scholarly journals Peer Review #2 of "GeNET: a web application to explore and share Gene Co-expression Network Analysis data (v0.1)"

2017 ◽  
Author(s):  
V Pancaldi
Keyword(s):  
Network Analysis ◽  
Peer Review ◽  
Web Application ◽  
Analysis Data

scholarly journals GeNET: a web application to explore and share Gene Co-expression Network Analysis data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3678 ◽  
Author(s):  
Amit P. Desai ◽  
Mehdi Razeghin ◽  
Oscar Meruvia-Pastor ◽  
Lourdes Peña-Castillo
Keyword(s):  
Network Analysis ◽  
Web Application ◽  
Gene Network ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Analysis Data ◽  
Published Data ◽  
Online Tool ◽  
The Public ◽  
Gene Sets

Gene Co-expression Network Analysis (GCNA) is a popular approach to analyze a collection of gene expression profiles. GCNA yields an assignment of genes to gene co-expression modules, a list of gene sets statistically over-represented in these modules, and a gene-to-gene network. There are several computer programs for gene-to-gene network visualization, but these programs have limitations in terms of integrating all the data generated by a GCNA and making these data available online. To facilitate sharing and study of GCNA data, we developed GeNET. For researchers interested in sharing their GCNA data, GeNET provides a convenient interface to upload their data and automatically make it accessible to the public through an online server. For researchers interested in exploring GCNA data published by others, GeNET provides an intuitive online tool to interactively explore GCNA data by genes, gene sets or modules. In addition, GeNET allows users to download all or part of the published data for further computational analysis. To demonstrate the applicability of GeNET, we imported three published GCNA datasets, the largest of which consists of roughly 17,000 genes and 200 conditions. GeNET is available at bengi.cs.mun.ca/genet.

scholarly journals A network approach on the relation between apathy and depression symptoms with dementia and functional disability

2019 ◽  
Vol 31 (11) ◽  
pp. 1655-1663 ◽  
Author(s):  
Lennard L. van Wanrooij ◽  
Denny Borsboom ◽  
Eric P. Moll van Charante ◽  
Edo Richard ◽  
Willem A. van Gool
Keyword(s):  
Network Analysis ◽  
Functional Disability ◽  
Geriatric Depression Scale ◽  
Depression Scale ◽  
Analysis Data ◽  
Future Research ◽  
Depression Symptoms ◽  
Dementia Risk ◽  
Strongly Connected ◽  
Sum Scores

ABSTRACTBackground:Studies on the association between depression and dementia risk mostly use sum scores on depression questionnaires to model symptomatology severity. Since individual items may contribute differently to this association, this approach has limited validity.Methods:We used network analysis to investigate the functioning of individual Geriatric Depression Scale (GDS-15) items, of which, based on studies that used factor analysis, 3 are generally considered to measure apathy (GDS-3A) and 12 depression (GDS-12D). Functional disability and future dementia were also included in our analysis. Data were extracted from 3229 participants of the Prevention of Dementia by Intensive Vascular care trial (preDIVA), analyzed as a single cohort, yielding 20,542 person-years of observation. We estimated a sparse network by only including connections between variables that could not be accounted for by variance in other variables. For this, we used a repeated L1 regularized regression procedure.Results:This procedure resulted in a selection of 59/136 possible connections. GDS-3A items were strongly connected to each other and with varying strength to several GDS-12D items. Functional disability was connected to all three GDS-3A items and the GDS-12D items “helplessness” and “worthlessness”. Future dementia was only connected to the GDS-12D item “memory problems”, which was in turn connected to the GDS-12D items “unhappiness” and “helplessness” and all three GDS-3A items.Conclusion:Network analysis reveals interesting relationships between GDS items, functional disability and dementia risk. We discuss what implications our results may have for (future) research on the associations between depression and/or apathy with dementia.

scholarly journals Application of Network Analysis for Development and Promotion of Sustainable Tourism in Public Forests

2014 ◽  
Vol 56 (2) ◽  
pp. 105-112 ◽  
Author(s):  
Michał Brach ◽  
Dariusz Górski
Keyword(s):  
Network Analysis ◽  
Spatial Data ◽  
Traffic Management ◽  
Web Application ◽  
Sustainable Tourism ◽  
Route Planning ◽  
Gis Technology ◽  
Anthropogenic Pressures ◽  
Tourist Attractions ◽  
Web Mapping

Abstract The issue of sustainable tourism within valuable natural areas has been extensively discussed ever since the emergence of sustainable development philosophy in the 1990s. In view of growing public interest in nature recreation and tourism development, the importance of addressing this subject matter has hitherto increased significantly. The main objective of the present paper was to offer a tool for supporting development and promotion of sustainable tourism in Poland’s forests managed by the State Forests - National Forest Holding. GIS technology, and specific tools for network analysis were used in the project. During task realization, only free and open software sources were used. The work was performed based on the example of the Forest District Żołędowo (Regional Directorate of State Forests in Toruń, Poland) with the use of District’s spatial data resources. A web application was created to present information about tourist attractions and infrastructure on an interactive map with tools for route planning. As a result, there has been developed the web mapping application which provides general access to tourism related information and enables planning touristic routes by pre-specified criteria. Implemented routing algorithms can help traffic management and further protection of the areas vulnerable to anthropogenic pressures. The system created not only promotes attractive tourist sites but also, supports targeting tourist traffic, and accordingly - adds to the progress of sustainable tourism

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