植物在不同的生長發育階段或遭遇逆境時，都需要調節相關基因的表現量來幫助自身適應不同的環境。其中最重要的調控方式就是利用轉錄因子(transcription factors)結合到啟動子(promoter)上的近端調控因子(cis-elements)來控制下游基因的表現。因此，若想了解其中複雜的調控關係，研究轉錄因子和基因組(genome)上的結合位置 (transcription factor binding sites，簡稱TFBSs)顯然是一個相當重要的工作。近年來各種高通量技術蓬勃發展，其中染色質免疫沉澱測序(chromatin immunoprecipitation sequencing，簡稱ChIP-seq)被廣泛應用於分析整個基因組上可能的轉錄因子結合位置或尋找會被某個轉錄因子所調控的基因群。所以，若能將這些實驗資料進行全面且條理性的分析統整，勢必更能了解轉錄因子與基因之間的調控關係。到目前為止，只有3個公開資料庫有提供植物ChIP-seq實驗資料，分別為PCSD、ChIPBase v2.0和Expresso。但ChIPBase v2.0和Expresso分別只收錄來自阿拉伯芥(Arabidopsis thaliana)的26和20種轉錄因子。此外，PCSD也只提供關於阿拉伯芥、水稻(Oryza sativa)和玉米(Zea mays)三種植物的轉錄因子和其調控基因的基本資訊，使用者無法直接分析任意啟動子序列上是否存在實驗驗證的TFBSs。基於以上原因，本研究主要的目的為建立一個整合多種植物物種之ChIP-seq資料庫。我們由Gene Expression Omnibus (GEO)和Sequence Read Archive (SRA)中蒐集了阿拉伯芥、水稻、玉米、大豆(Glycine max)、番茄(Solanum lycopersicum)、棉花(Gossypium hirsutum)和深山南芥(Arabidopsis lyrata)共7種植物之ChIP-seq實驗資料，涵蓋662個samples和99種蛋白質(包含轉錄因子、組織蛋白和其他DNA結合蛋白)。以上所有資料經由系統性的流程處理，並由AQUAS及MACS2分析，最終獲得4,574,337筆蛋白質結合位置以及1,233,999筆蛋白質與基因之結合關係資訊。最後建立一個名為Plant ChIP-seq Database(簡稱PCBase)的資料庫以方便植物學家快速了解基因組DNA上多種蛋白質的結合位置。PCBase提供基因搜尋(Gene Search)，蛋白質搜尋(Protein Search)，啟動子分析(Promoter Analysis)，基因組瀏覽(Genome Browser)及資料下載(Download)等五大功能來全面分析植物染色質狀態。使用者除了能輕易獲得轉錄因子和其轉錄因子結合位置座標及調控基因外，所有由ChIP-seq實驗資料得來的轉錄因子結合位置權重(TF binding position weight matrices)皆可用於分析任一段啟動子序列。我們希望PCBase可以幫助植物領域研究人員在研究植物的轉錄調控機制時更加便利。目前PCBase可由以下網址免費取得：http://pcbase.itps.ncku.edu.tw/

Transcription factors (TFs) can bind to cis-elements on promoters and regulate gene expression during plant development and stresses responsiveness. Therefore, investigation of TFs and their binding sites (TFBSs) is important to understand the gene regulatory mechanisms. Recently, a high-throughput technology, chromatin immunoprecipitation sequencing (ChIP-seq), was applied to rapidly explore the binding sequences on a genome and regulatory genes of a TF in many studies. Consequently, the collection and analysis of ChIP-seq experimental data will be useful to further identify the relationships among TFs, TFBSs, and TF-targeted genes. Until now, only three databases provide ChIP-seq data from plants, those are PCSD (including Arabidopsis thaliana, Oryza sativa (rice), Zea mays (maize)), ChIPBase v2.0 and Expresso (including Arabidopsis thaliana), respectively. However, only 26 and 20 TFs can be accessed from ChIPBase v2.0 and Expresso, individually. Additionally, PCSD only provides the information of TFs and their target-genes; the experimental TF binding motifs can’t be applied in promoter analysis. Based on the above, the aim of this study is to construct a comprehensive plant ChIP-seq database. We collected ChIP-seq experimental data from seven plants including Arabidopsis thaliana, Oryza sativa (rice), Zea mays (maize), Glycine max (soybean), Solanum lycopersicum (tomato), Gossypium hirsutum (cotton) and Arabidopsis lyrata. The number of samples obtained from Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) are 662, which