First hands on Listeriomics

From Listeriomics Wiki
Revision as of 09:47, 19 October 2016 by Cbecavin (talk | contribs) (Access to all genomics features)

Jump to: navigation, search


Home page

Through the home page of the Listeriomics website different tools can be accessed.

Printscreen of the home webpage of the Listeriomics website


Access to all "omics" datasets

Genomic datasets summary page
Genomics button

It gives access to the genomic tools. One can use it to access strain name, serotype, lineage, and isolation information, along with a complete phylogram of the Listeria strains. By double clicking on a strain the list of annotated genes will appear in a new summary panel.

Transcriptomic datasets summary page
Transcriptomics button

It gives access to all transcriptomic tools. A summary table shows every dataset available and a precise description of the biological conditions used to generate them. Filters are available to select a particular type of biological condition and data. A vast variety of datasets are available. In total, 4 different types of technology (Gene Expression array, Tiling array, RNASeq, TSS) are included for 7 different Listeria monocytogenes strains grown in 4 different broth media and 7 intracellular conditions.

Proteomic datasets summary page
Proteomics button

It gives access to all proteomic tools. A summary table of the 74 proteomics datasets. Once datasets are selected one can visualize them through an heatmap showing the presence or absence of each Listeria protein in a specific biological condition. Finally, each proteomic dataset can be displayed on the genome viewer along with transcriptomic datasets.

Access to all genomics features

Genomic datasets summary page
Gene panel

For each Listeria gene four different information panels are available in the gene viewer. The first one gives all general information about the position of the gene, possible annotated function, nucleotide sequence and amino acid sequence. The second panel provides an instant view of the conservation of a specific gene in other Listeria strains. It dynamically displays on the Listeria phylogram presence of absence of homology to the selected gene in each existing Listeria strain. It also displays a summary table of all homologs with their similarity percentages and amino acid sequences. One can then create a multi-alignment file of the homologs. A third panel uses the expression atlas to show in which transcriptomics datasets the selected gene is differently expressed. The cut-off on the Log(Fold Change) value for detecting such elements can be changed by the user. Finally the fourth panel displays every proteomics dataset in which the protein coded by the selected gene has been detected.

Transcriptomic datasets summary page
Small RNA panel

On a first webpage, all general information about discovered small RNAs in Listeria monocytogenes can be browsed here. Then by clicking on one small RNA one can access each Small RNA panel.

For each RNA element it displays in a viewer their positions, nucleotide sequence and predicted secondary structure at 37°C. Additionally, a table displays all the supplementary information provided with each small RNA discovery in Listeria. This gives a way to control to what extent a specific RNA has been observed in the different publications. A second panel uses the expression atlas to show in which transcriptomics datasets the selected small RNA is differently expressed. The cut-off on the Log(Fold Change) value for detecting such elements can be changed by the user.

Quick access to genome viewer with “omics” datasets in three biological conditions

Genome viewer displaying transcriptomic datasets of L. mono. EGD-e grown at 37°C in BHI at exponential phase
Listeria monocytogenes EGD-e grown in BHI 37°C exponential phase

The genome of EGD-e strain is displayed using the genome viewer with all its annotated genes, non-coding RNA, small RNA and predicted operon, along with RNASeq, tiling arrays, and gene expression arrays, transcription start sites (TSS), transcription termination sites (TermSeq), and Ribosome Profiling (RiboSeq).

Genome viewer displaying transcriptomic datasets of L. mono. EGD-e grown at 37°C in BHI at stationary phase
Listeria monocytogenes EGD-e grown in BHI 37°C exponential phase

The genome of EGD-e strain is displayed using the genome viewer along with RNASeq, transcription start sites, tiling arrays, gene expression arrays, and proteomics data.

Genome viewer displaying transcriptomic datasets of L. mono. EGD-e grown intracellularly in mouse macrophage
Listeria monocytogenes EGD-e grown intracellularly in mouse macrophage

The genome of EGD-e strain is displayed using the genome viewer along with RNASeq, and transcription start sites.

Other tools

Summary of all Small RNAs available in the Listeriomics database
L. mono. EGD-e small RNAs information

All general information about small RNAs discovery can be browsed here. By clicking on one small RNA one can access specific small RNA panel to get more information.

Data selection loading dialog
Load previous data selection

Dialog to load previously saved data selection to re-access quickly the data. The data selection is saved through the genome viewer.

Submit your data to Listeriomics
Submit your data to Listeriomics

Submission panel to submit the data to Listeriomics. If one wants its “omics” datasets to be on Listeriomics website faster, a webpage form is available to do so. Submitting the form will send an email to the Listeriomics webmasters which will then download the datasets from the repositories and integrate them.

Co-expression panel to discover potential regulation between genes and small RNAs
Access to the co-expression network tool

One can select one or many genome features and discover correlations with other genome features using the co-expression network tools.