ArticleNucleic acids research2004
POBO, transcription factor binding site verification with bootstrapping.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes.Functional & integrative genomics · 2023Article
- Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure.Functional & integrative genomics · 2022Article
- Article
- Vascular Plant One-Zinc-Finger (VOZ) Transcription Factors Are Positive Regulators of Salt Tolerance in Arabidopsis.International journal of molecular sciences · 2018Article
- Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity.PLoS pathogens · 2018Article
- Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato.Molecular biology reports · 2018Article
- Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress.Scientific reports · 2016Article
- Identification and expression analyses of MYB and WRKY transcription factor genes in Papaver somniferum L.Physiology and molecular biology of plants : an international journal of functional plant biology · 2015Article
- Small RNA profiling reveals regulation of Arabidopsis miR168 and heterochromatic siRNA415 in response to fungal elicitors.BMC genomics · 2014Article
- Expression-based network biology identifies immune-related functional modules involved in plant defense.BMC genomics · 2014Article
- Identification of a novel type of WRKY transcription factor binding site in elicitor-responsive cis-sequences from Arabidopsis thaliana.Plant molecular biology · 2014Article
- System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato.Plant physiology · 2013Article
- EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in Arabidopsis.Plant physiology · 2013Article
- ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.FEBS open bio · 2013Article
- Arabidopsis TNL-WRKY domain receptor RRS1 contributes to temperature-conditioned RPS4 auto-immunity.Frontiers in plant science · 2013Article
- Crosstalk between the circadian clock and innate immunity in Arabidopsis.PLoS pathogens · 2013Article
- Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation.BMC plant biology · 2012Article
- Expression analysis in response to drought stress in soybean: Shedding light on the regulation of metabolic pathway genes.Genetics and molecular biology · 2012Article
- Expression pattern of drought stress marker genes in soybean roots under two water deficit systems.Genetics and molecular biology · 2012Article
- A high resolution genome-wide scan of HNF4α recognition sites infers a regulatory gene network in colon cancer.PloS one · 2011Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors can either activate or repress target genes by binding onto short nucleotide sequence motifs in the promoter regions of these genes. Here, we present POBO, a promoter bootstrapping program, for gene expression data. POBO can be used to detect, compare and verify predetermined transcription factor binding site motifs in the promoters of one or two clusters of co-regulated genes. The program calculates the frequencies of the motif in the input promoter sets. A bootstrap analysis detects significantly over- or underrepresented motifs. The output of the program presents bootstrapped results in picture and text formats. The program was tested with published data from transgenic WRKY70 microarray experiments. Intriguingly, motifs recognized by the WRKY transcription factors of plant defense pathways are similarly enriched in both up- and downregulated clusters. POBO analysis suggests slightly modified hypothetical motifs that discriminate between up- and downregulated clusters. In conclusion, POBO allows easy, fast and accurate verification of putative regulatory motifs. The statistical tests implemented in POBO can be useful in eliminating false positives from the results of pattern discovery programs and increasing the reliability of true positives. POBO is freely available from http://ekhidna.biocenter.helsinki.fi:9801/pobo.
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