tspex: a tissue-specificity calculator for gene expression data

Abstract When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/

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GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

BMC Bioinformatics ◽

10.1186/1471-2105-8-457 ◽

2007 ◽

Vol 8 (1) ◽

pp. 457 ◽

Cited By ~ 8

Author(s):

André Fujita ◽

João R Sato ◽

Carlos E Ferreira ◽

Mari C Sogayar

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

Large Scale ◽

Expression Data ◽

User Friendly

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CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses

10.1101/255075 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sebastian Proost ◽

Marek Mutwil

Keyword(s):

Gene Expression ◽

Open Source ◽

Gene Expression Data ◽

Expression Profiles ◽

Specific Gene ◽

Expression Data ◽

Comparative Analyses ◽

Network Analyses ◽

Link Type ◽

User Friendly

ABSTRACTThe recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source, user-friendly web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

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CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data

Bioinformatics ◽

10.1093/bioinformatics/btl641 ◽

2007 ◽

Vol 23 (6) ◽

pp. 771-773

Author(s):

C. Girardot ◽

O. Sklyar ◽

S. Grosz ◽

W. Huber ◽

E. E. M. Furlong

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

Web Application ◽

Expression Data ◽

Chip Data ◽

On Chip

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A decoupled, modular and scriptable architecture for tools to curate data platforms

10.1101/2020.09.28.282699 ◽

2020 ◽

Author(s):

Moritz Langenstein ◽

Henning Hermjakob ◽

Manuel Bernal Llinares

Keyword(s):

Web Application ◽

Production Systems ◽

Source Code ◽

Black Box ◽

Command Line ◽

Web Interface ◽

Link Type ◽

Data Platform ◽

The Web

AbstractMotivationCuration is essential for any data platform to maintain the quality of the data it provides. Existing databases, which require maintenance, and the amount of newly published information that needs to be surveyed, are growing rapidly. More efficient curation is often vital to keep up with this growth, requiring modern curation tools. However, curation interfaces are often complex and difficult to further develop. Furthermore, opportunities for experimentation with curation workflows may be lost due to a lack of development resources, or a reluctance to change sensitive production systems.ResultsWe propose a decoupled, modular and scriptable architecture to build curation tools on top of existing platforms. Instead of modifying the existing infrastructure, our architecture treats the existing platform as a black box and relies only on its public APIs and web application. As a decoupled program, the tool’s architecture gives more freedom to developers and curators. This added flexibility allows for quickly prototyping new curation workflows as well as adding all kinds of analysis around the data platform. The tool can also streamline and enhance the curator’s interaction with the web interface of the platform. We have implemented this design in cmd-iaso, a command-line curation tool for the identifiers.org registry.AvailabilityThe cmd-iaso curation tool is implemented in Python 3.7+ and supports Linux, macOS and Windows. Its source code and documentation are freely available from https://github.com/identifiers-org/cmd-iaso. It is also published as a Docker container at https://hub.docker.com/r/identifiersorg/[email protected]

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