20. Stroud H, Greenberg MVC, Feng S et al
(2013) Comprehensive analysis of silencing
mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352–364.
https://doi.org/10.1016/j.cell.2012.10.054
21. Roudier F, Ahmed I, Be ´rard C et al (2011)
Integrative epigenomic mapping defines four
main chromatin states in Arabidopsis. EMBO
J 30:1928–1938. https://doi.org/10.1038/
emboj.2011.103
22. Sullivan AM, Bubb KL, Sandstrom R et al
(2015) DNase I hypersensitivity mapping,
genomic footprinting, and transcription factor
networks in plants. Curr Plant Biol 3–4:40–47.
https://doi.org/10.1016/j.cpb.2015.10.001
23. Kawakatsu T, Huang SC, Jupe F et al (2016)
Epigenomic diversity in a global collection of
Arabidopsis
thaliana
accessions.
Cell
166:492–505.
https://doi.org/10.1016/j.
cell.2016.06.044
24. Winter D, Vinegar B, Nahal H et al (2007) An
“electronic fluorescent pictograph” browser
for exploring and analyzing large-scale
biological data sets. PloS One 2:e718
25. Schmid M, Davison TS, Henz SR et al (2005)
A gene expression map of Arabidopsis thaliana
development. Nat Genet 37:501–506. https://
doi.org/10.1038/ng1543
26. Nakabayashi K, Okamoto M, Koshiba T et al
(2005) Genome-wide profiling of stored
mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J Cell Mol Biol
41:697–709.
https://doi.org/10.1111/j.
1365-313X.2005.02337.x
27. Brady SM, Sarkar SF, Bonetta D, McCourt P
(2003) The ABSCISIC ACID INSENSITIVE
3 (ABI3) gene is modulated by farnesylation
and is involved in auxin signaling and lateral
root development in Arabidopsis. Plant J
34:67–75. https://doi.org/10.1046/j.1365313X.2003.01707.x
28. Klepikova AV, Kasianov AS, Gerasimov ES et al
(2016) A high resolution map of the Arabidopsis thaliana developmental transcriptome based
on RNA-seq profiling. Plant J 88:1058–1070.
https://doi.org/10.1111/tpj.13312
29. Hruz T, Laule O, Szabo G et al (2008) Genevestigator v3: a reference expression database
for the meta-analysis of transcriptomes. Adv
Bioinforma 2008:420747. https://doi.org/
10.1155/2008/420747
30. Toufighi K, Brady SM, Austin R et al (2005)
The botany array resource: e-Northerns,
expression angling, and promoter analyses.
Plant J 43:153–163. https://doi.org/10.
1111/j.1365-313X.2005.02437.x
31. Brady SM, Orlando DA, Lee J-Y et al (2007) A
high-resolution root spatiotemporal map
reveals dominant expression patterns. Science
318:801–806. https://doi.org/10.1126/sci
ence.1146265
32. Aoki Y, Okamura Y, Tadaka S et al (2016)
ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression.
Plant Cell Physiol 57:e5–e5. https://doi.org/
10.1093/pcp/pcv165
33. Obayashi T, Kinoshita K (2009) Rank of correlation coefficient as a comparable measure for
biological significance of gene coexpression.
DNA Res Int J Rapid Publ Rep Genes Genomes 16:249–260. https://doi.org/10.1093/
dnares/dsp016
34. Dubreucq B, Berger N, Vincent E et al (2000)
The Arabidopsis AtEPR1 extensin-like gene is
specifically expressed in endosperm during seed
germination. Plant J Cell Mol Biol 23:643–652
35. Nole-Wilson S, Tranby TL, Krizek BA (2005)
AINTEGUMENTA-like (AIL) genes are
expressed in young tissues and may specify meristematic or division-competent states. Plant
Mol Biol 57:613–628. https://doi.org/10.
1007/s11103-005-0955-6
36. Austin RS, Hiu S, Waese J et al (2016) New
BAR tools for mining expression data and
exploring Cis-elements in Arabidopsis thaliana.
Plant J Cell Mol Biol. https://doi.org/10.
1111/tpj.13261
37. Higo K, Ugawa Y, Iwamoto M, Higo H
(1998) PLACE: a database of plant cis-acting
regulatory DNA elements. Nucleic Acids Res
26:358–359. https://doi.org/10.1093/nar/
26.1.358
38. Bailey TL, Boden M, Buske FA et al (2009)
MEME SUITE: tools for motif discovery and
searching. Nucleic Acids Res 37:W202–W208.
https://doi.org/10.1093/nar/gkp335
39. O’Malley RC, Huang S-SC, Song L et al
(2016) Cistrome and epicistrome features
shape the regulatory DNA landscape. Cell
165:1280–1292. https://doi.org/10.1016/j.
cell.2016.04.038
40. Grant CE, Bailey TL, Noble WS (2011)
FIMO: scanning for occurrences of a given
motif. Bioinformatics 27:1017–1018. https://
doi.org/10.1093/bioinformatics/btr064
41. McLeay RC, Bailey TL (2010) Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics
11:165.
https://doi.org/10.1186/14712105-11-165
42. Brady SM, Zhang L, Megraw M et al (2011) A
stele-enriched gene regulatory network in the
Arabidopsis root. Mol Syst Biol 7:459. https://
doi.org/10.1038/msb.2010.114
43. Gaudinier A, Zhang L, Reece-Hoyes JS et al
(2011) Enhanced Y1H assays for Arabidopsis.
