Bioinformatics Software Developed by Wei Lab

http://prosper.ffr.mtu.edu/ (click to download)

 

These software and algorithms have been used to identify the following genes and gene regulatory networks that govern various biological processes, pathways, and complex traits:

 

A.    TGMI (Triple-Gene mutual Information)

 

(1)   MYC2, which reduces stomatal density and improves water use efficiency (Xia et al, 2024. New Phytologist 2024 Jan 23) (https://doi.org/10.1111/nph.19531)

(2)   VND7/MYB69/WRKY4/HAT22/KNAT7/SHN2, which govern lignin biosynthesis pathway (Zhang et al. 2020. Frontiers of Plant Science 11:2022) (https://www.frontiersin.org/articles/10.3389/fpls.2020.00652/full )

(3)   29 TFs, which potentially regulate lignin biosynthetic pathway in maize. (Wang et al, 2024. Int. J. Mol. Sci. 2024, 25, 6710). (https://doi.org/10.3390/ijms25126710)

(4)     34 IsMYBs, 18 IsbHLHs, 15 IsWRKYs, 9 IsMADSs, and 3 IsWIPs regulators that potentially regulate Proanthocyanidins biosynthesis in I. stachyodes. (https://doi.org/10.1186/s12870-022-03794-4)

(5)     40 TFs were found to potentially regulate 62 anthocyanin biosynthesis pathway genes. Wang et al BMC Plant Biology (https://doi.org/10.1186/s12870-025-06053-4 )

 

B.    CollaborativeNET (originally called TF-Cluster)

 

(6)   NAC1/RAP2.11/HWS module, which regulates root development under low nitrogen (Wei, H. et al. 2013. New Phytologist 200 (2):483-497) (https://doi.org/10.1111/nph.12375)

(7)   A collaborative subnetwork, comprising BRN1, BRN2, SMB and FEZ, maintains the rootcap pluripotency identity (Nie et al. 2011. BMC Systems Biology 5: p53) (https://doi.org/10.1186/1752-0509-5-53)

(8)   A collaborative subnetwork, comprising 24 regulators including Nanog, Pou5f1, Oct4, and Sox2, governs human stem cell pluripotency (Nie et al. 2011. BMC Systems Biology 5: p53) (https://doi.org/10.1186/1752-0509-5-53)

(9)   Three collaborative subnetworks, which govern regeneration in Arabidopsis (Islam et al. 2023. aBiotech. 4:332-351 (https://doi.org/10.1007/s42994-023-00121-9) 

 

C.    Bottom-up GGM Algorithm

 

(10) ERF016, which negative regulates plant vegetative growth by altering the accumulation of sugars produced through photosynthesis. (Chen et al. 2025. Plant Biotechnology Journal 0:1-6). (https://doi.org/10.1111/pbi.70265 )  

(11) MYB40 and WRKY75, which regulate the number of adventitious roots at the basal-ends of stem cuttings in poplar under low phosphorus (Wang et al. 2022. Plant Biotechnology Journal, 20(8):1561-1577.) (https://doi.org/10.1111/pbi.13833)

(12) HOX52, which accelerates regeneration of adventitious roots and increases their number (Wei, M et al. 2021. New Phytologist. 228(4): 1369-1385) (https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16778)

(13) UNE12, which regulates the development of secondary vascular tissue (Song et al. 2023. Plant Physiology 192(2):1046-1062) (https://doi.org/10.1093/plphys/kiad152 )

(14) NAC83, which functions as a high-hierarchical regulator that control lignin pathway under salt stress condition (Lei et al. 2022. Plant Molecular Biology 109:689-702) ( https://link.springer.com/article/10.1007/s11103-022-01267-8 )

(15) A three-layered hierarchical network, including MYB021, 52, 42, 48, VND1, NST1, HB1,   ARF2,3,7,8, and UNE12, modulates lignin monomer polymerization. (Lu et al., 2013. PNAS 110(26): 10848-10853) (https://doi.org/10.1073%2Fpnas.1308936110)

 

D.    Top-down GGM Algorithm:

 

