News
PearGRN is released now!
Note: The multi-omics integrative network is constructed based on omics data from pear fruit samples.
Introduction
pearGRN (Pear Integrative Gene Regulatory Network Database) is a comprehensive resource designed to consolidate various omics regulatory networks, facilitating the retrieval of gene regulatory relationships and protein interactions. It provides a platform to predict key genes associated with important breeding-related traits.
The database offers several tools including BLAST, Expression, Jbrowse, Gene Search, Node Search, Network Creation, Network Comparison, TF Regulation, Interact Finder, TraitConnect and ML Predictor, making it an essential resource for researchers in pear genetics and genomics.
PearGRN is hosted by the Central of Pearl Engineering Technology Research at Nanjing Agricultural University and aims to support advanced genetic research and breeding projects in pears.
Citations: Li, H., Qiao, X., Huo, Y., Li, L., Qi, K., Xie, Z., Rui, W., Yang, Y., Li, Q., Zou, Y., et al. (2025). A multi-omics integrative gene network of pear (Pyrus). J. Integr. Plant Biol. 00: 1–20. https://doi.org/10.1111/jipb.70117
Network Information
| Network | Node number | Edge number | TF number | Gene number | Transitivity | Avg. distance | Modules (≥5 genes) | Hub gene |
|---|---|---|---|---|---|---|---|---|
| High Confidence Coexpression Network | 22175 | 637942 | 1937 | 20238 | 0.334 | 3.970 | 1401 | 2217 |
| Moderate Confidence Coexpression Network | 27881 | 1284858 | 2071 | 25810 | 0.191 | 2.811 | 1415 | 2780 |
| Low Confidence Coexpression Network | 29913 | 2111196 | 2204 | 27709 | 0.160 | 2.533 | 1495 | 2991 |
| Non-coding RNA Network | 25700 | 1626783 | 1776 | 23924 | 0.800 | 5.244 | 929 | 2484 |
| 3D Inter Network | 3032 | 5237 | 214 | 2818 | 0.019 | 2.594 | 228 | 261 |
| 3D Intra Network | 8591 | 16743 | 637 | 7954 | 0.045 | 3.754 | 559 | 805 |
| 3D Genome Network | 10964 | 21980 | 793 | 10171 | 0.050 | 4.552 | 737 | 1059 |
| ATAC-seq-based TF-target Regulatory Network | 9717 | 194238 | 1094 | 8623 | 0.012 | 2.510 | 22 | 956 |
| PWM-based TF-target Regulatory Network | 39473 | 395509 | 2908 | 36565 | 0.004 | 2.606 | 101 | 3799 |
| TF-target Regulatory Network | 40005 | 567927 | 2924 | 37081 | 0.006 | 2.498 | 29 | 3830 |
| Pcorr Network | 2304 | 269130 | 209 | 2095 | 1.000 | 1.000 | 21 | 492 |
| cPPI Network | 6790 | 64003 | 723 | 6067 | 0.117 | 3.434 | 269 | 670 |
| Interactome Network | 8666 | 333115 | 860 | 7806 | 0.944 | 3.312 | 262 | 825 |
| Structure-based PPI Network | 14765 | 195350 | 1911 | 12854 | 0.399 | 4.233 | 732 | 1468 |
| Integrative Network | 45678 | 3157357 | 2979 | 42699 | 0.260 | 2.572 | 597 | 4564 |