-
1
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y. Hochberg Y. ( 1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Series B, 57, 289 300.
-
(1995)
J. Roy. Stat. Soc. Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
2
-
-
0000835913
-
A general method for the isolation of RNA complementary to DNA
-
Bolton E.T. McCarthy B.J. ( 1962) A general method for the isolation of RNA complementary to DNA. Proc. Natl Acad. Sci. USA, 48, 1390 1397.
-
(1962)
Proc. Natl Acad. Sci. USA
, vol.48
, pp. 1390-1397
-
-
Bolton, E.T.1
McCarthy, B.J.2
-
3
-
-
1242316281
-
ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
Buck M.J. Lieb J.D. ( 2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83, 349 360.
-
(2004)
Genomics
, vol.83
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
4
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley S. Bekiranov S. Ng H.H. et al. ( 2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 116, 499 509.
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
-
5
-
-
1642412791
-
Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones
-
Chua Y.L. Mott E. Brown A.P. MacLean D. Gray J.C. ( 2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. Plant J. 37, 789 800.
-
(2004)
Plant J.
, vol.37
, pp. 789-800
-
-
Chua, Y.L.1
Mott, E.2
Brown, A.P.3
MacLean, D.4
Gray, J.C.5
-
7
-
-
0037276041
-
Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response
-
Dong J. Chen C. Chen Z. ( 2003) Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol. Biol. 51, 21 37.
-
(2003)
Plant Mol. Biol.
, vol.51
, pp. 21-37
-
-
Dong, J.1
Chen, C.2
Chen, Z.3
-
8
-
-
0035983849
-
In vivo interaction between NPR1 and transcription factor TGA2 leads to salicylic acid-mediated gene activation in Arabidopsis
-
Fan W. Dong X. ( 2002) In vivo interaction between NPR1 and transcription factor TGA2 leads to salicylic acid-mediated gene activation in Arabidopsis. Plant Cell, 14, 1377 1389.
-
(2002)
Plant Cell
, vol.14
, pp. 1377-1389
-
-
Fan, W.1
Dong, X.2
-
10
-
-
0347859216
-
Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data
-
Hudson M.E. Quail P.H. ( 2003) Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data. Plant Physiol. 133, 1605 1616.
-
(2003)
Plant Physiol.
, vol.133
, pp. 1605-1616
-
-
Hudson, M.E.1
Quail, P.H.2
-
11
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer V.R. Horak C.E. Scafe C.S. Botstein D. Snyder M. Brown P.O. ( 2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533 538.
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
12
-
-
0027263978
-
Plant bZIP protein DNA binding specificity
-
Izawa T. Foster R. Chua N.H. ( 1993) Plant bZIP protein DNA binding specificity. J. Mol. Biol. 230, 1131 1144.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 1131-1144
-
-
Izawa, T.1
Foster, R.2
Chua, N.H.3
-
13
-
-
0034761018
-
In vivo target promoter-binding activities of a xenobiotic stress-activated TGA factor
-
Johnson C. Boden E. Desai M. Pascuzzi P. Arias J. ( 2001) In vivo target promoter-binding activities of a xenobiotic stress-activated TGA factor. Plant J. 28, 237 243.
-
(2001)
Plant J.
, vol.28
, pp. 237-243
-
-
Johnson, C.1
Boden, E.2
Desai, M.3
Pascuzzi, P.4
Arias, J.5
-
14
-
-
0042421723
-
Salicylic acid and NPR1 induce the recruitment of trans-activating TGA factors to a defense gene promoter in Arabidopsis
-
Johnson C. Boden E. Arias J. ( 2003) Salicylic acid and NPR1 induce the recruitment of trans-activating TGA factors to a defense gene promoter in Arabidopsis. Plant Cell, 15, 1846 1858.
-
(2003)
Plant Cell
, vol.15
, pp. 1846-1858
-
-
Johnson, C.1
Boden, E.2
Arias, J.3
-
15
-
-
0034284437
-
Repbase update: A database and an electronic journal of repetitive elements
-
Jurka J. ( 2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418 420.
-
(2000)
Trends Genet.
, vol.16
, pp. 418-420
-
-
Jurka, J.1
-
16
-
-
0024982034
-
Two tobacco DNA-binding proteins with homology to the nuclear factor CREB
-
Katagiri F. Lam E. Chua N.H. ( 1989) Two tobacco DNA-binding proteins with homology to the nuclear factor CREB. Nature, 340, 727 730.