contain 99 proteins (TF/Histone/DNA binding protein). AQUAS and MACS2 programs systematically processed all of the raw data to identify the protein binding sites. Finally, we constructed a database named Plant ChIP-seq Database (PCBase) to comprehensively analyze plant chromatin status. There are five main functions in PCBase, such as Gene Search, Protein Search, Promoter Analysis, Genome Browser, and Download. The target genes and TFBS coordinates of a TF can be effectively retrieved. All experimental TF binding matrices can be utilized in any input promoter sequence. We hope this database can help scientists to study the transcriptional regulatory mechanisms in plants. This database is freely available at: http://pcbase.itps.ncku.edu.tw/

Adkins, N. L., Hagerman, T. A., & Georgel, P. (2006). GAGA protein: a multi-faceted transcription factor. Biochem Cell Biol, 84(4), 559-567. doi:10.1139/o06-062
Aghamirzaie, D., Raja Velmurugan, K., Wu, S., Altarawy, D., Heath, L. S., & Grene, R. (2017). Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data. F1000Res, 6, 372. doi:10.12688/f1000research.10041.1
Alam, M. M., Nakamura, H., Ichikawa, H., Miyao, A., Hirochika, H., Kobayashi, K., . . . Nishiguchi, M. (2014). Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice. Rice (N Y), 7(1), 9. doi:10.1186/s12284-014-0009-2
Aparicio, O., Geisberg, J. V., & Struhl, K. (2004). Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Cell Biol, Chapter 17, Unit 17 17. doi:10.1002/0471143030.cb1707s23
Ashraf, M., & Foolad, M. R. (2007). Roles of glycine betaine and proline in improving plant abiotic stress resistance. Environmental and Experimental Botany, 59(2), 206-216. doi:10.1016/j.envexpbot.2005.12.006
Bailey, T. L. (2011). DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27(12), 1653-1659. doi:10.1093/bioinformatics/btr261
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., . . . Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 37(Web Server issue), W202-208. doi:10.1093/nar/gkp335
Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol, 2, 28-36.
Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., . . . Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129(4), 823-837. doi:10.1016/j.cell.2007.05.009
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., . . . Smith, A. J. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456(7218), 53-59. doi:10.1038/nature07517
Berger, N., Dubreucq, B., Roudier, F., Dubos, C., & Lepiniec, L. (2011). Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell, 23(11), 4065-4078. doi:10.1105/tpc.111.087866
Binott, J. J., Owuoche, J. O., & Bartels, D. (2017). Physiological and molecular characterization of Kenyan barley (Hordeum vulgare L.) seedlings for salinity and drought tolerance. Euphytica, 213(7). doi:UNSP 139
10.1007/s10681-017-1924-2
Buck, M. J., & Lieb, J. D. (2004). ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83(3), 349-360.
