Figure 1.
Pipeline of data collection, curation and recording in SyStemCell.
Figure 2.
Database content of SyStemCell.
(A) Summary of original papers on seven levels of regulation, where transcription products possess the largest proportion of all recorded papers in SyStemCell. (B) Summary of Top 5 stem cell types from original papers, where the proportion of ESC (Embryonic Stem Cells) ranks the first. MSC, Mesenchymal Stem Cells; HSC/HPC, Hematopoietic Stem/Progenitor Cells; NSC, Neural Stem Cells and iPSC, induced Pluripotent Stem Cells. (C) Summary of entry across seven regulatory levels. The entry counts are log2 transformed for each level. (D) Pie plot of regulatory levels occupied by all 43,434 genes in SyStemCell.
Figure 3.
Queries retrieved from SyStemCell, using mouse gene “Pou5f1” (Oct4) as an example.
(A) Multi-level summary page and external annotation (only partial displayed). (B) DNA CpG Methylation information. (C) Histone modification information (only partial displayed) and (D) microRNA regulation information.
Figure 4.
Browse page and dynamic selecting box.
(A) Browse page for seven levels of regulatory information in SyStemCell. (B) Dynamic selecting box (using histone modification H3K27me3 in mouse ES and fibroblasts cells as an example). “Child” boxes are only displayed when their “Parent” boxes are selected.
Figure 5.
Co-Localization analysis page and example.
(A) Analysis can be carried in two organisms (human and mouse) and three regulation levels (CpG hydroxy/methylation, histone modification and transcription factor binding) (B) Correlation matrix created by selecting interested modifiers/regulators (Pou5f1, Nr5a2, Sox2, Nanog, H3K4me3 and H3K27me3) in mouse. The color of red and shape close to slash indicate more positive correlation, while the color of blue and shape close to backslash indicate negative correlation, and the color of grey and shape like circle indicate no correlation. (C) Venn-diagram of Pou5f1 targeted genes and Nr5a2 targeted genes. Gene list in each part of the plot can be downloaded separately to run enrichment analysis in DAVID.
Figure 6.
Conserved co-regulatory network in both Homo sapiens and Mus musculus species.
Each interconnected edge (representing a pair of modifier/regulator) must satisfy three criteria, i.e., existed in both human and mouse, the Bonforroni adjusted p<0.001 and the intersection genes of the pair was enriched at least 2-fold. The gene symbols are shown as in Mus musculus species. The node size is in proportion to its degree and color represents different types of modifier/regulator, red, DNA hydroxy/methylation; blue, hisotone modification and yellow, transcription factor.
Table 1.
Nodes with high coreness in combinatorial TF-miRNA network of mouse ESC.
Figure 7.
Motif patterns in the mouse ESC combinatorial network.
Green nodes represent TFs, and red nodes represent miRNAs. Nodes in rectangle shape are ESC core TFs according to literatures. All the edges are retrieved from SystemCell except those in purple, which are supplemented by predicted miRNA-target relationships.