Summary

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Home page of the Listeriomics website

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:

  1. What are the known functions of a genomic feature in a given strain and homologies in closely related strains?
  2. What are the biological conditions in which a genomic feature is transcribed?
  3. What are the biological conditions in which a genomic feature is translated?
  4. 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

Screenshots