scholarly journals An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Bhaskar Dutta ◽  
Alaleh Azhir ◽  
Louis-Henri Merino ◽  
Yongjian Guo ◽  
Swetha Revanur ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Rnai Screen ◽  
Integrated Analysis ◽  
Expression Data ◽  
Web Based ◽  
Optimal Thresholds ◽  
Analysis Workflow ◽  
Genome Scale ◽  
Sirna Screens ◽  
Selection Of

Abstract RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

scholarly journals Magellan: A Web Based System for the Integrated Analysis of Heterogeneous Biological Data and Annotations; Application to DNA Copy Number and Expression Data in Ovarian Cancer

2006 ◽  
Vol 2 ◽  
pp. 117693510600200 ◽  
Author(s):  
Chris B. Kingsley ◽  
Wen-Lin Kuo ◽  
Daniel Polikoff ◽  
Andy Berchuck ◽  
Joe W. Gray ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Analytical Methods ◽  
Patient Survival ◽  
Biological Data ◽  
Integrated Analysis ◽  
Comparative Genomic ◽  
Expression Data ◽  
Data Set ◽  
Web Based ◽  
Web Based System

Recent advances in high throughput biological methods allow researchers to generate enormous amounts of data from a single experiment. In order to extract meaningful conclusions from this tidal wave of data, it will be necessary to develop analytical methods of sufficient power and utility. It is particularly important that biologists themselves be able to perform many of these analyses, such that their background knowledge of the experimental system under study can be used to interpret results and direct further inquiries. We have developed a web-based system, Magellan, which allows the upload, storage, and analysis of multivariate data and textual or numerical annotations. Data and annotations are treated as abstract entities, to maximize the different types of information the system can store and analyze. Annotations can be used in analyses/visualizations, as a means of subsetting data to reduce dimensionality, or as a means of projecting variables from one data type or data set to another. Analytical methods are deployed within Magellan such that new functionalities can be added in a straightforward fashion. Using Magellan, we performed an integrated analysis of genome-wide comparative genomic hybridization (CGH), mRNA expression, and clinical data from ovarian tumors. Analyses included the use of permutation-based methods to identify genes whose mRNA expression levels correlated with patient survival, a nearest neighbor classifier to predict patient survival from CGH data, and curated annotations such as genomic position and derived annotations such as statistical computations to explore the quantitative relationship between CGH and mRNA expression data.

scholarly journals Correction: Corrigendum: An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Bhaskar Dutta ◽  
Alaleh Azhir ◽  
Louis-Henri Merino ◽  
Yongjian Guo ◽  
Swetha Revanur ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Rnai Screen ◽  
Web Based

scholarly journals Comprehensive Analysis of Transcriptome and Metabolome Reveals the Flavonoid Metabolic Pathway Is Associated with Fruit Peel Coloration of Melon

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2830
Author(s):  
Aiai Zhang ◽  
Jing Zheng ◽  
Xuemiao Chen ◽  
Xueyin Shi ◽  
Huaisong Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Fruit Peel ◽  
External Quality ◽  
Color Formation ◽  
Peel Color ◽  
Dark Green

The peel color is an important external quality of melon fruit. To explore the mechanisms of melon peel color formation, we performed an integrated analysis of transcriptome and metabolome with three different fruit peel samples (grey-green ‘W’, dark-green ‘B’, and yellow ‘H’). A total of 40 differentially expressed flavonoids were identified. Integrated transcriptomic and metabolomic analyses revealed that flavonoid biosynthesis was associated with the fruit peel coloration of melon. Twelve differentially expressed genes regulated flavonoids synthesis. Among them, nine (two 4CL, F3H, three F3′H, IFS, FNS, and FLS) up-regulated genes were involved in the accumulation of flavones, flavanones, flavonols, and isoflavones, and three (2 ANS and UFGT) down-regulated genes were involved in the accumulation of anthocyanins. This study laid a foundation to understand the molecular mechanisms of melon peel coloration by exploring valuable genes and metabolites.

scholarly journals SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays

Cell Systems ◽  
2021 ◽  
Author(s):  
Samuel Katz ◽  
Jian Song ◽  
Kyle P. Webb ◽  
Nicolas W. Lounsbury ◽  
Clare E. Bryant ◽  
...  
Keyword(s):  
Web Based ◽  
Iterative Analysis ◽  
Network Approaches ◽  
Genome Scale ◽  
Analysis Platform

scholarly journals INMEX—a web-based tool for integrative meta-analysis of expression data

