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)