Summary
Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format.
The main purpose of the website is to give scientists 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 are the known functions of a genomic feature in a given strain and homologies in closely related strains?
- What are the biological conditions in which a genomic feature is transcribed?
- What are the biological conditions in which a genomic feature is translated?
- What is the regulation network involved with a genomic feature of interest?
The website 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 hands on Listeriomics | General organization of the website and principal features |
Tools
Genomic tools | How-to access 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 analysis with the expression atlas |
Proteomic tools | How-to access proteomic dataset and display it or perform an analysis with the protein atlas |
Co-expression network tools | How-to access to the co-expression network and search for potential co-regulation of genomic feature |
Submit your datasets | How-to access to the submit section of Listeriomics in which you can inform us of important database update to make |
Viewers
Genome viewer | How-to use the genome viewer for visualizing "omics" datasets |
Transcriptomic HeatMap viewer | How-to use the transcriptomic heatmap viewer and decipher differently expressed genomic features |
Proteomic HeatMap viewer | How-to use the proteomic heatmap viewer and decipher detected protein in every proteomic experiment |
Database
The Listeriomics database includes all complete genomes, transcriptomes and proteomes published on Listeria species to date. It allows scientists 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:
- 83 Listeria complete genomes
- 492 transcriptome datasets
- 74 proteome datasets
The whole database can be downloaded Here