Cheneby, J., Gheorghe, M., Artufel, M., Mathelier, A., & Ballester, B. (2018). ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Res, 46(D1), D267-D275. doi:10.1093/nar/gkx1092
Chien, C. H., Chow, C. N., Wu, N. Y., Chiang-Hsieh, Y. F., Hou, P. F., & Chang, W. C. (2015). EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. BMC Genomics, 16 Suppl 2, S6. doi:10.1186/1471-2164-16-S2-S6
Chow, C. N., Zheng, H. Q., Wu, N. Y., Chien, C. H., Huang, H. D., Lee, T. Y., . . . Chang, W. C. (2016). PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Res, 44(D1), D1154-1160. doi:10.1093/nar/gkv1035
Cifuentes-Esquivel, N., Celiz-Balboa, J., Henriquez-Valencia, C., Mitina, I., Arrano-Salinas, P., Moreno, A. A., . . . Orellana, A. (2018). bZIP17 regulates the expression of genes related to seed storage and germination, reducing seed susceptibility to osmotic stress. J Cell Biochem. doi:10.1002/jcb.26882
D'Amato, G., Vitale, C., Rosario, N., Neto, H. J. C., Chong-Silva, D. C., Mendonca, F., . . . D'Amato, M. (2017). Climate change, allergy and asthma, and the role of tropical forests. World Allergy Organ J, 10(1), 11. doi:10.1186/s40413-017-0142-7
Dai, X., Wang, Y., & Zhang, W. H. (2016). OsWRKY74, a WRKY transcription factor, modulates tolerance to phosphate starvation in rice. J Exp Bot, 67(3), 947-960. doi:10.1093/jxb/erv515
Davis, C. A., Hitz, B. C., Sloan, C. A., Chan, E. T., Davidson, J. M., Gabdank, I., . . . Cherry, J. M. (2018). The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res, 46(D1), D794-D801. doi:10.1093/nar/gkx1081
Delmer, D. P. (2005). Agriculture in the developing world: Connecting innovations in plant research to downstream applications. Proc Natl Acad Sci U S A, 102(44), 15739-15746. doi:10.1073/pnas.0505895102
Diao, W., Snyder, J. C., Wang, S., Liu, J., Pan, B., Guo, G., . . . Dawood, M. (2018). Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network. Int J Mol Sci, 19(4). doi:10.3390/ijms19041028
Edgar, R., Domrachev, M., & Lash, A. E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res, 30(1), 207-210.
Fernandez-Pozo, N., Menda, N., Edwards, J. D., Saha, S., Tecle, I. Y., Strickler, S. R., . . . Mueller, L. A. (2015). The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. Nucleic Acids Res, 43(Database issue), D1036-1041. doi:10.1093/nar/gku1195
Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., . . . Bateman, A. (2016). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res, 44(D1), D279-285. doi:10.1093/nar/gkv1344
Gong, R., Cao, H., Zhang, J., Xie, K., Wang, D., & Yu, S. (2018). Divergent functions of the GAGA-binding transcription factor family in rice. Plant J, 94(1), 32-47. doi:10.1111/tpj.13837
Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., . . . Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res, 40(Database issue), D1178-1186. doi:10.1093/nar/gkr944
Gordon, A., & Hannon, G. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit.
Grant, D., Nelson, R. T., Cannon, S. B., & Shoemaker, R. C. (2010). SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res, 38(Database issue), D843-846. doi:10.1093/nar/gkp798
Gruber, M., Alahakoon, U., Taheri, A., Nagubushana, N., Zhou, R., Aung, B., . . . Hegedus, D. D. (2018). The biochemical composition and transcriptome of cotyledons from Brassica napus lines expressing the AtGL3 transcription factor and exhibiting reduced flea beetle feeding. BMC Plant Biol, 18(1), 64. doi:10.1186/s12870-018-1277-6
Halbritter, F., Kousa, A. I., & Tomlinson, S. R. (2014). GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. Nucleic Acids Res, 42(Database issue), D851-858. doi:10.1093/nar/gkt966
Heyman, J., Cools, T., Vandenbussche, F., Heyndrickx, K. S., Van Leene, J., Vercauteren, I., . . . De Veylder, L. (2013). ERF115 controls root quiescent center cell division and stem cell replenishment. Science, 342(6160), 860-863. doi:10.1126/science.1240667
Institute, B. (2018). Picard Toolkit. Broad Institute, GitHub repository, http://broadinstitute.github.io/picard/.
