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Protocols

PhenoGram specifications

Information


Unique identifier OMICS_11755
Name PhenoGram
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainer


  • person_outline Daniel Wolfe

Information


Unique identifier OMICS_11755
Name PhenoGram
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
RMagick
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Daniel Wolfe

Publication for PhenoGram

PhenoGram citations

 (10)
library_books

Disease relevant modifications of the methylome and transcriptome by particulate matter (PM2.5) from biomass combustion

2017
Epigenetics
PMCID: 5739103
PMID: 28742980
DOI: 10.1080/15592294.2017.1356555

[…] ally methylated CpG positions to their nearest TSSs were calculated with the help of the DistanceToNearest-function of the “GenomicRanges” package, and plotted against their corresponding Dbvalue.The phenogram shown in the manuscript is a collage of 3 different phenograms (for hypomethylated CpGs, hypermethylated CpGs, and Giemsa bands). Each phenogram was generated using the web application Pheno […]

call_split

Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer Saldino syndrome

2017
Hum Genomics
PMCID: 5517791
PMID: 28724397
DOI: 10.1186/s40246-017-0111-9
call_split See protocol

[…] ype lists for each of the proband, maternal, and paternal exome data. Variant read depth and variant calls were confirmed visually with the Integrated Genomics Viewer (IGV). Data were visualized with PhenoGram (Center for System Genomics, Pennsylvania State University; http://visualization.ritchielab.psu.edu/). […]

library_books

Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy?

2017
Genome Biol Evol
PMCID: 5737724
PMID: 28854631
DOI: 10.1093/gbe/evx119

[…] native forms in the bona fide (+) data set were retrieved from Ensembl (genome version: GRCh38) (). The ideogram representing the chromosomal localization of these genes was created with the software PhenoGram (http://ritchielab.psu.edu/). Additionally, a circular diagram displaying the genomic distances between genes encoding alternative forms (distinct AnEnPi cluster of the same EC) as well as g […]

library_books

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

2016
BMC Genomics
PMCID: 5162099
PMID: 27986076
DOI: 10.1186/s12864-016-3377-8

[…] ze cutoffs of eight for a di-, six for a tri-, and four for tetra-, penta-, and hexanucleotide repeats were used to report SSRs. A maximum distance of 100 bp was allowed between two SSRs. A web based PhenoGram [] was used to visualize the distribution of the SNP loci across the switchgrass pseudomolecules, each line representing a SNP locus with its base pair coordinate. […]

library_books

Genome wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress responsive and development related members

2016
Sci Rep
PMCID: 5133618
PMID: 27910910
DOI: 10.1038/srep38260

[…] The resulting p-values were corrected using the Bonferroni method to accommodate bias due to multiple comparisons.The chromosomal distribution and duplication state of the genes was visualised using PhenoGram (http://visualization.ritchielab.psu.edu/phenograms/plot - © 2012 Ritchie Lab). The predicted exon–intron structure was retrieved from the V1 annotation of the grapevine genome (http://genom […]

library_books

Phenome Wide Association Study to Explore Relationships between Immune System Related Genetic Loci and Complex Traits and Diseases

2016
PLoS One
PMCID: 4980020
PMID: 27508393
DOI: 10.1371/journal.pone.0160573

[…] We used Synthesis-View [], PhenoGram [], and Cytoscape [], to visualize the results. Synthesis-View was used to visualize the SNP-phenotype associations and to plot associations matching previously reported associations in the […]

Citations

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PhenoGram institution(s)
Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
PhenoGram funding source(s)
This work was supported by the following funding agencies and grants: 5U01 HG004798-03, 5R01 LM010040-02, and U19 HL065962-10.

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