Difference between revisions of "Summary"

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Image:BHIViewer.png|Genome viewer
 
Image:BHIViewer.png|Genome viewer
 
Image:genomes.png|Genome webpage
 
Image:genomes.png|Genome webpage
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Image:GenomeviewerChangeView.png|Example of the zoom capability of the Genome Viewer
 
Image:Genepanel.png|Gene webpage
 
Image:Genepanel.png|Gene webpage
 
Image:Synteny.png|Synteny webpage
 
Image:Synteny.png|Synteny webpage

Revision as of 10:47, 19 October 2016

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. Use Listeriomics for deciphering regulatory mechanisms of your genome element of interest

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?
  5. What do I know about my gene/small RNA function, and is it present in other strains?
  6. Is my genomic element transcribed, and in which biological condition?
  7. Is my genome element translated, and in which biological condition can I find the protein?
  8. Is my gene/small RNA a regulator or does it regulate another genomic element?

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
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

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


Screenshots