Jackson, S. P., & Bartek, J. (2009). The DNA-damage response in human biology and disease. Nature, 461(7267), 1071-1078. doi:10.1038/nature08467
Jafari, M., Ansari-Pour, N., Azimzadeh, S., & Mirzaie, M. (2017). A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology. PLoS One, 12(12), e0189922. doi:10.1371/journal.pone.0189922
Jin, J., Tian, F., Yang, D. C., Meng, Y. Q., Kong, L., Luo, J., & Gao, G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res, 45(D1), D1040-D1045. doi:10.1093/nar/gkw982
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science, 316(5830), 1497-1502. doi:10.1126/science.1141319
Kel, A. E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V., & Wingender, E. (2003). MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res, 31(13), 3576-3579.
Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., . . . Yates, A. (2018). Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res, 46(D1), D802-D808. doi:10.1093/nar/gkx1011
Kharchenko, P. V., Tolstorukov, M. Y., & Park, P. J. (2008). Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol, 26(12), 1351-1359. doi:10.1038/nbt.1508
Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T. A., . . . Ren, B. (2005). A high-resolution map of active promoters in the human genome. Nature, 436(7052), 876-880. doi:10.1038/nature03877
Kiranmai, K., Lokanadha Rao, G., Pandurangaiah, M., Nareshkumar, A., Amaranatha Reddy, V., Lokesh, U., . . . Sudhakar, C. (2018). A Novel WRKY Transcription Factor, MuWRKY3 (Macrotyloma uniflorum Lam. Verdc.) Enhances Drought Stress Tolerance in Transgenic Groundnut (Arachis hypogaea L.) Plants. Front Plant Sci, 9, 346. doi:10.3389/fpls.2018.00346
Kobayashi, K., Suzuki, T., Iwata, E., Nakamichi, N., Suzuki, T., Chen, P., . . . Ito, M. (2015). Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J, 34(15), 1992-2007. doi:10.15252/embj.201490899
Kodama, Y., Shumway, M., Leinonen, R., & International Nucleotide Sequence Database, C. (2012). The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res, 40(Database issue), D54-56. doi:10.1093/nar/gkr854
Koh, P. W., Pierson, E., & Kundaje, A. (2017). Denoising genome-wide histone ChIP-seq with convolutional neural networks. Bioinformatics, 33(14), i225-i233. doi:10.1093/bioinformatics/btx243
Kooiker, M., Airoldi, C. A., Losa, A., Manzotti, P. S., Finzi, L., Kater, M. M., & Colombo, L. (2005). BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK. Plant Cell, 17(3), 722-729. doi:10.1105/tpc.104.030130
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., . . . Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res, 40(Database issue), D1202-1210. doi:10.1093/nar/gkr1090
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10(3), R25. doi:10.1186/gb-2009-10-3-r25
Lazniewska, J., Macioszek, V. K., Lawrence, C. B., & Kononowicz, A. K. (2010). Fight to the death: Arabidopsis thaliana defense response to fungal necrotrophic pathogens. Acta Physiologiae Plantarum, 32(1), 1-10. doi:10.1007/s11738-009-0372-6
Lee, J., Shim, D., Moon, S., Kim, H., Bae, W., Kim, K., . . . Ryu, H. (2018). Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato. Plant Physiol Biochem, 127, 553-560. doi:10.1016/j.plaphy.2018.04.031
Li, D., Fu, X., Guo, L., Huang, Z., Li, Y., Liu, Y., . . . Liu, X. (2016). FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc Natl Acad Sci U S A, 113(33), 9375-9380. doi:10.1073/pnas.1602960113
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352
Liu, M., Chen, Y., Chen, Y., Shin, J. H., Mila, I., Audran, C., . . . Bouzayen, M. (2018). The tomato Ethylene Response Factor Sl-ERF.B3 integrates ethylene and auxin signaling via direct regulation of Sl-Aux/IAA27. New Phytol. doi:10.1111/nph.15165
Liu, S., Kracher, B., Ziegler, J., Birkenbihl, R. P., & Somssich, I. E. (2015). Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. Elife, 4, e07295. doi:10.7554/eLife.07295
Liu, Y., Tian, T., Zhang, K., You, Q., Yan, H., Zhao, N., . . . Su, Z. (2018). PCSD: a plant chromatin state database. Nucleic Acids Res, 46(D1), D1157-D1167. doi:10.1093/nar/gkx919
Machanick, P., & Bailey, T. L. (2011). MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics, 27(12), 1696-1697. doi:10.1093/bioinformatics/btr189
Martin, M. (2011). CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17. doi:10.14806/ej.17.1.200
Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., . . . Wingender, E. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res, 31(1), 374-378.
