Table 3.
Data Analysis Tools Used in Stem Cell Databases
| Database | Data Analysis Tools |
|---|---|
| 1. SyStemCell | 1.1 Co-localization analysis; 1.2 Venn Diagram plotting; 1.3 DAVID enrichment analysis |
| 2. CODEX | 2.1 Motif discovery analysis and peak profile correlation analysis |
| 3. ESTOOLS Data@Hand | 3.1 Differential expression analysis; 3.2 Co-expression analysis; 3.3 Clustering and heatmap analysis; 3.4 Gene expression profiling; 3.5 Sample-wise clustering and dendrogram generation; 3.6 GO and KEGG enrichment |
| 4. Stem Cell Discovery Engine | 4.1 Gene list comparison by gene signatures, molecular signatures, and pathways |
| 5. StemFormatics | 5.1 Gene clustering and heatmap analysis through Hamlet; 5.2 Hierarchical clustering and comparative marker selection through GenePattern module |
| 6. LINCS | 6.1 Drug pathway browser; 6.2 LINCS analytics; 6.3 Drug/Cell line Browser; 6.4 Repurposing App; etc. |
| 7. LifeMap Discovery | 7.1 Partnered with custom GeneAnalytics gene analysis suite |
| 8. StemMapper | 8.1 Heatmap, Principal Components Analysis, and Pearson correlation analysis |
| 9. ESCAPE | 9.1 Enrichment analysis and lineage prediction |
| 10. SKiP Stem Cell Knowledge and Information Portal | - None |
| 11. hPSCreg | - None |
| 12. CellNet | 12.1 R software analysis of protein and transcription regulatory interactions |
| 13. StemCellNet | 13.1 Web-based analysis of molecular networks; 13.2 Statistical analysis examining physical protein interaction, transcriptional reg. interactions; |
| 13.3 Online statistical analysis platform allowing up to 500 genes input | |
| 14. HSC-explorer | 14.1 Bioinformatics resource allowing the search of pathways correlated to hematopoiesis; |
| 14.2 Web-based analysis platform allowing visualization of data. Diagrams can be downloaded as SBML, graphML, or jpg files; | |
| 14.3 Database is linked to EntrezGene, KEGG, miRBAse, Gene Ontology, or CORUM | |
| 15. CORTECON | 15.1 R-analysis using developing cerebral cortex transcriptome in humans; 15.2 Online resource allowing multiple views of developing cortex data |
| 16. ESCD | 16.1 Online repository which contains perturbation and ChIP experiments in ESCs |