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PageMan specifications
Information
| Unique identifier | OMICS_19183 |
|---|---|
| Name | PageMan |
| Software type | Pipeline/Workflow |
| Interface | Graphical user interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Programming languages | Java |
| Computer skills | Medium |
| Stability | Stable |
| Maintained | Yes |
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Versioning
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Maintainers
- person_outline Axel Nagel
- person_outline Dirk Steinhauser
- person_outline Bjorn Usadel
- person_outline Yves Gibon
- person_outline Oliver Bläsing
Publication for PageMan
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
PageMan citations
(38)De novo transcriptome analysis and gene expression profiling of an oleaginous microalga Scenedesmus acutus TISTR8540 during nitrogen deprivation induced lipid accumulation
[…] comparative transcriptome analysis, the organism-specific mapping files were generated from protein reference sequences by the Mercator pipeline. Over-representation analysis was performed using the PAGEMAN program using the Fisher’s exact test with a cutoff of 2. […]
Genome Wide Analysis of Long Non Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process
[…] d in carbohydrate, protein, lipid, and phytohormone metabolism; cell division/cycle; and photosynthesis activation. Unlike GO and KEGG enrichment analyses in the present study, the MapMan pathway and PageMan programs were used to explore the putative functions of the differentially expressed genes identified by RNA-seq in the study of Liu et al. []. Liu et al. [,] analyzed the transcriptomic and p […]
Perturbation of Auxin Homeostasis and Signaling by PINOID Overexpression Induces Stress Responses in Arabidopsis
[…] ationship between PID-modulated auxin homeostasis and signaling, and the observed stress responses.PIDOE plants also showed changes in levels of other hormones and their responsive genes, as shown by PageMan, hormone quantification and expression changes in our transcriptome data (Figure , Supplementary Figure , and Data ). The involvement of multiple hormones suggests involvement of complex and i […]
Molecular characterization of the acquisition of longevity during seed maturation in soybean
[…] principal component analysis (). Data from the two biological replicates were highly similar, with between 98% and 97% similarity between the two biological replicates of stage 7.2 and stage 9.Using Pageman (MAPMAN, GABI Germany), a gene ontology (GO) enrichment was performed to obtain an overview of the different biological processes that are overrepresented at the different stages of seed matur […]
Chloroplast Redox Status Modulates Genome Wide Plant Responses during the Non host Interaction of Tobacco with the Hemibiotrophic Bacterium Xanthomonas campestris pv. vesicatoria
[…] even when their function is approximate, and the same gene can belong to more than one BIN or subBIN ().Pathway over-representation analyses between lines or treatment comparisons were performed with PageMan (). The analysis was carried out separately for induced (FC > 2 and FDR < 0.05) and repressed (FC < 0.5 and FDR < 0.05) genes using Fisher’s exact test with Bonferroni correction (FDR < 0.05). […]
Alteration in Auxin Homeostasis and Signaling by Overexpression Of PINOID Kinase Causes Leaf Growth Defects in Arabidopsis thaliana
[…] s were classified into groups based on gene ontology (GO) information obtained from the TAIR Database2 by using MapMan () and overrepresented functions and gene enrichment studies were carried out by PageMan () and Cytoscape (using the BiNGO plugin) software. […]
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