Gene tools

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General organization[edit]

The gene webpage can be accessed either from the home webpage of Listeriomics website or by double-clicking on a genome in the genomic webpage.

Printscreen of the Gene webpage of the Listeriomics website


Chromosome selection

Here one can select a specific genome among the 50 Listeria strains available. Then one has to select a chromosome. In Listeria species, in general the first one is a circular chromosome and the second one is a plasmid. With a star are indicated genomes for which transcriptomic datasets are available.

Gene search and selection

In this list, all the genes available for a specific chromosome are displayed. One can search for a gene locus, a gene name, or even key words which can be found in the annotation of each gene. A click on an element of the list will display all related information on the Gene information panel.

Omics selection panel

For each Listeria gene four different information panels are available.

  • General information: The position of the gene, possible annotated function, nucleotide sequence and amino-acid sequence.
  • Gene conservation in other Listeria strains : It dynamically displays on the Listeria phylogram presence or absence of homolog 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.
  • Synteny viewer to display conservation of whole group of genes in different Listeria strains
  • Expression atlas: It shows 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.
  • Protein atlas: It displays every proteomics dataset in which the protein coded by the selected gene has been detected.
Gene information panel

The panel in which all information will be displayed

How-to access gene annotation?[edit]

Gene annotation panel of the Gene webpage
Click on General information on the Omics selection panel
  • Genome viewer: Displays the gene in the genome viewer to see surrounding genome features.
  • General information: Every general information available on gene position, product, Cluster of Orthologous Gene (COG) and summary of gene conservation.
  • Supplementary information: All supplementary information available on the gene annotation such as conserved motif or alternative annotation.
  • Sequences: DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast.
  • Localization information: A graphical representation of the predicted localization of the protein is displayed. Sub-cellular localization prediction was performed in Listeria monocytogenes EGD-e strain in Renier et al. Plos One 2012. For proteins from a strain different from EGD-e, the localization of its homolog EGD-e protein is shown.
Sequence information panel of the Gene webpage
DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast.

Is my gene conserved?[edit]

Gene conservation panel of the Gene webpage
Click on Homologs on the Omics selection panel
  • Export to fasta file: Select a list of genes in the conservation table and export all their amino acid sequences to a multi-sequence fasta file. This is for exporting sequences to a multi sequence alignment software.
  • Gene conservation on Listeria species: It displays on Listeria species phylogram the conservation of a specific protein, with its similarity percentage shown.
  • Gene conservation table: All information about the protein conservation and the strains in which it is conserved are displayed here. One can select some proteins and export their sequence in fasta format, or double-click on a protein to display its information on the gene webpage.
Synteny panel of the Gene webpage
A synteny viewer is available to see the conservation of whole groups of genes. It uses SynTView architecture [1].

Is my gene transcribed?[edit]

Expression atlas panel of the Gene webpage
Click on Expression Atlas on the Omics selection panel
  • Cut-off selection: Select the value of Log(Fold Change) used to detect differential expression.
  • Send to Genome viewer of Heatmap viewer: Display selected datasets in the genome viewer in which the gene will be highlighted, or to the heatmap viewer to show the values of Log(Fold-change).
  • Datasets in which the gene is over-expressed: List of relative value expression data in which the gene is over-expressed (i.e. Log(FC) > cut-off).
  • Datasets in which the gene is under-expressed: List of relative value expression data in which the gene is under-expressed (i.e. Log(FC) < - cut-off).
  • Datasets in which the gene has no differential expression: List of relative value expression data in which the gene is not differentially expressed (i.e. - cut-off < Log(FC) < cut-off).

Is my gene translated?[edit]

Protein atlas panel of the Gene webpage
Click on Proteomes on the Omics selection panel
  • List of datasets in which the corresponding protein has been detected: List of protein expression data in which the protein has been detected.
  1. Lechat P., Souche E., Moszer I. 2013. SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics. BMC Bioinformatics. 2013 Sep 22;14:277. doi: 10.1186/1471-2105-14-277.