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 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 )

 

B.    CollaborativeNET (originally called TF-Cluster)

 

(3)   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)

(4)   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)

(5)   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)

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

 

 

C.    Bottom-up GGM Algorithm

 

(7)   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)

(8)   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)

(9)   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 )

(10)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 )

(11)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:

 

(10)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)

(11)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 )

(12)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 )

(13)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)

(14)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)

 

E.     BWERF (Backward Elimination Random Forest)

 

(15) 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)

(16) 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)

(17) 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(&):1159-1172) (https://doi.org/10.1093/treephys/tpz025)

(18) 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)

 

 

 

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