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https://doi.org/10.1093/pcp/pcu174
87. Warde-Farley D, Donaldson SL, Comes O et al
(2010) The GeneMANIA prediction server:
biological network integration for gene prioritization and predicting gene function. Nucleic
Acids Res 38:W214–W220. https://doi.org/
10.1093/nar/gkq537
88. Xie K, Zhang J, Yang Y (2014) Genome-wide
prediction of highly specific guide RNA spacers
for CRISPR–Cas9-mediated genome editing
in model plants and major crops. Mol Plant
7:923–926. https://doi.org/10.1093/mp/
ssu009
Arabidopsis Bioinformatics
89
(2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317–329. https://doi.
org/10.1104/pp.107.103465
68. Katari MS, Nowicki SD, Aceituno FF et al
(2010) VirtualPlant: a software platform to
support systems biology research. Plant Physiol
152:500–515. https://doi.org/10.1104/pp.
109.147025
69. Mostafavi S, Ray D, Warde-Farley D et al
(2008) GeneMANIA: a real-time multiple
association network integration algorithm for
predicting gene function. Genome Biol 9:S4
70. Cui H, Levesque MP, Vernoux T et al (2007)
An evolutionarily conserved mechanism delimiting SHR movement defines a single layer
of endodermis in plants. Science 316:421–425.
https://doi.org/10.1126/science.1139531
71. de Lucas M, Davie `re J-M, Rodrı ´guez-Falco ´ n M
et al (2008) A molecular framework for light
and gibberellin control of cell elongation.
Nature 451:480–484. https://doi.org/10.
1038/nature06520
72. Dill A, Jung HS, Sun TP (2001) The DELLA
motif is essential for gibberellin-induced degradation of RGA. Proc Natl Acad Sci U S A
98:14162–14167. https://doi.org/10.1073/
pnas.251534098
73. Waese J, Fan J, Pasha A et al (2017) ePlant:
visualizing and exploring multiple levels of data
for hypothesis generation in plant biology.
Plant Cell 29:1806–1821. https://doi.org/
10.1105/tpc.17.00073
74. Kulkarni SR, Vaneechoutte D, Van de Velde J,
Vandepoele K (2018) TF2Network: predicting
transcription factor regulators and gene regulatory networks in Arabidopsis using publicly
available binding site information. Nucleic
Acids Res 46:e31. https://doi.org/10.1093/
nar/gkx1279
75. Ramirez CL, Foley JE, Wright DA et al (2008)
Unexpected failure rates for modular assembly
of engineered zinc fingers. Nat Methods
5:374–375.
https://doi.org/10.1038/
nmeth0508-374
76. Christian M, Qi Y, Zhang Y, Voytas DF (2013)
Targeted mutagenesis of Arabidopsis thaliana
using engineered TAL effector nucleases. G3
Genes Genomes Genet 3:1697–1705. https://
doi.org/10.1534/g3.113.007104
77. Feng Z, Zhang B, Ding W et al (2013) Efficient
genome editing in plants using a CRISPR/Cas
system. Cell Res 23:1229–1232. https://doi.
org/10.1038/cr.2013.114
78. Nekrasov V, Staskawicz B, Weigel D et al
(2013) Targeted mutagenesis in the model
plant Nicotiana benthamiana using Cas9
RNA-guided endonuclease. Nat Biotechnol
31:691–693. https://doi.org/10.1038/nbt.
2655
79. Schwab R, Ossowski S, Riester M et al (2006)
Highly specific gene silencing by artificial
MicroRNAs in Arabidopsis. Plant Cell
18:1121–1133.
https://doi.org/10.1105/
tpc.105.039834
80. Ossowski S, Schwab R, Weigel D (2008) Gene
silencing in plants using artificial microRNAs
and other small RNAs. Plant J Cell Mol Biol
53:674–690.
https://doi.org/10.1111/j.
1365-313X.2007.03328.x
81. O’Malley RC, Ecker JR (2010) Linking genotype to phenotype using the Arabidopsis
unimutant collection. Plant J Cell Mol Biol
61:928–940.
https://doi.org/10.1111/j.
1365-313X.2010.04119.x
82. O’Malley RC, Barragan CC, Ecker JR (2015)
A user’s guide to the Arabidopsis T-DNA insertion mutant collections. Methods Mol Biol
Clifton NJ 1284:323–342. https://doi.org/
10.1007/978-1-4939-2444-8_16
83. IAIC (2012) Taking the next step: building an
Arabidopsis information portal. Plant Cell
Online 24:2248–2256. https://doi.org/10.
1105/tpc.112.100669
84. Mi H, Dong Q, Muruganujan A et al (2010)
PANTHER version 7: improved phylogenetic
trees, orthologs and collaboration with the
Gene Ontology Consortium. Nucleic Acids
Res 38:D204–D210. https://doi.org/10.
1093/nar/gkp1019
85. Lee I, Ambaru B, Thakkar P et al (2010) Rational association of genes with traits using a
genome-scale gene network for Arabidopsis
thaliana. Nat Biotechnol 28:149–156.
https://doi.org/10.1038/nbt.1603
86. Kakei Y, Shimada Y (2015) AtCAST3.0
update: a web-based tool for analysis of transcriptome data by searching similarities in gene
expression profiles. Plant Cell Physiol 56:e7.
https://doi.org/10.1093/pcp/pcu174
87. Warde-Farley D, Donaldson SL, Comes O et al
(2010) The GeneMANIA prediction server:
biological network integration for gene prioritization and predicting gene function. Nucleic
Acids Res 38:W214–W220. https://doi.org/
10.1093/nar/gkq537
88. Xie K, Zhang J, Yang Y (2014) Genome-wide
prediction of highly specific guide RNA spacers
for CRISPR–Cas9-mediated genome editing
in model plants and major crops. Mol Plant
7:923–926. https://doi.org/10.1093/mp/
ssu009
Arabidopsis Bioinformatics
89