27. Note that the ABRC has recently rolled out its own interface
for ordering T-DNA insertion lines and has disintermediated
itself from TAIR, but the SIGnAL page still links to TAIR. Just
click through as necessary.
References
1. Reuter JA, Spacek DV, Snyder MP (2015)
High-throughput sequencing technologies.
Mol Cell 58:586–597. https://doi.org/10.
1016/j.molcel.2015.05.004
2. Chory J, Ecker JR, Briggs S et al (2000)
National
Science
Foundation-Sponsored
Workshop Report: “The 2010 Project” functional genomics and the virtual plant. A blueprint for understanding how plants are built
and how to improve them. Plant Physiol
123:423–426. https://doi.org/10.1104/pp.
123.2.423
3. Reiser L, Subramaniam S, Li D, Huala E
(2017) Using the Arabidopsis Information
Resource (TAIR) to find information about
arabidopsis genes. Curr Protoc Bioinforma
60:1.11.1–1.11.45.
https://doi.org/10.
1002/cpbi.36
4. Alonso JM, Stepanova AN, Leisse TJ et al
(2003) Genome-wide insertional mutagenesis
of Arabidopsis thaliana. Science 301:653–657.
https://doi.org/10.1126/science.1086391
5. Krishnakumar V, Hanlon MR, Contrino S et al
(2015) Araport: the Arabidopsis information
portal. Nucleic Acids Res 43:D1003–D1009.
https://doi.org/10.1093/nar/gku1200
6. Finkelstein RR, Somerville CR (1990) Three
classes of abscisic acid (ABA)-insensitive mutations of arabidopsis define genes that control
overlapping subsets of ABA responses. Plant
Physiol 94:1172–1179
7. Brady SM, Provart NJ (2009) Web-queryable
large-scale data sets for hypothesis generation
in plant biology. Plant Cell 21:1034–1051.
https://doi.org/10.1105/tpc.109.066050
8. Usadel B, Obayashi T, Mutwil M et al (2009)
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.
Plant Cell Environ 32:1633–1651. https://
doi.org/10.1111/j.1365-3040.2009.
02040.x
9. IAIC (2019) Arabidopsis bioinformatics
resources: The current state, challenges, and
priorities for the future. Plant Direct 3:
e00109. https://doi.org/10.1002/pld3.109
10. Mu J, Tan H, Zheng Q et al (2008) LEAFY
COTYLEDON1 is a key regulator of fatty acid
biosynthesis in Arabidopsis. Plant Physiol
148:1042–1054. https://doi.org/10.1104/
pp.108.126342
11. 1001 Genomes Consortium (2016) 1,135
genomes reveal the global pattern of polymorphism
in
Arabidopsis
thaliana.
Cell
166:481–491.
https://doi.org/10.1016/j.
cell.2016.05.063
12. Kersey PJ, Allen JE, Allot A et al (2018)
Ensembl Genomes 2018: an integrated omics
infrastructure for non-vertebrate species.
Nucleic Acids Res 46:D802–D808. https://
doi.org/10.1093/nar/gkx1011
13. Hubbard T, Barker D, Birney E et al (2002)
The Ensembl genome database project.
Nucleic Acids Res 30:38–41. https://doi.
org/10.1093/nar/30.1.38
14. McCarty DR, Carson CB, Stinard PS, Robertson DS (1989) Molecular analysis of
viviparous-1: an abscisic acid-insensitive
mutant of maize. Plant Cell 1:523–532.
https://doi.org/10.1105/tpc.1.5.523
15. Van Bel M, Diels T, Vancaester E et al (2018)
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant
genomics.
Nucleic
Acids
Res
46:
D1190–D1196. https://doi.org/10.1093/
nar/gkx1002
16. Mi H, Muruganujan A, Casagrande JT,
Thomas PD (2013) Large-scale gene function
analysis with the PANTHER classification system. Nat Protoc 8:1551–1566. https://doi.
org/10.1038/nprot.2013.092
17. Mi H, Muruganujan A, Huang X et al (2019)
Protocol Update for large-scale genome and
gene function analysis with the PANTHER
classification system (v.14.0). Nat Protoc
14:703. https://doi.org/10.1038/s41596019-0128-8
18. Nelson ADL, Haug-Baltzell AK, Davey S et al
(2018) EPIC-CoGe: managing and analyzing
genomic data. Bioinformatics 34:2651–2653.
https://doi.org/10.1093/bioinformatics/
bty106
19. The EPIC Planning Committee TEP (2012)
Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment.
