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CatMap specifications

Information


Unique identifier OMICS_18320
Name CatMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability No
Maintained No

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Publication for CatMap

CatMap in pipelines

 (3)
2017
PMCID: 5311056
PMID: 28224043
DOI: 10.1038/hgv.2017.4

[…] consortium database (http://exac.broadinstitute.org/) and our internal university college london exomes consortium database comprising of 1,980 exomes. variants were then cross-referenced with catmap (http://cat-map.wustl.edu/) for variants in known cataract genes. wes data were also analyzed by exomedepth to identify any potential causative exonic copy number variations. the gcnt2 variant […]

2014
PMCID: 4169242
PMID: 25232726
DOI: 10.1371/journal.pgen.1004619

[…] transcripts present on at least four arrays for fat body, or at least five for gut were kept for further analysis. fdr was controlled using the described procedure . for gene ontology enrichment, catmap , or david ease analyses were performed., for qpcr analysis rna was isolated from five to 10 midguts, five fat bodies or five guts and fat bodies with trizol, converted into cdna and qpcr […]

2010
PMCID: 2841611
PMID: 20333234
DOI: 10.1371/journal.pgen.1000881

[…] from further analysis. flybase gene ids were mapped to gene ontology (go) ids (version 1.107)., for functional analysis using all expressed genes, we used the wilcoxon rank sum test implemented in catmap . ranks of genes were based on the bayes t-statistic for differential expression and, for a given functional category, the significance of the rank sum for all genes in the category […]


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CatMap in publications

 (23)
PMCID: 5913218
PMID: 29686395
DOI: 10.1038/s41467-018-03795-8

[…] spin configurations. molecular orbitals (mos) of fe3n2 and their corresponding contributions from fe3 and n2 were obtained from fragment mo analyses., microkinetic modeling was carried out using the catmap software package. the model was constructed by numerically solving the differential equations that describe the coverage of each surface intermediates under the steady-state approximation. […]

PMCID: 5739433
PMID: 29267365
DOI: 10.1371/journal.pone.0189881

[…] infancy or during childhood and displays variable clinical morphology including posterior polar opacities, nuclear opacities, cortical opacities and total lens opacities (https://sites.wustl.edu/catmap). currently, the epha2 mutation spectrum includes 14 missense mutations predicted to result in amino-acid substitutions, one nonsense mutation, and five frame-shift mutations predicted […]

PMCID: 5746853
PMID: 29296669
DOI: 10.1021/acscentsci.7b00442

[…] transfer which occurs on the ns to ps time scale.,, a steady-state, mean-field microkinetic model was used to determine theoretical turnover frequencies. the catalysis microkinetic analysis package (catmap) was used to solve the set of coupled differential equations that describe the reaction rates. we assume a co pressure of 1 mbar based on the experimental faradaic efficiency under co2 […]

PMCID: 5355364
PMID: 28273481
DOI: 10.1016/j.cmet.2017.02.005

[…] (a). this revealed that the average ranking of the ovarian-expressed transcripts () was smaller than expected by chance when compared with randomly selected gene lists of the same size (p = 0.09, catmap; ; b). all other tissue gene sets were less similar to the whole genome. thus, the ovarian transcriptome may have been constrained toward encoding aas in the proportions required to maximize […]

PMCID: 5343483
PMID: 28262694
DOI: 10.1038/ncomms14621

[…] finally, more accurate modelling of kinetics on the surface to choose the most interesting species to study is desirable. integration of these methods with existing microkinetic codes such as catmap would simplify this process. we have found that the chosen criterion (highest transition-state energy in a pathway) has worked well for determining the rate-limiting step in the networks […]


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CatMap institution(s)
Complex Systems Division, Department of Theoretical Physics, Lund University, Lund, Sweden
CatMap funding source(s)
Supported by the Swedish Foundation for Strategic Research and the Swedish Foundation for Strategic Research through the Lund Center for Stem Cell Biology and Cell Therapy.

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