Table 7.
Complexity of Rubrics Characterizing Stem Cell Research Databases
| Stem Cells Database Rubrics | Complexity of Each Rubric | Complexity Breakdown | % of Databases with the Rubric |
|---|---|---|---|
| Summary | N/A | N/A | 100% |
| Stem Cell Lineage | 8 | Adult stem/progenitor cell; embryonic progenitor cell; ESC; fetal stem/progenitor cell; iPSC; cell lines; primary cells; and tissue/cell composite | 100% |
| Stem Cell Species | 5 | human, mouse, rat, pig, macac | 100% |
| Publications | N/A | N/A | 88% |
| Stem Cell Type/Name | Thousands of stem cell types | 88% | |
| Data analysis tools | 28 | Co-localization analysis; Venn Diagram plotting; DAVID-enriched analysis; peak profile correlation analysis; gene set control analysis; motif discovery analysis; differential expression analysis; clustering and heatmap analysis; gene expression; GO and KEGG enrichment; gene list comparison, and 15 more | 88% |
| Organization | N/A | N/A | 75% |
| Sequencing Platform | Next Generation Sequencing | Illumina, others | 75% |
| Cell Surface Markers | Large number of cell surface proteins | 56% | |
| Disease State of Donor | Large number of diseases | X-linked juvenile retinoschisis; Pathological myopia; Short rib-thoracic dysplasia syndrome; DFNB4, | 50% |
| Pendred syndrome; Xp22.2 Exon; Childhood acute B-lymphoblastic leukemia; Parkinson’s disease; | |||
| Alzheimer’s disease; Fragile X-syndrome and others | |||
| Tissue Type | Large number of tissue types | Blood; Adipose; Mesenchymal Stem Cells; Endothelium; Bone; Heart; Cartlidge; Liver; Amnion; | 44% |
| Tooth; Placenta; Uterus; Epithelial Cells; Umbilical Cord, and others | |||
| Cell Culture Conditions and Treatment | Variety of conditions | 44% | |
| PI/Corresponding Researcher | N/A | N/A | 38% |
| Transcription Factors Expression/Regulation | 210 (CODEX); +9 other databases | RUNX1; CBFB; CEBPA; CTDP1; EP300; ERG; FUSELF1; ERG; FLI1; GATA2; HDAC1; MYH11 | 38% |
| RUNX3; CDK7; CDK9; POLR2A; BCL6; BCOR; SMRT; ZNF143; SPI1; BACH2, and others | |||
| Microarray Data | 420 microarray datasets (StemFormatics); +5 other databases | 38% | |
| Gene Expression Data | 10,401 (LifeMap Discovery); 5813 (ESCAPE); +4 other databases | 31% | |
| miRNA Expression/Transcription Profiling | N/A | N/A | 31% |
| Stem Cell Subtype | 132 (CODEX); +3 other databases | [CL]CMK; [PC]CD34+ acute myeloid leukemia blast cells; [CL]Kasumi-1+ scrambled siRNA; | 25% |
| [CL]ME-1; [CL]NB4; [CL]Lymphoblastoid; [PC] H1 ES derived angiogenic hematopoietic progenitor; | |||
| [PC] H7 ES derived anterior foregut, and others | |||
| Epigenetic modifications | 72 (CODEX); +11 other databases (Histone Modifications) | H3K4me1; H2A.Zac; H3K9Ac; H3K9K14ac; H2AFZ/H2A.Z; H3K4me3; H4K20me3; H3K27ac; | 25% |
| H3K27me3; H3K4me2; Ab4729; H3K79me2; H3Y41ph, and others | |||
| Sex of the donor | 2 | Female, male | 19% |
| Age of the Donor | N/A | N/A | 19% |
| Differentiation Status | N/A | N/A | 19% |
| Karyotype | N/A | N/A | 19% |
| Mutation Status of a Donor | Large number of abnormalities listed (CODEX); +2 other databases | Trisomy 21; translocation t(16,21; Acute Monocytic Leukemia; cervical adenocarcinoma; | 19% |
| p53 mutation; K562 erythrocytic leukaemia cells; erythrocytic leukemia cells; and others | |||
| Immunoprecipitation Antibody | N/A | N/A | 19% |
| Gene Annotation | N/A | N/A | 13% |
| miRNA-based Regulation/Interactions | N/A | N/A | 13% |
| Clinical Trials for Cell Therapies | 568 (LifeMap Discovery) | 6% | |
| Ethnicity of the Donor | N/A | N/A | 6% |
| Developmental Stage | N/A | N/A | 6% |
| Cell Derivation Process | N/A | N/A | 6% |
| Cell Morphology | N/A | N/A | 6% |
| Phenotype Quality | N/A | N/A | 6% |
| Tissue Histology | N/A | N/A | 6% |
| Protein Phosphorylation | N/A | N/A | 6% |