Plant Cell 24:2257–2261. https://doi.org/
10.1105/tpc.112.100636
86
G. Alex Mason et al.
for ordering T-DNA insertion lines and has disintermediated
itself from TAIR, but the SIGnAL page still links to TAIR. Just
click through as necessary.
References
1. Reuter JA, Spacek DV, Snyder MP (2015)
High-throughput sequencing technologies.
Mol Cell 58:586–597. https://doi.org/10.
1016/j.molcel.2015.05.004
2. Chory J, Ecker JR, Briggs S et al (2000)
National
Science
Foundation-Sponsored
Workshop Report: “The 2010 Project” functional genomics and the virtual plant. A blueprint for understanding how plants are built
and how to improve them. Plant Physiol
123:423–426. https://doi.org/10.1104/pp.
123.2.423
3. Reiser L, Subramaniam S, Li D, Huala E
(2017) Using the Arabidopsis Information
Resource (TAIR) to find information about
arabidopsis genes. Curr Protoc Bioinforma
60:1.11.1–1.11.45.
https://doi.org/10.
1002/cpbi.36
4. Alonso JM, Stepanova AN, Leisse TJ et al
(2003) Genome-wide insertional mutagenesis
of Arabidopsis thaliana. Science 301:653–657.
https://doi.org/10.1126/science.1086391
5. Krishnakumar V, Hanlon MR, Contrino S et al
(2015) Araport: the Arabidopsis information
portal. Nucleic Acids Res 43:D1003–D1009.
https://doi.org/10.1093/nar/gku1200
6. Finkelstein RR, Somerville CR (1990) Three
classes of abscisic acid (ABA)-insensitive mutations of arabidopsis define genes that control
overlapping subsets of ABA responses. Plant
Physiol 94:1172–1179
7. Brady SM, Provart NJ (2009) Web-queryable
large-scale data sets for hypothesis generation
in plant biology. Plant Cell 21:1034–1051.
https://doi.org/10.1105/tpc.109.066050
8. Usadel B, Obayashi T, Mutwil M et al (2009)
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.
Plant Cell Environ 32:1633–1651. https://
doi.org/10.1111/j.1365-3040.2009.
02040.x
9. IAIC (2019) Arabidopsis bioinformatics
resources: The current state, challenges, and
priorities for the future. Plant Direct 3:
e00109. https://doi.org/10.1002/pld3.109
10. Mu J, Tan H, Zheng Q et al (2008) LEAFY
COTYLEDON1 is a key regulator of fatty acid
biosynthesis in Arabidopsis. Plant Physiol
148:1042–1054. https://doi.org/10.1104/
pp.108.126342
11. 1001 Genomes Consortium (2016) 1,135
genomes reveal the global pattern of polymorphism
in
Arabidopsis
thaliana.
Cell
166:481–491.
https://doi.org/10.1016/j.
cell.2016.05.063
12. Kersey PJ, Allen JE, Allot A et al (2018)
Ensembl Genomes 2018: an integrated omics
infrastructure for non-vertebrate species.
Nucleic Acids Res 46:D802–D808. https://
doi.org/10.1093/nar/gkx1011
13. Hubbard T, Barker D, Birney E et al (2002)
The Ensembl genome database project.
Nucleic Acids Res 30:38–41. https://doi.
org/10.1093/nar/30.1.38
14. McCarty DR, Carson CB, Stinard PS, Robertson DS (1989) Molecular analysis of
viviparous-1: an abscisic acid-insensitive
mutant of maize. Plant Cell 1:523–532.
https://doi.org/10.1105/tpc.1.5.523
15. Van Bel M, Diels T, Vancaester E et al (2018)
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant
genomics.
Nucleic
Acids
Res
46:
D1190–D1196. https://doi.org/10.1093/
nar/gkx1002
16. Mi H, Muruganujan A, Casagrande JT,
Thomas PD (2013) Large-scale gene function
analysis with the PANTHER classification system. Nat Protoc 8:1551–1566. https://doi.
org/10.1038/nprot.2013.092
17. Mi H, Muruganujan A, Huang X et al (2019)
Protocol Update for large-scale genome and
gene function analysis with the PANTHER
classification system (v.14.0). Nat Protoc
14:703. https://doi.org/10.1038/s41596019-0128-8
18. Nelson ADL, Haug-Baltzell AK, Davey S et al
(2018) EPIC-CoGe: managing and analyzing
genomic data. Bioinformatics 34:2651–2653.
https://doi.org/10.1093/bioinformatics/
bty106
19. The EPIC Planning Committee TEP (2012)
Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment.
Plant Cell 24:2257–2261. https://doi.org/
10.1105/tpc.112.100636
86
G. Alex Mason et al.