Visualizing genomic information across chromosomes with PhenoGram

Daniel Wolfe, Scott Dudek, Marylyn Deriggi Ritchie, Sarah A. Pendergrass

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

Background: With the abundance of information and analysis results being collected for genetic loci, user-friendly and flexible data visualization approaches can inform and improve the analysis and dissemination of these data. A chromosomal ideogram is an idealized graphic representation of chromosomes. Ideograms can be combined with overlaid points, lines, and/or shapes, to provide summary information from studies of various kinds, such as genome-wide association studies or phenome-wide association studies, coupled with genomic location information. To facilitate visualizing varied data in multiple ways using ideograms, we have developed a flexible software tool called PhenoGram which exists as a web-based tool and also a command-line program. Results: With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail. We have now used PhenoGram to produce a variety of different plots, and provide these as examples herein. These plots include visualization of the genomic coverage of SNPs from a genotyping array, highlighting the chromosomal coverage of imputed SNPs, copy-number variation region coverage, as well as plots similar to the NHGRI GWA Catalog of genome-wide association results. Conclusions: PhenoGram is a versatile, user-friendly software tool fostering the exploration and sharing of genomic information. Through visualization of data, researchers can both explore and share complex results, facilitating a greater understanding of these data.

Original languageEnglish (US)
Article number18
JournalBioData Mining
Volume6
Issue number1
DOIs
StatePublished - Oct 18 2013

Fingerprint

Chromosomes
Base Pairing
Chromosome
Genomics
Single Nucleotide Polymorphism
National Human Genome Research Institute (U.S.)
Genes
Software
Color
Research Personnel
Coverage
Software Tools
Genetic Loci
Foster Home Care
Visualization
Information Dissemination
Genome-Wide Association Study
Annotation
Line
Genome

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Wolfe, D., Dudek, S., Ritchie, M. D., & Pendergrass, S. A. (2013). Visualizing genomic information across chromosomes with PhenoGram. BioData Mining, 6(1), [18]. https://doi.org/10.1186/1756-0381-6-18
Wolfe, Daniel ; Dudek, Scott ; Ritchie, Marylyn Deriggi ; Pendergrass, Sarah A. / Visualizing genomic information across chromosomes with PhenoGram. In: BioData Mining. 2013 ; Vol. 6, No. 1.
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Wolfe, D, Dudek, S, Ritchie, MD & Pendergrass, SA 2013, 'Visualizing genomic information across chromosomes with PhenoGram', BioData Mining, vol. 6, no. 1, 18. https://doi.org/10.1186/1756-0381-6-18

Visualizing genomic information across chromosomes with PhenoGram. / Wolfe, Daniel; Dudek, Scott; Ritchie, Marylyn Deriggi; Pendergrass, Sarah A.

In: BioData Mining, Vol. 6, No. 1, 18, 18.10.2013.

Research output: Contribution to journalArticle

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