(16) SND1-mediated multilayered hierarchical gene network (ML-hGRN). ChIP-PCR analysis indicated that 97% regulatory relationships predicted were true (Lin et al. 2013. Plant Cell 25(11): 4324-41. (https://doi.org/10.1105/tpc.113.117697)

(17) ERF1, which regulates five middle-level hub genes including WRKY53, WRKY70, MKP20, GIA1 and ERF9 under cold stress. These hub genes, in turn, govern downstream stress response and tolerance genes (Lv et al. 2021. Forestry Research 1:11) (https://doi.org/10.48130/FR-2021-0013 )

(18) GRF5-mediated hierarchical network, which regulates the leaf size in poplar by regulating multiple middle-level hub genes including CKX1, TCP4, LBD38, WIND1, GIF1, and TGA1 (Wu et al. 2021. New Phytologist 230(2):612-628. (https://doi.org/10.1111%2Fnph.17179 )

(19) miRNA397, which targets 14 laccase genes for regulation to increase lignin monomer polymerization (Lu et al. 2013. PNAS 110(26): 10848-10853) (https://doi.org/10.1073%2Fpnas.1308936110)

(20)  GL3, which governs biosynthesis of cuticular waxes through regulating 92 target genes including gl1, gl4, gl6, cer8, gl8, gl26 (Zhao et al. 2023. Plant Cell  35(8):2736-2749. (https://doi.org/10.1093/plcell/koad155)

(21)  A four-layered GRN mediated by PtLBD7 involved in hydrolase activity and a four-layered GRN mediated by PtLBD20 involved in detoxification, oxidative stress, and epidermal cell differentiation. (Dang et al. BMC Genomics. 2024. 25(1):920) (https://doi.org/10.1186/s12864-024-10848-4)

 

 

E.     BWERF (Backward Elimination Random Forests)

 

(22) GRF15-mediated gene regulatory network, in which growth-regulating factor 15 (PagGRF15) and its target, high-affinity K+ transporter 6 (PagHAK6), were identified as an important regulatory module in the salt stress response. (Xu et al. 2023. Plant Physiology. 191(4):2367-2384) (https://doi.org/10.1093/plphys/kiac600)

(23) bHLH10, which regulates photosynthesis, oxidoreductase activity and membrane properties under drought stress and cold stress (Xu et al. 2023. Frontiers in Plant Science 14:2023) (https://doi.org/10.3389/fpls.2023.1155504)

(24) DRE1A, FEZ, and MYC1 module, which regulates metal cd-caused stress response and tolerance (Xie et al. 2023. Tree Physiology 43(4): 630-642.  (https://doi.org/10.1093/treephys/tpac147)

(25) Three-layered gene regulatory network, which contains 157 regulatory relationships between TFs and Calvin–Benson–Bassham cycle. These gene regulatory relationships are supported by PlantPAN2.0. (Wang et al. Tree physiology 39(7):1159-1172) (https://doi.org/10.1093/treephys/tpz025)

(26) Three-layered gene regulatory network built in a bottom-up fashion to identify WRKY18, which can directly bind the W-box elements in the promoter of a transmembrane leucine-rich repeat receptor-like kinase, PagSOBIR1 gene, to trigger pattern–triggered immunity (PTI) and effector–triggered immunity (ETI) (Chen et al. 2024. Plant, Cell and Environment. Page 1-19) (https://doi.org/10.1111/pce.14860)

(27) WRKYs regulated ML-hGRN in response to nitrate. (Chen et al. 2022. Genes 13(12), 2324; (https://doi.org/10.3390/genes13122324)

(28) Two four-layered hGRNs comprising PtLBD7, and PtLBD20 (Dang et al. 2024. BMC Genomics. 2024. 25(1):920). (https://doi.org/10.1186/s12864-024-10848-4)

(29) One four-layered hGRN with bZIP75 located on the second level (Hu, et al. 2024. Environmental and Experimental Botany. 106051. (https://doi.org/10.1016/j.envexpbot.2024.106051)

 

F.  Regression based methods

 

(30)irx8 and irx13, which function in secondary cell wall formation.

(Persson and Wei et al. 2005. Proc Natl Acad Sci USA, 102(24): 8633-8638. (https://doi.org/10.1073/pnas.0503392102 )

 

 

 

Sample networks built by these methods/algorithms (click the link)