-
(1989)
Nature
, vol.340
, pp. 727-730
-
-
Katagiri, F.1
Lam, E.2
Chua, N.H.3
-
17
-
-
0037350568
-
Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray
-
Kim H. Snesrud E.C. Haas B. Cheung F. Town C.D. Quackenbush J. ( 2003) Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res. 13, 327 340.
-
(2003)
Genome Res.
, vol.13
, pp. 327-340
-
-
Kim, H.1
Snesrud, E.C.2
Haas, B.3
Cheung, F.4
Town, C.D.5
Quackenbush, J.6
-
18
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim T.H. Barrera L.O. Zheng M. Qu C. Singer M.A. Richmond T.A. Wu Y. Green R.D. Ren B. ( 2005) A high-resolution map of active promoters in the human genome. Nature, 436, 876 880.
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
Barrera, L.O.2
Zheng, M.3
Qu, C.4
Singer, M.A.5
Richmond, T.A.6
Wu, Y.7
Green, R.D.8
Ren, B.9
-
19
-
-
33644760394
-
Genomic survey of gene expression diversity in Arabidopsis thaliana
-
Kliebenstein D.J. West M.A. van Leeuwen H. Kim K. Doerge R.W. Michelmore R.W. St Clair D.A. ( 2006) Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics, 172, 1179 1189.
-
(2006)
Genetics
, vol.172
, pp. 1179-1189
-
-
Kliebenstein, D.J.1
West, M.A.2
Van Leeuwen, H.3
Kim, K.4
Doerge, R.W.5
Michelmore, R.W.6
St Clair, D.A.7
-
20
-
-
2942518343
-
Mapping global histone acetylation patterns to gene expression
-
Kurdistani S.K. Tavazoie S. Grunstein M. ( 2004) Mapping global histone acetylation patterns to gene expression. Cell, 117, 721 733.
-
(2004)
Cell
, vol.117
, pp. 721-733
-
-
Kurdistani, S.K.1
Tavazoie, S.2
Grunstein, M.3
-
21
-
-
0029152188
-
Binding site requirements and differential representation of TGA factors in nuclear ASF-1 activity
-
Lam E. Lam Y.K. ( 1995) Binding site requirements and differential representation of TGA factors in nuclear ASF-1 activity. Nucleic Acids Res. 23, 3778 3785.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 3778-3785
-
-
Lam, E.1
Lam, Y.K.2
-
22
-
-
0024746306
-
Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants
-
Lam E. Benfey P.N. Gilmartin P.M. Fang R.X. Chua N.H. ( 1989) Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Proc. Natl Acad. Sci. USA, 86, 7890 7894.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 7890-7894
-
-
Lam, E.1
Benfey, P.N.2
Gilmartin, P.M.3
Fang, R.X.4
Chua, N.H.5
-
23
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I. Rinaldi N.J. Robert F. et al. ( 2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799 804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
-
24
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
Lippman Z. Gendrel A.V. Black M. et al. ( 2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471 476.
-
(2004)
Nature
, vol.430
, pp. 471-476
-
-
Lippman, Z.1
Gendrel, A.V.2
Black, M.3
-
26
-
-
0036852098
-
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
-
Nuwaysir E.F. Huang W. Albert T.J. et al. ( 2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749 1755.
-
(2002)
Genome Res.
, vol.12
, pp. 1749-1755
-
-
Nuwaysir, E.F.1
Huang, W.2
Albert, T.J.3
-
27
-
-
0034161329
-
Mapping chromosomal proteins in vivo by formaldehyde-crosslinked- chromatin immunoprecipitation
-
Orlando V. ( 2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99 104.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 99-104
-
-
Orlando, V.1
-
28
-
-
0030039808
-
Binding specificity and tissue-specific expression pattern of the Arabidopsis bZIP transcription factor TGA2
-
de Pater S. Pham K. Memelink J. Kijne J. ( 1996) Binding specificity and tissue-specific expression pattern of the Arabidopsis bZIP transcription factor TGA2. Mol. Gen. Genet. 250, 237 239.
-
(1996)
Mol. Gen. Genet.
, vol.250
, pp. 237-239
-
-
De Pater, S.1
Pham, K.2
Memelink, J.3
Kijne, J.4
-
29
-
-
2342501846
-
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
-
Redman J.C. Haas B.J. Tanimoto G. Town C.D. ( 2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 38, 545 561.
-
(2004)
Plant J.
, vol.38
, pp. 545-561
-
-
Redman, J.C.1
Haas, B.J.2
Tanimoto, G.3
Town, C.D.4
-
30
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren B. Robert F. Wyrick J.J. et al. ( 2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306 2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
-
31
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
In. Krawetz, S. Misener, S., eds). Totowa, NJ: Humana Press, pp.
