MapMan protocols

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MapMan specifications

Information


Unique identifier OMICS_10372
Name MapMan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 3.6.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Axel Nagel <>

Information


Unique identifier OMICS_10372
Name MapMan
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 3.6.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Axel Nagel <>

Publications for MapMan

MapMan in pipelines

 (71)
2018
PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] (sbicolor_v1.4_79) [] by using tophat version 2.0.4 []. differentially expressed genes were identified by using cuffdiff version 2.2.0 [], with the gene models annotated in sbicolor ver1.4 []., mapman (3.5.1 r2) software [] was used to map the ratio of expression (lodged to intact) of each gene to known metabolic pathways. the log2 value was calculated after adding 1 to the fpkm […]

2018
PMCID: 5768701
PMID: 29335449
DOI: 10.1038/s41598-017-18850-5

[…] ncbi (www.ncbi.nlm.nih.gov) and gene ontology consortium databases (http://geneontology.org/). all the degs were then mapped against the arabidopsis “ath_agi_locus_tair10_aug2012.m02” database in mapman to identify transcription factors (tfs). mapman identifies tfs based on its comparison with the reference genome. the tfs thus obtained were validated manually using the annotated list […]

2018
PMCID: 5809557
PMID: 29434236
DOI: 10.1038/s41598-018-21187-2

[…] above conditions. the annotation of probe sets was obtained from affymetrix and loaded in the partek genomics suite software (partek incorporated, st. louis, usa). for the functional study of degs mapman software was used since it has a more completed database for functional assignations. the slyc_affy_sgn_build2_070709 database was loaded and used for this functional analysis. the statistical […]

2018
PMCID: 5827756
PMID: 29483524
DOI: 10.1038/s41598-018-21866-0

[…] cufflinks program (version 2.0.0) with default parameters. the degs were filtered by p-value ≤0.01, fdr ≤0.05 and log fold change > 1, and these degs were used further for pathway analysis using mapman (version 3.5.1r2)., first-strand cdna was synthesized from dnasei treated total rna using superscript iii (invitrogen). the qrt-pcr reaction was carried out for selected degs (supplementary […]

2018
PMCID: 5849761
PMID: 29535363
DOI: 10.1038/s41598-018-22798-5

[…] tailored for plant omics data, to annotate assembled unigenes and differentially expressed genes. mercator assigns each sequence to functional bins that can be visualized on the pathways using mapman., quality-trimmed reads were aligned to the assembled sugarcane transcriptome using bowtie 2 with default alignment parameters. bowtie 2 was instructed to add rg headers (lb, pl, pu, and sm) […]


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MapMan in publications

 (802)
PMCID: 5935972
PMID: 29728053
DOI: 10.1186/s12870-018-1301-x

[…] 1208 transcripts (62%) reversed their expression changes after 2 d of n resupply (20 dag), therefrom 665 being again upregulated and 543 being again downregulated., further analysis using mapman software [] sorted differentially regulated genes into functional classes. about 63% of all differentially regulated genes could at least be assigned to one functional class. a number […]

PMCID: 5928093
PMID: 29736251
DOI: 10.1038/s41438-018-0034-1

[…] identified, with more genes being upregulated in pillar (453) than downregulated (188) (dataset ). to evaluate potential changes in regulatory and/or metabolic pathways, all degs were examined using mapman. gene enrichment analysis revealed significant differential expression of genes involved in biotic and abiotic stress responses along with several other categories that are commonly associated […]

PMCID: 5913800
PMID: 29685101
DOI: 10.1186/s12870-018-1281-x

[…] intracellular).fig. 3, to further characterize the metabolic changes regulated by drought stress and water recovery, we visualized the metabolic responses to water deficit and recovery using the mapman program [] (see additional file : figure s7). there were 404 degs involved in six main metabolic activities related to the minor cho, cell wall, lipids, starch and sucrose, tca, as well […]

PMCID: 5913055
PMID: 29687350
DOI: 10.1186/s12284-018-0219-0

[…] of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. functional classification analysis with a mapman tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. comparative analysis of rice and arabidopsis demonstrated that genes involved […]

PMCID: 5910329
PMID: 29679239
DOI: 10.1186/s12284-018-0211-8

[…] were generated using the venndiagram function in r 3.2.1 with the limma package. principal component analysis (pca) was conducted using the pca function in r 3.2.1 with the factominer package. mapman analysis was conducted using mapman 3.6.0 (http://mapman.gabipd.org/web/guest) software., the observed root phenotypes indicated that both cultivated and wild rice varieties developed black, […]


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MapMan institution(s)
Max Planck Institute for Molecular Plant Physiology, Golm, Germany

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