A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. Liu, L., Ramsay, T., Zinkgraf, M., Sundell, D., Street, N. R., Filkov, V., & Groover, A. Plant J, 82(5):887–98, June, 2015. Edition: 2015/04/24![A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.
@article{liu_resource_2015,
title = {A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in {Populus}},
volume = {82},
issn = {1365-313X (Electronic) 0960-7412 (Linking)},
url = {https://www.ncbi.nlm.nih.gov/pubmed/25903933},
doi = {10.1111/tpj.12850},
abstract = {Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.},
language = {en},
number = {5},
urldate = {2021-06-07},
journal = {Plant J},
author = {Liu, L. and Ramsay, T. and Zinkgraf, M. and Sundell, D. and Street, N. R. and Filkov, V. and Groover, A.},
month = jun,
year = {2015},
note = {Edition: 2015/04/24},
keywords = {Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Gene Expression Profiling/methods, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant, Image Processing, Computer-Assisted, Molecular Sequence Data, Plant Proteins/*genetics/metabolism, Populus trichocarpa, Populus/*genetics/growth \& development, Transcription Factors/genetics/*metabolism, Wood/genetics/*growth \& development, Workflow, cambium, chromatin immunoprecipitation sequencing, secondary growth, transcription factor, wood formation},
pages = {887--98},
}
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Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.","language":"en","number":"5","urldate":"2021-06-07","journal":"Plant J","author":[{"propositions":[],"lastnames":["Liu"],"firstnames":["L."],"suffixes":[]},{"propositions":[],"lastnames":["Ramsay"],"firstnames":["T."],"suffixes":[]},{"propositions":[],"lastnames":["Zinkgraf"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Sundell"],"firstnames":["D."],"suffixes":[]},{"propositions":[],"lastnames":["Street"],"firstnames":["N.","R."],"suffixes":[]},{"propositions":[],"lastnames":["Filkov"],"firstnames":["V."],"suffixes":[]},{"propositions":[],"lastnames":["Groover"],"firstnames":["A."],"suffixes":[]}],"month":"June","year":"2015","note":"Edition: 2015/04/24","keywords":"Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Gene Expression Profiling/methods, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant, Image Processing, Computer-Assisted, Molecular Sequence Data, Plant Proteins/*genetics/metabolism, Populus trichocarpa, Populus/*genetics/growth & development, Transcription Factors/genetics/*metabolism, Wood/genetics/*growth & development, Workflow, cambium, chromatin immunoprecipitation sequencing, secondary growth, transcription factor, wood formation","pages":"887–98","bibtex":"@article{liu_resource_2015,\n\ttitle = {A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in {Populus}},\n\tvolume = {82},\n\tissn = {1365-313X (Electronic) 0960-7412 (Linking)},\n\turl = {https://www.ncbi.nlm.nih.gov/pubmed/25903933},\n\tdoi = {10.1111/tpj.12850},\n\tabstract = {Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. 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