-
Rozen S. Skaletski H.J. ( 2000) primer3 on the WWW for general users and for biologist programmers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology ( Krawetz S. Misener S., eds). Totowa, NJ : Humana Press, pp. 365 386.
-
(2000)
Bioinformatics Methods and Protocols: Methods in Molecular Biology
, pp. 365-386
-
-
Rozen, S.1
Skaletski, H.J.2
-
33
-
-
2642570305
-
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
-
Schubeler D. MacAlpine D.M. Scalzo D. et al. ( 2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263 1271.
-
(2004)
Genes Dev.
, vol.18
, pp. 1263-1271
-
-
Schubeler, D.1
MacAlpine, D.M.2
Scalzo, D.3
-
34
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth G.K. ( 2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, pp. 3
-
-
Smyth, G.K.1
-
35
-
-
20144386497
-
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
-
Stolc V. Samanta M.P. Tongprasit W. et al. ( 2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl Acad. Sci. USA, 102, 4453 4458.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4453-4458
-
-
Stolc, V.1
Samanta, M.P.2
Tongprasit, W.3
-
36
-
-
18744377158
-
Microarray-based detection and genotyping of viral pathogens
-
Wang D. Coscoy L. Zylberberg M. Avila P.C. Boushey H.A. Ganem D. DeRisi J.L. ( 2002) Microarray-based detection and genotyping of viral pathogens. Proc. Natl Acad. Sci. USA, 99, 15687 15692.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 15687-15692
-
-
Wang, D.1
Coscoy, L.2
Zylberberg, M.3
Avila, P.C.4
Boushey, H.A.5
Ganem, D.6
Derisi, J.L.7
-
37
-
-
0034353112
-
Arabidopsis microarray service facilities
-
Wisman E. Ohlrogge J. ( 2000) Arabidopsis microarray service facilities. Plant Physiol. 124, 1468 1471.
-
(2000)
Plant Physiol.
, vol.124
, pp. 1468-1471
-
-
Wisman, E.1
Ohlrogge, J.2
-
38
-
-
0037200201
-
A new non-linear normalization method for reducing variability in DNA microarray experiments
-
Workman C. Jensen L.J. Jarmer H. Berka R. Gautier L. Nielser H.B. Saxild H.H. Nielsen C. Brunak S. Knudsen S. ( 2002) A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol. 3, 1 16.
-
(2002)
Genome Biol.
, vol.3
, pp. 1-16
-
-
Workman, C.1
Jensen, L.J.2
Jarmer, H.3
Berka, R.4
Gautier, L.5
Nielser, H.B.6
Saxild, H.H.7
Nielsen, C.8
Brunak, S.9
Knudsen, S.10
-
39
-
-
0242300620
-
Empirical analysis of transcriptional activity in the Arabidopsis genome
-
Yamada K. Lim J. Dale J.M. et al. ( 2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842 846.
-
(2003)
Science
, vol.302
, pp. 842-846
-
-
Yamada, K.1
Lim, J.2
Dale, J.M.3
-
40
-
-
26944438704
-
Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression
-
Zanetti M.E. Chang I.F. Gong F. Galbraith D.W. Bailey-Serres J. ( 2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol. 138, 624 635.
-
(2005)
Plant Physiol.
, vol.138
, pp. 624-635
-
-
Zanetti, M.E.1
Chang, I.F.2
Gong, F.3
Galbraith, D.W.4
Bailey-Serres, J.5
-
41
-
-
0345376974
-
Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance
-
Zhang Y. Tessaro M.J. Lassner M. Li X. ( 2003) Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance. Plant Cell, 15, 2647 2653.
-
(2003)
Plant Cell
, vol.15
, pp. 2647-2653
-
-
Zhang, Y.1
Tessaro, M.J.2
Lassner, M.3
Li, X.4
-
42
-
-
0034141963
-
NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid
-
Zhou J.M. Trifa Y. Silva H. Pontier D. Lam E. Shah J. Klessig D.F. ( 2000) NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid. Mol. Plant Microbe Interact. 13, 191 202.
-
(2000)
Mol. Plant Microbe Interact.
, vol.13
, pp. 191-202
-
-
Zhou, J.M.1
Trifa, Y.2
Silva, H.3
Pontier, D.4
Lam, E.5
Shah, J.6
Klessig, D.F.7
-
43
-
-
0034524684
-
Large-scale profiling of the Arabidopsis transcriptome
-
Zhu T. Wang X. ( 2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 124, 1472 1476.
-
(2000)
Plant Physiol.
, vol.124
, pp. 1472-1476
-
-
Zhu, T.1
Wang, X.2
|