Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 15598839

Visualizing information across multidimensional post-genomic structured and textual databases.

Ying Tao·Carol Friedman·Yves A Lussier
View original source ↗Export metadata ↓

Abstract

MOTIVATION: Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. RESULTS: We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. AVAILABILITY: PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ CONTACT: Lussier@dbmi.columbia.edu.

Explore related subjects

Computer GraphicsDatabase Management SystemsDatabases, BibliographicDatabases, GeneticDocumentationGene Expression ProfilingGenomicsHumansInformation Storage and RetrievalModels, BiologicalNatural Language ProcessingPeriodicals as TopicUser-Computer InterfaceJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ying Tao, Carol Friedman, Yves A Lussier. 2004-12-14. Visualizing information across multidimensional post-genomic structured and textual databases.. https://doi.org/10.1093/bioinformatics%2Fbti210

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2006

Short-latency disparity vergence eye movements: a response to disparity energy.

Vergence eye movements were elicited in human subjects by applying disparities to square-wave gratings lacking the fundamental ("missing fundamental", mf). Using a dichoptic arrangement, subjects viewed gratings that were identical at the two eyes except for a phase difference of 1/4 wavelength so that, based on the nearest-neighbor matches, the features and the 4n+1 harmonics (5th, 9th, etc.) all had binocular disparities of one sign, whereas the 4n-1 harmonics (3rd, 7th, etc.) all had disparities of the opposite sign. Further, the amplitude of the ith harmonic was proportional to 1/i. Using the electromagnetic search coil technique to record the positions of both eyes indicated that the earliest vergence eye movements elicited by these disparity stimuli had ultra-short latencies (minimum, <65 ms) and were always in the direction of the most prominent harmonic, the 3rd, but their magnitudes fell short of those elicited when the same disparities were applied to pure sinusoids whose spatial frequency and contrast matched those of the 3rd harmonic. This shortfall was evident in both the horizontal vergence responses recorded with vertical grating stimuli and the vertical vergence responses recorded with horizontal grating stimuli. When the next most prominent harmonic, the 5th, was removed from the mf stimulus (creating the "mf-5" stimulus) the vertical vergence responses showed almost no shortfall-indicating that it had been almost entirely due to that 5th harmonic-but the horizontal vergence responses still showed a small shortfall, at least with higher contrast stimuli. This small shortfall might represent a very minor contribution from higher harmonics and/or distortion products and/or a feature-based mechanism. We conclude that the earliest disparity vergence responses-especially vertical-were strongly dependent on the major Fourier components of the binocular images, consistent with early spatial filtering of the monocular visual inputs prior to their binocular combination as in the disparity-energy model of complex cells in striate cortex [Ohzawa, I., DeAngelis, G. C., & Freeman, R. D. (1990). Stereoscopic depth discrimination in the visual cortex: neurons ideally suited as disparity detectors. Science, 249, 1037-1041].

Computer Graphics↗
PubMed2006

Phenotype-genotype association grid: a convenient method for summarizing multiple association analyses.

BACKGROUND: High-throughput genotyping generates vast amounts of data for analysis; results can be difficult to summarize succinctly. A single project may involve genotyping many genes with multiple variants per gene and analyzing each variant in relation to numerous phenotypes, using several genetic models and population subgroups. Hundreds of statistical tests may be performed for a single SNP, thereby complicating interpretation of results and inhibiting identification of patterns of association. RESULTS: To facilitate visual display and summary of large numbers of association tests of genetic loci with multiple phenotypes, we developed a Phenotype-Genotype Association (PGA) grid display. A database-backed web server was used to create PGA grids from phenotypic and genotypic data (sample sizes, means and standard errors, P-value for association). HTML pages were generated using Tcl scripts on an AOLserver platform, using an Oracle database, and the ArsDigita Community System web toolkit. The grids are interactive and permit display of summary data for individual cells by a mouse click (i.e. least squares means for a given SNP and phenotype, specified genetic model and study sample). PGA grids can be used to visually summarize results of individual SNP associations, gene-environment associations, or haplotype associations. CONCLUSION: The PGA grid, which permits interactive exploration of large numbers of association test results, can serve as an easily adapted common and useful display format for large-scale genetic studies. Doing so would reduce the problem of publication bias, and would simplify the task of summarizing large-scale association studies.

Computer Graphics↗
PubMed2006

Verification of intensity modulated profiles using a pixel segmented liquid-filled linear array.

A liquid isooctane (C8H18) filled ionization chamber linear array developed for radiotherapy quality assurance, consisting of 128 pixels (each of them with a 1.7 mm pitch), has been used to acquire profiles of several intensity modulated fields. The results were compared with film measurements using the gamma test. The comparisons show a very good matching, even in high gradient dose regions. The volume-averaging effect of the pixels is negligible and the spatial resolution is enough to verify these regions. However, some mismatches between the detectors have been found in regions where low-energy scattered photons significantly contribute to the total dose. These differences are not very important (in fact, the measurements of both detectors are in agreement using the gamma test with tolerances of 3% and 3 mm in most of those regions), and may be associated with the film energy dependence. In addition, the linear array repeatability (0.27% one standard deviation) is much better than the film one ( approximately 3%). The good repeatability, small pixel size and high spatial resolution make the detector ideal for the real time profile verification of high gradient beam profiles like those present in intensity modulated radiation therapy and radiosurgery.

Computer Graphics↗