Difference between revisions of "Summary"
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| − | Image: | + | Image:Gene.png|Gene panel |
| − | Image: | + | Image:smallRNA.png|Small RNA panel |
| − | Image: | + | Image:transcriptome.png|Transcriptome panel |
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Revision as of 13:20, 16 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 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 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
- Genomeviewer.png
Genome viewer with tiling array, Proteomic data, TSS data, RNAseq, and genome annotation. Listeria grown in BHI 37°C in exponetial growth phase.
Genome panel
- Gene.png
Gene panel
Small RNA panel
Transcriptome panel
Proteome panel
Co-expression network panel
