Dataset Information

CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

ABSTRACT: CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG) format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

SUBMITTER: Chang YF

PROVIDER: S-EPMC3219657 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

Chang Yi-Feng YF Chang Chuan-Hsiung CH

PloS one 20111117 11

CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy ge ...[more]

PMID: 22114666

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Project description:PurposeTo compare three commonly used retinal vessel caliber measurement software systems, and propose an algorithm for conversion between measurement systems.MethodsWe used 120 retinal photographs to evaluate the agreement between three commonly used software (Retinal Analysis [RA], Integrative Vessel Analysis [IVAN], and Singapore I Vessel Assessment [SIVA]). Bland-Altman plots were used to evaluate agreement of retinal arteriolar (central retinal artery equivalent, CRAE) and venular (central retinal vein equivalent, CRVE) calibers. Pearson's correlation was used to assess the associations between systemic factors and retinal vessel calibers, and Z-test was used to compare the strength of the correlation coefficients across the three software systems. An algorithm was created to convert measurements, with paired t-test performed to evaluate the differences between SIVA-measured retinal calibers and SIVA-approximates converted from RA- and IVAN-measurements using the algorithm.ResultsDifferences between SIVA- and RA-measured calibers (CRAE: mean difference [MD] = -21.8 ?m, 95% limits of agreement [LOA], -47.3 to 3.7 ?m; CRVE: MD = -7.7 ?m, 95% LOA, -28.0 to 12.6 ?m), SIVA- and IVAN-measured calibers (CRAE: MD = -6.7 ?m, 95% LOA, -23.8 to 10.4 ?m; CRVE: MD = -18.2 ?m 95% LOA, -36.7 to 0.4 ?m) were large. However, the strength of correlations between systemic factors with SIVA-measured retinal calibers was not significantly different to that measured using RA and IVAN (P ? 0.332). SIVA-approximates converted from RA and IVAN measurements using the proposed algorithm was not significantly different from SIVA-measured calibers (P ? 0.20).ConclusionAbsolute measurements of retinal vessel calibers vary between three common software systems but associations with systemic factors were similar.Translational relevanceThe proposed algorithm allowed conversions of RA and IVAN measurements to SIVA-approximates. This conversion is important for future data pooling and establishment of normative values for retinal vascular caliber measurements.

Project description:BackgroundAnalysis of ciliary function for assessment of patients suspected of primary ciliary dyskinesia (PCD) and for research studies of respiratory and ependymal cilia requires assessment of both ciliary beat pattern and beat frequency. While direct measurement of beat frequency from high-speed video recordings is the most accurate and reproducible technique it is extremely time consuming. The aim of this study was to develop a freely available automated method of ciliary beat frequency analysis from digital video (AVI) files that runs on open-source software (ImageJ) coupled to Microsoft Excel, and to validate this by comparison to the direct measuring high-speed video recordings of respiratory and ependymal cilia. These models allowed comparison to cilia beating between 3 and 52 Hz.MethodsDigital video files of motile ciliated ependymal (frequency range 34 to 52 Hz) and respiratory epithelial cells (frequency 3 to 18 Hz) were captured using a high-speed digital video recorder. To cover the range above between 18 and 37 Hz the frequency of ependymal cilia were slowed by the addition of the pneumococcal toxin pneumolysin. Measurements made directly by timing a given number of individual ciliary beat cycles were compared with those obtained using the automated ciliaFA system.ResultsThe overall mean difference (± SD) between the ciliaFA and direct measurement high-speed digital imaging methods was -0.05 ± 1.25 Hz, the correlation coefficient was shown to be 0.991 and the Bland-Altman limits of agreement were from -1.99 to 1.49 Hz for respiratory and from -2.55 to 3.25 Hz for ependymal cilia.ConclusionsA plugin for ImageJ was developed that extracts pixel intensities and performs fast Fourier transformation (FFT) using Microsoft Excel. The ciliaFA software allowed automated, high throughput measurement of respiratory and ependymal ciliary beat frequency (range 3 to 52 Hz) and avoids operator error due to selection bias. We have included free access to the ciliaFA plugin and installation instructions in Additional file 1 accompanying this manuscript that other researchers may use.

Dataset Information

CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

Publications

CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

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