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Revision as of 15:09, 27 April 2015
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 features |
| 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 anlaysis with the expression atlas |
| Proteomic tools | How-to access proteomic dataset and display it or perform an analysis with the protein 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
It can be downloaded here DataListeriomics
Data have to be accessed and managed through the BACNET developemnt platform.
Screenshots
Genome viewer
Genome webpage
Gene webpage
Small RNA webpage
Transcriptome webpage
Proteome webpage
Co-expression network webpage
