Table 1. Resources for validating peak-TF-gene regulatory relationship.
While there is no existing experimental approach to validate all three factors in a trio at high resolution with high throughput, we resort to existing databases and orthogonal sequencing data to validate peak-gene, peak-TF, and TF-gene pairs, completing the loop.
| Validation | Database/Resource | Description | Organism | Tissue | PMID | GSE | GSM | URL |
|---|---|---|---|---|---|---|---|---|
| Peak-gene | FANTOM5 (HACER) | Tissue-specific enhancer database | Human | Blood cell lines | 24670763 | NA | NA | http://bioinfo.vanderbilt.edu/AE/HACER |
| 4DGenome (HACER) | Tissue-specific enhancer database | Human | Blood cell lines | 25788621 | NA | NA | http://bioinfo.vanderbilt.edu/AE/HACER | |
| EnhancerAtlas2.0 | Tissue-specific enhancer database | Human | Blood cell lines | 31740966 | NA | NA | http://www.enhanceratlas.org | |
| GTEx | Tissue-specific cis-eQTLs | Human | Whole blood | 29022597 | NA | NA | https://gtexportal.org | |
| PLAC-seq | Enhancer-promoter interactions by PLAC-seq (rep 1) | Mouse | Embryonic forebrain at day 16.5 | 31695190 | GSE130399 | GSM3819641 | https://www.ncbi.nlm.nih.gov/geo | |
| Enhancer-promoter interactions by PLAC-seq (rep 2) | GSM3819642 | |||||||
| Super-enhancer | H3K4me1 and H3K27ac ChIP-seq | Mouse | Transit-amplifying cell (TAC) from mouse hair follicle | 25799994 | GSE61316 | GSM1502001 | https://www.ncbi.nlm.nih.gov/geo | |
| GSM1502003 | ||||||||
| Peak-TF | Cistrome | A data portal for ChIP-Seq and chromatin accessibility data in human and mouse | Human | B lymphocyte, T lymphocyte, monocyte | 27789702 | Supplementary Table S2 | http://cistrome.org | |
| TF ChIP-seq | Olig2 ChIP-seq | Rat | Oligodendrocyte precursor cell (OPC) | 23332759 | GSE42454 | GSM1040156 | https://www.ncbi.nlm.nih.gov/geo | |
| Immature oligodendrocyte (iOL) | GSM1040157 | |||||||
| Mature oligodendrocyte (mOL) | GSM1040158 | |||||||
| Neurog2 ChIP-seq | Mouse | Embryonic cerebral cortex at day 14.5 | 27600842 | GSE63620 | GSM1553880 | |||
| Eomes ChIP-seq | GSM1553879 | |||||||
| Tbr1 ChIP-seq | Embryonic whole cortex at day 15.5 | 27325115 | GSE71384 | GSM1833461 | ||||
| TF-gene | knockTF | A database of human gene expression profiles with knockdown/knockout of transcription factors | Human | Blood cells | 31598675 | NA | NA | http://www.licpathway.net/KnockTF |
| hTFtarget | A database of human transcription factors and their targets | Human | Blood cells | 32858223 | NA | NA | https://bio.tools/hTFtarget | |