Meek, D. W. (2009). Tumour suppression by p53: a role for the DNA damage response? Nat Rev Cancer, 9(10), 714-723. doi:10.1038/nrc2716
Mei, S., Qin, Q., Wu, Q., Sun, H., Zheng, R., Zang, C., . . . Liu, X. S. (2017). Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res, 45(D1), D658-D662. doi:10.1093/nar/gkw983
Meister, R. J., Williams, L. A., Monfared, M. M., Gallagher, T. L., Kraft, E. A., Nelson, C. G., & Gasser, C. S. (2004). Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter. Plant J, 37(3), 426-438.
Nawrath, C., & Metraux, J. P. (1999). Salicylic acid induction-deficient mutants of Arabidopsis express PR-2 and PR-5 and accumulate high levels of camalexin after pathogen inoculation. Plant Cell, 11(8), 1393-1404.
O'Malley, R. C., Huang, S. C., Song, L., Lewsey, M. G., Bartlett, A., Nery, J. R., . . . Ecker, J. R. (2016). Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell, 165(5), 1280-1292. doi:10.1016/j.cell.2016.04.038
Ogita, N., Okushima, Y., Tokizawa, M., Yamamoto, Y. Y., Tanaka, M., Seki, M., . . . Umeda, M. (2018). Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis. Plant J, 94(3), 439-453. doi:10.1111/tpj.13866
Pajoro, A., Madrigal, P., Muino, J. M., Matus, J. T., Jin, J., Mecchia, M. A., . . . Kaufmann, K. (2014). Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol, 15(3), R41. doi:10.1186/gb-2014-15-3-r41
Park, P. J. (2009). ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet, 10(10), 669-680. doi:10.1038/nrg2641
Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., . . . Young, R. A. (2000). Genome-wide location and function of DNA binding proteins. Science, 290(5500), 2306-2309. doi:10.1126/science.290.5500.2306
Rogers, E. E., & Ausubel, F. M. (1997). Arabidopsis enhanced disease susceptibility mutants exhibit enhanced susceptibility to several bacterial pathogens and alterations in PR-1 gene expression. Plant Cell, 9(3), 305-316.
Sakai, H., Lee, S. S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., . . . Itoh, T. (2013). Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol, 54(2), e6. doi:10.1093/pcp/pcs183
Santi, L., Wang, Y., Stile, M. R., Berendzen, K., Wanke, D., Roig, C., . . . Salamini, F. (2003). The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J, 34(6), 813-826.
Schutzendubel, A., & Polle, A. (2002). Plant responses to abiotic stresses: heavy metal-induced oxidative stress and protection by mycorrhization. J Exp Bot, 53(372), 1351-1365.
Shinya Oki, T. O., Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno. (2018). Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions. bioRxiv, ChIP-Atlas,doi: https://doi.org/10.1101/262899.
Simonini, S., & Kater, M. M. (2014). Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance. J Exp Bot, 65(6), 1455-1465. doi:10.1093/jxb/eru003
Singh, K., Foley, R. C., & Onate-Sanchez, L. (2002). Transcription factors in plant defense and stress responses. Curr Opin Plant Biol, 5(5), 430-436.
Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., & Holmes, I. H. (2009). JBrowse: a next-generation genome browser. Genome Res, 19(9), 1630-1638. doi:10.1101/gr.094607.109
Sun, T., Zhang, Y., Li, Y., Zhang, Q., Ding, Y., & Zhang, Y. (2015). ChIP-seq reveals broad roles of SARD1 and CBP60g in regulating plant immunity. Nat Commun, 6, 10159. doi:10.1038/ncomms10159
Teller, S. (2013). Data Visualization with d3.js. Bibliometrics, 194.
