Supplemental Data

Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Complete normalized array data represented on an MA scatter-plot. Each circle represents a probe set plotted by the M value (fold change between term and midgestation samples) and the A value (mean estimated log intensity of term and midgestation samples). Red circles denote those probe sets that reach statistical significance by a moderated t-test and Bonferroni correction (P < 0.05).
• Supplemental Figure 2 - Heat map of differentially expressed genes with complete annotation. The normalized log intensity values for all 505 differentially expressed probe sets were centered to the median value of each probe set and colored on a range of –2 to +2, with yellow indicating high expression and blue indicating low expression. Columns represent a single placental array, and each row represents a single probe set. Arrays are arranged from left to right by increasing gestational age. Rows are then placed in rank order by fold change of the mean term (n = 9) versus mean midgestation (n = 27) values. The gene name, fold change, and probe set identity are provided for each row.
• Supplemental Figure 3 - K-means clusters of coexpressed differentially expressed genes. Differentially expressed probe sets were clustered into 11 groups using K-means (Euclidean). The seven remaining clusters are presented here as heat maps of the normalized log intensity data, permitting visual assessment of signal intensity and change over gestation (E through K). Arrays (columns) are arranged from left to right by increasing gestational age. Each probe set is annotated with gene symbol, fold change, chromosomal location and the GenBank accession number (ACC#).
• Supplemental Figure 4 - Ingenuity Pathway Analysis of functional categories for the differentially expressed genes. Functional categories (molecular and cellular; physiological processes) that contain a significant number of differentially expressed genes at a threshold of >–(log) 1.25 are shown along with gene symbol (See Supplemental Table 5 for alphabetical listing of gene symbols.)
• Supplemental Figure 5 - Differentially expressed genes that map to the Wnt-β catenin pathway. Based on the canonical pathways from GeneMapp, KEGG and IPA we created a diagram of the Wnt-β catenin pathway mapped to the array data. The differentially expressed genes are shown as either upregulated (red) or downregulated (green) at term (See Supplemental Table 5 for alphabetical listing of gene symbols.)
• Supplemental Figure 6 - Differentially expressed genes networked by using Ingenuity Pathway Analysis. Network analysis resulted in networks containing 10 to 28 differentially expressed genes. The top functions included in each network are listed at the top of the network. Molecules are placed in their subcellular location, and shapes indicate functional class (e.g., enzyme, transporter; see legend on figure). Solid arrows show direct relationships supported by published experimental data; dashed arrows show indirect relationships. Standard symbol names are provided as Supplemental Table 5. Shades of red (upregulated at term) and green (downregulated at term) reflect relative fold change. Asterisks denote duplicate probe sets; bold symbol names are the differentially expressed genes.
• Supplemental Table 1 - Assay-On-Demand or Primer/Probe Set Used for Q-PCR
• Supplemental Table 2 - Clinical Data for Basal Plate Samples
• Supplemental Table 3 - Canonical Pathways Analysis of Differentially Expressed Genes
• Supplemental Table 4 - Functional Annotation from Protein Modeling with ModBase Links and Updated Affymetrix Annotation
• Supplemental Table 5 - Complete alphebetical listing of differentially expressed probe sets.