at E14.5-E15.5.
Genes that were related to blood coagulation and complement cascades and exhibited 2-fold up-regulation between E14.5 and E15.5 were filtered and integrated into a network using Ingenuity Pathway Analysis (www.ingenuity.com). Genes related to blood coagulation and complement cascades are tethered to the label with green lines. The saturation of red shading indicates the degree of up-regulation.
Figure 5.
Validation of proteomic changes by western blot.
Expression of select proteins in the mouse liver at E11.5, E14.5, E15.5, and 3 dpp. Proteins that were analyzed included those exhibiting a type A pattern of expression (left column), those related to the mobilization of hematopoietic stem cells (middle column), and those related to liver function or other functions (right column). GAPDH served as an internal control.
Figure 6.
Validation of transcriptomic changes by RT-PCR.
The mRNA expression of select mouse liver genes at E11.5, E14.5, E15.5, and 3 dpp. Genes that were analyzed included genes related to hematopoiesis (left column) and genes related to liver function and development (right column). GAPDH served as an internal control.