Torstein Hønsi, G. H., Gert Vaartjes, Hilde Instefjord, Guro Myrkaskog, Anne Jorunn Fjærestad, Jon Arild Nygård, Øystein Moseng, Anita Nesse, Gjertrud Fretheim, Mustapha Mekhatria, Katharina von Oltersdorff-Kalettka, Linda Svendsen, Vidar Brekke, Sarah Elizabeth Miller Skjeldestad, Georg Nesse, Christer Vasseng, Elisabeth Fjøsne Ese, Cathrine Helene Ulverud,Henrik Holmberg, Kulbir Kainth, Grzegorz Iwacz,Paweł Fus, Sebastian Bochan, Kacper Madej, Grzegorz Blachliński. (2018). Highcharts JS v6.1.0 (2018-04-13). (c) 2009-2016 Torstein Honsi, License: www.highcharts.com/license.
Wang, C., Deng, P., Chen, L., Wang, X., Ma, H., Hu, W., . . . He, G. (2013). A wheat WRKY transcription factor TaWRKY10 confers tolerance to multiple abiotic stresses in transgenic tobacco. PLoS One, 8(6), e65120. doi:10.1371/journal.pone.0065120
Wang, J., Zhuang, J., Iyer, S., Lin, X. Y., Greven, M. C., Kim, B. H., . . . Weng, Z. (2013). Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res, 41(Database issue), D171-176. doi:10.1093/nar/gks1221
Wasternack, C., & Hause, B. (2013). Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann Bot, 111(6), 1021-1058. doi:10.1093/aob/mct067
Wildermuth, M. C., Dewdney, J., Wu, G., & Ausubel, F. M. (2001). Isochorismate synthase is required to synthesize salicylic acid for plant defence. Nature, 414(6863), 562-565. doi:Doi 10.1038/35107108
Wold, B., & Myers, R. M. (2008). Sequence census methods for functional genomics. Nat Methods, 5(1), 19-21. doi:10.1038/nmeth1157
Wong, K. C., Chan, T. M., Peng, C., Li, Y., & Zhang, Z. (2013). DNA motif elucidation using belief propagation. Nucleic Acids Res, 41(16), e153. doi:10.1093/nar/gkt574
Woods-Tor, A., Studholme, D. J., Cevik, V., Telli, O., Holub, E. B., & Tor, M. (2018). A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana. Front Plant Sci, 9, 265. doi:10.3389/fpls.2018.00265
Yevshin, I., Sharipov, R., Valeev, T., Kel, A., & Kolpakov, F. (2017). GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res, 45(D1), D61-D67. doi:10.1093/nar/gkw951
Yu, J., Jung, S., Cheng, C. H., Ficklin, S. P., Lee, T., Zheng, P., . . . Main, D. (2014). CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res, 42(Database issue), D1229-1236. doi:10.1093/nar/gkt1064
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., . . . Liu, X. S. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol, 9(9), R137. doi:10.1186/gb-2008-9-9-r137
Zhang, Y. X., Yang, Y. A., Fang, B., Gannon, P., Ding, P. T., Li, X., & Zhang, Y. L. (2010). Arabidopsis snc2-1D Activates Receptor-Like Protein-Mediated Immunity Transduced through WRKY70. Plant Cell, 22(9), 3153-3163. doi:10.1105/tpc.110.074120
Zhou, K. R., Liu, S., Sun, W. J., Zheng, L. L., Zhou, H., Yang, J. H., & Qu, L. H. (2017). ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res, 45(D1), D43-D50. doi:10.1093/nar/gkw965
Zhou, N., Tootle, T. L., & Glazebrook, J. (1999). Arabidopsis PAD3, a gene required for camalexin biosynthesis, encodes a putative cytochrome P450 monooxygenase. Plant Cell, 11(12), 2419-2428.
Zhou, Q., Zhang, S., Chen, F., Liu, B., Wu, L., Li, F., . . . Liu, G. (2018). Genome-wide identification and characterization of the SBP-box gene family in Petunia. BMC Genomics, 19(1), 193. doi:10.1186/s12864-018-4537-9