2013 ◽  
Vol 41 (W1) ◽  
pp. W63-W70 ◽  
Author(s):  
Jianguo Xia ◽  
Christopher D. Fjell ◽  
Matthew L. Mayer ◽  
Olga M. Pena ◽  
David S. Wishart ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Expression Data ◽  
Web Based

scholarly journals Carnavalesk taalgebruik en de constructie van lokale identiteiten

2012 ◽  
Vol 1 (1) ◽  
pp. 15-40 ◽  
Author(s):  
Leonie M.E.A. Cornips ◽  
Vincent de Rooij ◽  
Irene Stengs
Keyword(s):  
Interdisciplinary Approach ◽  
Integrated Analysis ◽  
Cultural Elements ◽  
Language And Culture ◽  
Norms And Values ◽  
Southern Netherlands ◽  
Interdisciplinary Study ◽  
The City ◽  
Selection Of

This article aims to encourage the interdisciplinary study of ‘languaculture,’ an approach to language and culture in which ideology, linguistic and cultural forms, as well as praxis are studied in relation to one another. An integrated analysis of the selection of linguistic and cultural elements provides insight into how these choices arise from internalized norms and values, and how people position themselves toward received categories and hegemonic ideologies. An interdisciplinary approach will stimulate a rethinking of established concepts and methods of research. It will also lead to a mutual strengthening of linguistic, sociolinguistic, and anthropological research. This contribution focuses on Limburg and the linguistic political context of this Southern-Netherlands region where people are strongly aware of their linguistic distinctiveness. The argument of the paper is based on a case study of languaculture, viz. the carnivalesque song ‘Naar Talia’ (To Italy) by the Getske Boys from the city of Heerlen.

Sistem Informasi Geografis (Sig) Properti Di Kota Tanjungpinang Berbasis Website

2019 ◽  
Vol 8 (1) ◽  
pp. 39-47
Author(s):  
Zulfachmi ◽  
Angger Andrea Amanda ◽  
Dedy Jauhari
Keyword(s):  
Information System ◽  
Geographic Information System ◽  
Unified Modeling Language ◽  
Geographic Information ◽  
Web Based ◽  
Unified Modeling ◽  
The Public ◽  
Property Specification ◽  
System Requirements ◽  
Selection Of

The increasing need for property in Tanjungpinang City is very growing, especially in the housing sector. Selection of property based on location and facilities and infrastructure is always a consideration for the community in making decisions to buy a property. Difficulty finding property location information in a certain area often occurs, resulting in people not getting references about the properties offered in Tanjungpinang City. The purpose of this research is to create a web-based geographic information system (GIS) regarding the distribution of the number of properties on offer, especially in Tanjungpinang City using a web-based mapping approach. In the development of Property GIS the author uses the Waterfall method and in the analysis of system requirements it is modeled with UML (Unified Modeling Language) and implemented with the PHP programming language and MySQLI database. It is hoped that the results of making this property's geographic information system can help the public to find out information about the distribution of properties offered, such as the location of property coordinates, addresses, prices, property photos, property specification data and property developer data.

scholarly journals Methods and applications for visualization of SNOMED CT concept sets

2014 ◽  
Vol 05 (01) ◽  
pp. 127-152 ◽  
Author(s):  
E. Sundvall ◽  
K.R. Gøeg ◽  
A.R. Højen
Keyword(s):  
Content Management ◽  
Graph Layout ◽  
Snomed Ct ◽  
Focus Group Interviews ◽  
Web Based ◽  
Hierarchical Relations ◽  
Potential Applications ◽  
Group Interviews ◽  
And Training ◽  
Selection Of

SummaryInconsistent use of SNOMED CT concepts may reduce comparability of information in health information systems. Terminology implementation should be approached by common strategies for navigating and selecting proper concepts. This study aims to explore ways of illustrating common pathways and ancestors of particular sets of concepts, to support consistent use of SNOMED CT and also assess potential applications for such visualizations.The open source prototype presented is an interactive web-based re-implementation of the terminology visualization tool TermViz that provides an overview of concepts and their hierarchical relations. It provides terminological features such as interactively rearranging graphs, fetching more concept nodes, highlighting least common parents and shared pathways in merged graphs etc.Four teams of three to four people used the prototype to complete a terminology mapping task and then, in focus group interviews, discussed the user experience and potential future tool usage. Potential purposes discussed included SNOMED CT search and training, consistent selection of concepts and content management.The evaluation indicated that the tool may be useful in many contexts especially if integrated with existing systems, and that the graph layout needs further tuning and development.Citation: Højen AR, Sundvall E, Gøeg KR. Methods and applications for visualization of SNOMED CT concept sets. Appl Clin Inf 2014; 5: 127–152http://dx.doi.org/10.4338/ACI-2013-09-RA-0071

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