Arabidopsis Bioinformatics
87
(2013) Comprehensive analysis of silencing
mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352–364.
https://doi.org/10.1016/j.cell.2012.10.054
21. Roudier F, Ahmed I, Be ´rard C et al (2011)
Integrative epigenomic mapping defines four
main chromatin states in Arabidopsis. EMBO
J 30:1928–1938. https://doi.org/10.1038/
emboj.2011.103
22. Sullivan AM, Bubb KL, Sandstrom R et al
(2015) DNase I hypersensitivity mapping,
genomic footprinting, and transcription factor
networks in plants. Curr Plant Biol 3–4:40–47.
https://doi.org/10.1016/j.cpb.2015.10.001
23. Kawakatsu T, Huang SC, Jupe F et al (2016)
Epigenomic diversity in a global collection of
Arabidopsis
thaliana
accessions.
Cell
166:492–505.
https://doi.org/10.1016/j.
cell.2016.06.044
24. Winter D, Vinegar B, Nahal H et al (2007) An
“electronic fluorescent pictograph” browser
for exploring and analyzing large-scale
biological data sets. PloS One 2:e718
25. Schmid M, Davison TS, Henz SR et al (2005)
A gene expression map of Arabidopsis thaliana
development. Nat Genet 37:501–506. https://
doi.org/10.1038/ng1543
26. Nakabayashi K, Okamoto M, Koshiba T et al
(2005) Genome-wide profiling of stored
mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J Cell Mol Biol
41:697–709.
https://doi.org/10.1111/j.
1365-313X.2005.02337.x
27. Brady SM, Sarkar SF, Bonetta D, McCourt P
(2003) The ABSCISIC ACID INSENSITIVE
3 (ABI3) gene is modulated by farnesylation
and is involved in auxin signaling and lateral
root development in Arabidopsis. Plant J
34:67–75. https://doi.org/10.1046/j.1365313X.2003.01707.x
28. Klepikova AV, Kasianov AS, Gerasimov ES et al
(2016) A high resolution map of the Arabidopsis thaliana developmental transcriptome based
on RNA-seq profiling. Plant J 88:1058–1070.
https://doi.org/10.1111/tpj.13312
29. Hruz T, Laule O, Szabo G et al (2008) Genevestigator v3: a reference expression database
for the meta-analysis of transcriptomes. Adv
Bioinforma 2008:420747. https://doi.org/
10.1155/2008/420747
30. Toufighi K, Brady SM, Austin R et al (2005)
The botany array resource: e-Northerns,
expression angling, and promoter analyses.
Plant J 43:153–163. https://doi.org/10.
1111/j.1365-313X.2005.02437.x
31. Brady SM, Orlando DA, Lee J-Y et al (2007) A
high-resolution root spatiotemporal map
reveals dominant expression patterns. Science
318:801–806. https://doi.org/10.1126/sci
ence.1146265
32. Aoki Y, Okamura Y, Tadaka S et al (2016)
ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression.
Plant Cell Physiol 57:e5–e5. https://doi.org/
10.1093/pcp/pcv165
33. Obayashi T, Kinoshita K (2009) Rank of correlation coefficient as a comparable measure for
biological significance of gene coexpression.
DNA Res Int J Rapid Publ Rep Genes Genomes 16:249–260. https://doi.org/10.1093/
dnares/dsp016
34. Dubreucq B, Berger N, Vincent E et al (2000)
The Arabidopsis AtEPR1 extensin-like gene is
specifically expressed in endosperm during seed
germination. Plant J Cell Mol Biol 23:643–652
35. Nole-Wilson S, Tranby TL, Krizek BA (2005)
AINTEGUMENTA-like (AIL) genes are
expressed in young tissues and may specify meristematic or division-competent states. Plant
Mol Biol 57:613–628. https://doi.org/10.
1007/s11103-005-0955-6
36. Austin RS, Hiu S, Waese J et al (2016) New
BAR tools for mining expression data and
exploring Cis-elements in Arabidopsis thaliana.
Plant J Cell Mol Biol. https://doi.org/10.
1111/tpj.13261
37. Higo K, Ugawa Y, Iwamoto M, Higo H
(1998) PLACE: a database of plant cis-acting
regulatory DNA elements. Nucleic Acids Res
26:358–359. https://doi.org/10.1093/nar/
26.1.358
38. Bailey TL, Boden M, Buske FA et al (2009)
MEME SUITE: tools for motif discovery and
searching. Nucleic Acids Res 37:W202–W208.
https://doi.org/10.1093/nar/gkp335
39. O’Malley RC, Huang S-SC, Song L et al
(2016) Cistrome and epicistrome features
shape the regulatory DNA landscape. Cell
165:1280–1292. https://doi.org/10.1016/j.
cell.2016.04.038
40. Grant CE, Bailey TL, Noble WS (2011)
FIMO: scanning for occurrences of a given
motif. Bioinformatics 27:1017–1018. https://
doi.org/10.1093/bioinformatics/btr064
41. McLeay RC, Bailey TL (2010) Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics
11:165.
https://doi.org/10.1186/14712105-11-165
42. Brady SM, Zhang L, Megraw M et al (2011) A
stele-enriched gene regulatory network in the
Arabidopsis root. Mol Syst Biol 7:459. https://
doi.org/10.1038/msb.2010.114
43. Gaudinier A, Zhang L, Reece-Hoyes JS et al
(2011) Enhanced Y1H assays for Arabidopsis.
Arabidopsis Bioinformatics
87