Pear Integrative Gene Regulatory Network Database

PearGRN

Multi-omics gene regulatory networks for pear genetics and breeding

PearGRN consolidates co-expression, TF-target, non-coding RNA, 3D-genome and protein-interaction networks of pear (Pyrus) into one resource — for retrieving regulatory relationships, exploring expression dynamics and prioritising candidate genes behind breeding traits.

42,341Genes
4,167lncRNAs
1,238circRNAs
226miRNAs
15Networks
3.16MEdges
PearGRN logo
News PearGRN is released now! — The multi-omics integrative network is constructed based on omics data from pear fruit samples.
About

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 Center of Pear Engineering Technology Research at Nanjing Agricultural University and aims to support advanced genetic research and breeding projects in pears.

Citation
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
Browse

Network Gallery

Four representative views of the resource — open any of them in the interactive network viewer.

Integrative Network
Integrative Network 45,678 nodes · 3.16M edges
TF-target Regulatory Network
TF-target Regulatory 40,005 nodes · 567,927 edges
Coexpression Network
Coexpression Network 22,175 nodes · 637,942 edges
Interactome Network
Interactome Network 8,666 nodes · 333,115 edges
Statistics

Network Information

Topological properties of all 15 networks. Click a column header to sort.

Network Nodes Edges TFs Genes Transitivity Avg. distance Modules Hub genes
High Confidence Coexpression Network22,175637,9421,93720,2380.3343.9701,4012,217
Moderate Confidence Coexpression Network27,8811,284,8582,07125,8100.1912.8111,4152,780
Low Confidence Coexpression Network29,9132,111,1962,20427,7090.1602.5331,4952,991
Non-coding RNA Network25,7001,626,7831,77623,9240.8005.2449292,484
3D Inter Network3,0325,2372142,8180.0192.594228261
3D Intra Network8,59116,7436377,9540.0453.754559805
3D Genome Network10,96421,98079310,1710.0504.5527371,059
ATAC-seq-based TF-target Regulatory Network9,717194,2381,0948,6230.0122.51022956
PWM-based TF-target Regulatory Network39,473395,5092,90836,5650.0042.6061013,799
TF-target Regulatory Network40,005567,9272,92437,0810.0062.498293,830
Pcorr Network2,304269,1302092,0951.0001.00021492
cPPI Network6,79064,0037236,0670.1173.434269670
Interactome Network8,666333,1158607,8060.9443.312262825
Structure-based PPI Network14,765195,3501,91112,8540.3994.2337321,468
Integrative Network45,6783,157,3572,97942,6990.2602.5725974,564
Toolkit

Tools

Sixteen integrated tools for annotation, network analysis and structural biology.

Search & Annotation
Gene Search Annotation for genes, lncRNAs, circRNAs and miRNAs. GO Finder Find genes sharing GO terms, with any / all matching. RNA Expression Temporal expression across pear fruit development. Proteome Expression ↗ Protein abundance across tissues and stages. JBrowse Gene models and variants along the pear genome. BLAST Align sequences against the pear genome and proteome.
Network Analysis
Node Search All regulatory partners of a gene across networks. Network Creation Build a sub-network from your own gene list. Network Comparison Compare topology and shared edges between networks. TF Regulation Transcription factor – target relationships. Interact Finder Proteins interacting with your protein of interest. TraitConnect Link traits to candidate genes via the networks. ML Predictor Machine-learning gene–trait association prediction.
Protein Tools
Structure Viewer Interactive 3D protein structure view. Molecular Docking Pre-computed protein–protein docking models. Fold Aligner Structural alignment of two protein structures.