TransTableView Help

With TransTableView you can easily view conservation or presence/absence of binding sites upstream of all genes across a large number of genomes. Initially, the user is presented with a particular binding site alignment and asked to choose a group of genomes they wish to study. The results we provide are grouped by genome, showing each of the hits and their downstream gene, as well as a conservation score for each hit.

TransTableView Options

Help for TransTableView options
  • A - Enter a few letters of the taxon group you would like to study and the selection box below will show all matches which include those letters.
  • B - Select your choices from the taxon box and click on the button labeled "-->" to add your taxon group selection to the query.
  • C - Select the sensitivity score you would like to use as a cut-off.
    If default is selected, the default will be used (default is the lowest of the recommended thresholds).
  • D - Click "Submit Query" to submit your query for processing. Results might take many minutes if a large taxon group was selected.

TransTableView Results

Help for TransTableView results
  • A - The name of the genome.
  • B - This notes whether an ortholog of the curated transcription factor has been found in this genome. If it notes "TF present", you may click on this text to be taken to the gene page for the putitive transcription factor in this genome. If no transcription factor was found, it will display "TF absent".
  • C - This is the table of results for the genome listed in A. Each row is a particular hit with the PWM on the genome. There may be multiple hits for a particular gene, or the same hit might be assigned to more then one gene. It is up to the user to interperet this data since it has not been verified by a curator.
    • ID - The RegTransBase internal hit id.
    • Gene Name - The name of the gene in this organism which is in the vicinity of this hit.
    • Anno - If you click on this link, a hover box will appear with GenBank annotations applied to this gene.
    • Links - If you click on this link, a hover box will appear with a set of links to this gene in other databases.
    • View - If you hover over this link, a box will appear with an image of this genomic region showing genes, precomputed hits, and any experimental sites.
    • Distance - The distance from the center of this putitive binding site to the start of the gene.
    • Score - The p-value score given by MAST.
    • # Cons. Hits - The number of putitive binding sites found upstream of orthologus genes in other organisms.
    • Cons Score - A higher conservation score denotes a binding site which is conserved over a large phylogenetic distance while a small conservation score highlights that this site is conserved only among phylogeneticaly close organisms.
    • TTV - Click on this link to be taken to TransTreeView, a analysis tool which will show the conservation of this gene along side conservation of this binding site across the bacterial tree.
  • D - By clicking on the number under the column "# Cons. Hits", you will get a table which shows orthologus genes in other organisms which have a putitive binding site.
    • Genome - The name of the genome with this gene.
    • Phylo Distance - The phylogenetic distance from the query organism (A) to the organism listed on this row.
    • Gene - The name of the orthologus gene in the organism listed on this row.