Difference between revisions of "Summary"
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[[File:HomePageListeriomics.png|thumb|300px|right|Home page of the Listeriomics website]] | [[File:HomePageListeriomics.png|thumb|300px|right|Home page of the Listeriomics website]] | ||
| − | 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. | + | 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. |
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: | 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 biological conditions in which a genomic feature is translated? | # What are the biological conditions in which a genomic feature is translated? | ||
# What is the regulation network involved with a genomic feature of interest? | # What is the regulation network involved with a genomic feature of interest? | ||
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The website integrates different type of tools for “omics” data analyses: | The website integrates different type of tools for “omics” data analyses: | ||
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* A tool to explore gene conservation throughout ''Listeria'' strains. | * A tool to explore gene conservation throughout ''Listeria'' strains. | ||
* A co-expression network tool to discover new potential regulation. | * A co-expression network tool to discover new potential regulation. | ||
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= Tutorials = | = Tutorials = | ||
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| General organization of the website and principal features | | General organization of the website and principal features | ||
|} | |} | ||
| + | |||
| + | === Tools === | ||
| + | |||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
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| [[Proteomic tools]] | | [[Proteomic tools]] | ||
| How-to access proteomic dataset and display it or perform an analysis with the protein atlas | | 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 | ||
|} | |} | ||
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* 74 proteome datasets | * 74 proteome datasets | ||
| + | The whole database can be downloaded [http://listeriomics01.hosting.pasteur.fr/DatabaseListeriomics.zip Here] | ||
= Screenshots = | = Screenshots = | ||
<gallery widths=200px> | <gallery widths=200px> | ||
Image:BHIViewer.png|Genome viewer | Image:BHIViewer.png|Genome viewer | ||
| + | Image:GenomeviewerChangeView.png|Example of the zoom capability of the Genome Viewer | ||
Image:genomes.png|Genome webpage | Image:genomes.png|Genome webpage | ||
Image:Genepanel.png|Gene webpage | Image:Genepanel.png|Gene webpage | ||
| + | Image:Synteny.png|Synteny webpage | ||
Image:smallRNA.png|Small RNA webpage | Image:smallRNA.png|Small RNA webpage | ||
Image:transcriptome.png|Transcriptome webpage | Image:transcriptome.png|Transcriptome webpage | ||
| + | Image:Heatmap.png|Heatmap visualization of transcriptomics datasets | ||
Image:proteome.png|Proteome webpage | Image:proteome.png|Proteome webpage | ||
| + | Image:HeatmapProteomic.png|Heatmap visualization of proteomics datasets | ||
Image:SeqInfo.png|Sequence information panel | Image:SeqInfo.png|Sequence information panel | ||
Image:coexpression.png|Co-expression network webpage | Image:coexpression.png|Co-expression network webpage | ||
</gallery> | </gallery> | ||
Latest revision as of 14:01, 29 November 2022
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[edit]
| First hands on Listeriomics | General organization of the website and principal features |
Tools[edit]
| 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[edit]
| 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[edit]
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[edit]
Genome viewer
Example of the zoom capability of the Genome Viewer
Genome webpage
Gene webpage
Synteny webpage
Small RNA webpage
Transcriptome webpage
Heatmap visualization of transcriptomics datasets
Proteome webpage
Heatmap visualization of proteomics datasets
Sequence information panel
Co-expression network webpage
