Table 4.
Ontology-Based Applications in Stem Cell Databases
| Databases | Ontology Interactions |
|---|---|
| 1. SyStemCell | 1.1 Gene Ontology database; 1.2 Biocarta Pathway; 1.3 Biosystems Pathway, and 1.4 dbDEPC database (correlation analysis). |
| 2. CODEX | 2.1 Gene Quest (TF’s targets and gene associations for human samples; ChIPpeakAnno and peak-to-gene associations). |
| 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 Galaxy analysis software to enhance ontology searches. |
| 5. StemFormatics | 5.1 Gene clustering; 5.2 Hierarchical clustering and comparative marker selection through GenePattern module |
| 6. LINCS | 6.1 Drug-pathway browser, TieDIE (HMS LINCS); 6.2 Drug/Cell line Browser, Enrichr, Drug Response Browser (BD2K-LINCS DCIC); |
| 6.3 Omics Integrator (Neuro LINCS); 6.4 ICV App (LINCS Transcriptomics), etc. | |
| 7. LifeMap Discovery | 7.1 A detailed description of the developmental ontology of organ/tissues, anatomical compartments and cells; 7.2 Gene expression profiling in adult mammalian organs, tissues, anatomical compartments and cells, cultured stem, progenitor and primary cells, or cells derived via differentiation protocols to allow characterization of cells by gene expression patterns. |
| 8. StemMapper | 8.1 Heatmaps; 8.2. Correlation analysis. |
| 9. ESCAPE | 9.1 GOI enrichment with ESCAPE-listed genes RNAi screens, protein lists from IP-MS pull-downs, genes differentially expressed after knock-down or over-expression, and target genes for transcription factors and histone modifications as determined by ChIP-seq. |
| 10. SKiP Stem Cell Knowledge and Information Portal | n/a |
| 11. hPSCreg | n/a |
| 12. CellNet | 12.1 Analysis of protein and transcription regulatory interactions. |
| 13. StemCellNet | 13.1 Statistical analysis examining physical protein interaction, transcriptional reg. interactions; 13.2 Online statistical analysis platform allowing up to 500 genes input. |
| 14. HSC-explorer | 14.3 Database is linked to EntrezGene, KEGG, miRBAse, Gene Ontology, or CORUM. |
| 15. CORTECON | 15.1 Analysis using developing cerebral cortex transcriptome in humans. |
| 16. ESCD | 16.1 Query by Gene ID; 16.2 Query by GO term. |