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45. Taylor-Teeples M, Lin L, de Lucas M et al
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517:571–575.
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cascade through opposing activities of both
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and
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60. Yao Q, Bollinger C, Gao J et al (2012) P(3)DB:
an integrated database for plant protein phosphorylation. Front Plant Sci 3:206. https://
doi.org/10.3389/fpls.2012.00206
61. Yang W, Zhang W, Wang X (2017) Posttranslational control of ABA signalling: the
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doi.org/10.1111/pbi.12652
62. Willems P, Horne A, Parys TV et al (2019) The
plant PTM viewer, a central resource for
exploring plant protein modifications. Plant J
99(4):752–762. https://doi.org/10.1111/
tpj.14345
63. Orchard S, Ammari M, Aranda B et al (2014)
The MIntAct project—IntAct as a common
curation platform for 11 molecular interaction
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https://doi.org/10.1093/nar/gkt1115
64. Chatr-Aryamontri A, Oughtred R, Boucher L
et al (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res 45:
D369–D379. https://doi.org/10.1093/nar/
gkw1102
65. Li P, Zang W, Li Y et al (2011) AtPID: the
overall hierarchical functional protein interaction network interface and analytic platform for
Arabidopsis.
Nucleic
Acids
Res
39:
D1130–D1133. https://doi.org/10.1093/
nar/gkq959
66. Dong S, Lau V, Song R et al (2019) Proteomewide, structure-based prediction of proteinprotein interactions/new molecular interactions viewer. Plant Physiol 179:1893–1907.
https://doi.org/10.1104/pp.18.01216
88
G. Alex Mason et al.
10.1038/nmeth.1750
44. Li B, Gaudinier A, Tang M et al (2014)
Promoter-based integration in plant defense
regulation. Plant Physiol 166:1803–1820.
https://doi.org/10.1104/pp.114.248716
45. Taylor-Teeples M, Lin L, de Lucas M et al
(2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature
517:571–575.
https://doi.org/10.1038/
nature14099
46. de Lucas M, Pu L, Turco G et al (2016) Transcriptional regulation of arabidopsis polycomb
repressive complex 2 coordinates cell-type proliferation and differentiation. Plant Cell
28:2616–2631.
https://doi.org/10.1105/
tpc.15.00744
47. Murphy E, Vu LD, Van den Broeck L et al
(2016) RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral
root initiation. J Exp Bot 67:4863–4875.
https://doi.org/10.1093/jxb/erw281
48. Porco S, Larrieu A, Du Y et al (2016) Lateral
root emergence in Arabidopsis is dependent on
transcription factor LBD29 regulation of auxin
influx carrier LAX3. Dev Camb Engl
143:3340–3349. https://doi.org/10.1242/
dev.136283
49. Sparks EE, Drapek C, Gaudinier A et al (2016)
Establishment
of
expression
in
the
SHORTROOT-SCARECROW transcriptional
cascade through opposing activities of both
activators
and
repressors.
Dev
Cell
39:585–596.
https://doi.org/10.1016/j.
devcel.2016.09.031
50. Ashburner M, Ball CA, Blake JA et al (2000)
Gene Ontology: tool for the unification of
biology. Nat Genet 25:25–29. https://doi.
org/10.1038/75556
51. Thimm O, Bl€ asing O, Gibon Y et al (2004)
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J
Cell Mol Biol 37:914–939
52. Tian T, Liu Y, Yan H et al (2017) agriGO v2.0:
a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res 45:
W122–W129.
https://doi.org/10.1093/
nar/gkx382
53. Carbon S, Ireland A, Mungall CJ et al (2009)
AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289.
https://doi.org/10.1093/bioinformatics/
btn615
54. Provart N, Zhu T (2003) A browser-based
functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol
2003:271–272
55. Mueller LA, Zhang P, Rhee SY (2003) AraCyc:
a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460. https://doi.
org/10.1104/pp.102.017236
56. Baud S, Boutin J-P, Miquel M et al (2002) An
integrated overview of seed development in
Arabidopsis thaliana ecotype WS. Plant Physiol
Biochem 40:151–160. https://doi.org/10.
1016/S0981-9428(01)01350-X
57. Hooper CM, Castleden IR, Tanz SK et al
(2017) SUBA4: the interactive data analysis
centre for Arabidopsis subcellular protein locations. Nucleic Acids Res 45:D1064–D1074.
https://doi.org/10.1093/nar/gkw1041
58. Gao J, Agrawal GK, Thelen JJ, Xu D (2009)
P3DB: a plant protein phosphorylation database. Nucleic Acids Res 37:D960–D962.
https://doi.org/10.1093/nar/gkn733
59. Yao Q, Ge H, Wu S et al (2014) P
3 DB 3.0:
From plant phosphorylation sites to protein
networks.
Nucleic
Acids
Res
42:
D1206–D1213. https://doi.org/10.1093/
nar/gkt1135
60. Yao Q, Bollinger C, Gao J et al (2012) P(3)DB:
an integrated database for plant protein phosphorylation. Front Plant Sci 3:206. https://
doi.org/10.3389/fpls.2012.00206
61. Yang W, Zhang W, Wang X (2017) Posttranslational control of ABA signalling: the
roles of protein phosphorylation and ubiquitination. Plant Biotechnol J 15:4–14. https://
doi.org/10.1111/pbi.12652
62. Willems P, Horne A, Parys TV et al (2019) The
plant PTM viewer, a central resource for
exploring plant protein modifications. Plant J
99(4):752–762. https://doi.org/10.1111/
tpj.14345
63. Orchard S, Ammari M, Aranda B et al (2014)
The MIntAct project—IntAct as a common
curation platform for 11 molecular interaction
databases. Nucleic Acids Res 42:D358–D363.
https://doi.org/10.1093/nar/gkt1115
64. Chatr-Aryamontri A, Oughtred R, Boucher L
et al (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res 45:
D369–D379. https://doi.org/10.1093/nar/
gkw1102
65. Li P, Zang W, Li Y et al (2011) AtPID: the
overall hierarchical functional protein interaction network interface and analytic platform for
Arabidopsis.
Nucleic
Acids
Res
39:
D1130–D1133. https://doi.org/10.1093/
nar/gkq959
66. Dong S, Lau V, Song R et al (2019) Proteomewide, structure-based prediction of proteinprotein interactions/new molecular interactions viewer. Plant Physiol 179:1893–1907.
https://doi.org/10.1104/pp.18.01216
88
G. Alex Mason et al.