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Protocols

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


No version available

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 citations

 (38)
library_books

De novo transcriptome analysis and gene expression profiling of an oleaginous microalga Scenedesmus acutus TISTR8540 during nitrogen deprivation induced lipid accumulation

2018
Sci Rep
PMCID: 5829077
PMID: 29487383
DOI: 10.1038/s41598-018-22080-8

[…] 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. […]

library_books

Genome Wide Analysis of Long Non Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process

2017
Int J Mol Sci
PMCID: 5796051
PMID: 29286332
DOI: 10.3390/ijms19010101

[…] 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 […]

library_books

Perturbation of Auxin Homeostasis and Signaling by PINOID Overexpression Induces Stress Responses in Arabidopsis

2017
Front Plant Sci
PMCID: 5539238
PMID: 28824662
DOI: 10.3389/fpls.2017.01308

[…] 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 […]

library_books

Molecular characterization of the acquisition of longevity during seed maturation in soybean

2017
PLoS One
PMCID: 5507495
PMID: 28700604
DOI: 10.1371/journal.pone.0180282

[…] 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 […]

call_split

Chloroplast Redox Status Modulates Genome Wide Plant Responses during the Non host Interaction of Tobacco with the Hemibiotrophic Bacterium Xanthomonas campestris pv. vesicatoria

2017
Front Plant Sci
PMCID: 5495832
PMID: 28725231
DOI: 10.3389/fpls.2017.01158
call_split See protocol

[…] 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). […]

call_split

Alteration in Auxin Homeostasis and Signaling by Overexpression Of PINOID Kinase Causes Leaf Growth Defects in Arabidopsis thaliana

2017
Front Plant Sci
PMCID: 5470171
PMID: 28659952
DOI: 10.3389/fpls.2017.01009
call_split See protocol

[…] 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. […]

Citations

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PageMan institution(s)
Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany; Deutsches Ressourcenzentrum für Genomforschung GmbH, Berlin, Germany; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
PageMan funding source(s)
Supported by the BMBF GABI grant nos. 0313110/ 0313112.

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