Difference between revisions of "Summary"

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[[File:HomePageListeriomics.png|thumb|300px|right|Home page of the Listeriomics website]]
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Listeriomics integrates all complete genomes, transcriptomes and proteomes published for <i>Listeria</i> species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format.
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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:
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# 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:
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* 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.
 
  
 
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= Tutorials =
 
 
 
{| class="wikitable"
 
|-
 
| [[First hands on Listeriomics]]
 
| General organization of the website and principal features
 
|}
 
 
 
=== Tools ===
 
 
 
{| class="wikitable"
 
|-
 
| [[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|Co-expression network tools]]
 
| How-to access to the co-expression network and search for potential co-regulation of genomic feature
 
|-
 
| [[Submit_Data|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 ===
 
 
 
{| class="wikitable"
 
|-
 
| [[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 [http://listeriomics01.hosting.pasteur.fr/DatabaseListeriomics.zip Here]
 
 
 
= Screenshots =
 
<gallery widths=200px>
 
Image:BHIViewer.png|Genome viewer
 
Image:GenomeviewerChangeView.png|Example of the zoom capability of the Genome Viewer
 
Image:genomes.png|Genome webpage
 
Image:Genepanel.png|Gene webpage
 
Image:Synteny.png|Synteny webpage
 
Image:smallRNA.png|Small RNA webpage
 
Image:transcriptome.png|Transcriptome webpage
 
Image:Heatmap.png|Heatmap visualization of transcriptomics datasets
 
Image:proteome.png|Proteome webpage
 
Image:HeatmapProteomic.png|Heatmap visualization of proteomics datasets
 
Image:SeqInfo.png|Sequence information panel
 
Image:coexpression.png|Co-expression network webpage
 
</gallery>
 

Revision as of 09:58, 8 August 2020

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