Difference between revisions of "Summary"
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The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for ''Listeria'' species. | The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for ''Listeria'' species. | ||
| + | The main purpose of the website is to give biologists a quick and easy access to tools created for answering the four questions one has when starting a study on a specific genomic element: | ||
| + | # What do I know about my gene/small RNA function, and is it present in other strains? | ||
| + | # Is my genomic element transcribed, and in which biological condition? | ||
| + | # Is my genome element translated, and in which biological condition can I find the protein? | ||
| + | # Is my gene/small RNA a regulator or does it regulate another genomic element? | ||
| + | |||
It integrates different type of tools for “omics” data analyses: | It integrates different type of tools for “omics” data analyses: | ||
| − | + | * A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets. | |
| − | + | * Expression and protein atlas, which are tools to connect every genomic feature (genes, smallRNAs, antisenseRNAs) or proteins to the most relevant “omics” data. | |
| − | + | * A tool to explore gene conservation throughout ''Listeria'' strains. | |
| − | + | * A co-expression network tool to discover new potential regulation. | |
= Tutorials = | = Tutorials = | ||
Revision as of 12:48, 16 April 2015
A web-based software for manipulating Listeria "omics" data.
Contents
Summary
The Listeriomics website is a web-based software design to manage genomic, transcriptomic and proteomic data for Listeria species. The main purpose of the website is to give biologists a quick and easy access to tools created for answering the four questions one has when starting a study on a specific genomic element:
- What do I know about my gene/small RNA function, and is it present in other strains?
- Is my genomic element transcribed, and in which biological condition?
- Is my genome element translated, and in which biological condition can I find the protein?
- Is my gene/small RNA a regulator or does it regulate another genomic element?
It integrates different type of tools for “omics” data analyses:
- A highly interactive genome viewer for display of gene expression arrays, tiling arrays, and RNA-Seq datasets along with proteomics and genomics datasets.
- Expression and protein atlas, which are tools to connect every genomic feature (genes, smallRNAs, antisenseRNAs) or proteins to the most relevant “omics” data.
- A tool to explore gene conservation throughout Listeria strains.
- A co-expression network tool to discover new potential regulation.
Tutorials
| First hand on Listeriomics | General organization of the website and principal featues |
| Genomic tools | How-to scroll all the genomes. |
| Gene tools | How-to access a specific gene and get information about its annotation, its conservation, its transcription or translation. |
| Small RNA tools | How-to access a specific Small RNA |
| Transcriptomic tools | How-to access transcriptomic dataset and display it or perform an anlysis through the expression atlas |
| Proteomic tools | How-to access proteomic dataset and display it or perform an anlysis through the expression atlas |
Database
The Listeriomics database includes all complete genomes, transcriptomes and proteomes published on 'Listeria' species to date. It allows biologists to analyse dynamically all these datasets in a user-friendly format, and can be used by bio-informaticians as a central database for systems biology analysis.
List of data available:
- 50 Listeria complete genomes
- 492 transcriptome datasets
- 74 proteome datasets
Screenshots
- MultiOmicsViewBacnet.png
Multi omics view: Tiling array, Proteomics, TSS data, RNAseq, Genome annotation. Desktop version
- SingleSourcingBacnet.png
Single sourcing allows to develop with same Java code a desktop and a web application
- SplashScreen.png
Splash screen of BACNET platform
- ListeriomicsWebsite.png
View of the Listeriomics website developed thanks to BACNET platform
- Environmentbacnet.png
View of Eclipse environment in which BACNET is developed
- HeatMapBacnet.png
HeatMap view (desktop version)
- VennDiagramBacnet.png
Venn Diagram view (desktop version)
- SmallRnaBacnet.png
Small RNA tool (desktop version)
- ExpressionAtlasWebBacnet.png
Expression Atlas tool (web version)
