Documentation

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Search options

In order to query BacRegNet enter a search item, such as a gene identifier (e.g. "cg2103") or a gene name (e.g. "dtxr") and search the database by different criteria ("in field") and in a specific organism ("Organism").
Statistics and Browsing

Statistics itemize the total numbers of certain elements included in BacRegNet. Besides the quantities of genes and proteins of all five organisms, statistics also provide information on the number of transcription factors and regulatory interactions included in BacRegNet. Specific information about the species are available on separate links. Additionally, one can start browsing genes, proteins and regulations of a certain organism.



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Main statistics

BacRegNet provides several statistical analysis features which are explicated in each case separately. For example, one can check the distribution of the number of transcription factors regulating a gene or the distribution of transcription factor binding site distances from target gene start.



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TFBScan

One can use all PSSMs included in BacRegNet to predict transcription factor binding sites in up to 10 user defined (upstream) sequences. To use this feature enter all sequences in FASTA format.



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CoMA

CoMa (Contradictions in Microarrays) is a new feature that allows you to check your microarray results against BacRegNet's data stock and thereby enables you to easily assess their quality.
Example: A possible contradiction could be a gene that is highly expressed although it's repressor gene is highly expressed as well.



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CoMA

The figure above shows the input form for CoMa by file upload. The alternative input options are used by similar (and also quite intuitive) forms.

On top an example for the required file layout is given: The file needs to be in ASCII encoding and must consist of lines that contain no other than one gene ID and one mValue or expression ratio separated by a tabulator character. (Hint: copy-pasting your data from a spreadsheet into a plain text editor should deliver exactly this format.)

The form offers four input options:

  1. mValue threshold: This option determines, which entries of your input are really processed by the algorithm. All genes having mValues with an absolute value smaller than the given threshold will be discarded.
  2. ignore autoregulations: Sometimes the instant occurs, that genes regulate their own expression level. Since this natural phenomenon matches the above stated contradiction criteria, we offer the possibility to ignore these cases in our algorithm.
  3. mValue/ratio: Here you should specify whether your file entries are mValues or still raw expression ratios. Ratios will be log2-transformed before being processed.
  4. file: Please enter the name of the file to be uploaded. Alternatively you may select it in a filechooser dialog (Click the 'Browse' button).




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Results

Search results display relevant data of a searched item like regulatory interactions between the search item and other genes.



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Details

Search results for transcription factors provide information relevant for the reconstruction of regulatory networks. BacRegNet is linked to other databases such as NCBI Entrez, GenDB, RegulonDB (for Escherichia coli K12 genes ) and PubMed.



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Attributes, position weight matrix and sequence logo

DNA-binding motifs are used to calculate position weight matrices. The corresponding sequence logo is displayed below and can also be downloaded in XML format. The distribution of the binding site distances from target gene start are illustrated by means of two histograms.



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TFBScan

BacRegNet integrates the transcription factor binding site matching tool PoSSuMsearch. There are two ways to access this feature. You can use the PWMs of all organisms to predict binding sites in the upstream region of the displayed gene. Additionally, if the actual gene codes for a transcription factor with known binding sites, one can use the corresponding PWM to detect potential binding sites in the upstream regions of all genes in the database.



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Results

Matching results display relevant data of the predicted binding site, the corresponding target gene and the pValue for the specific match that represents the statistical significance.



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GraphVis

Search results can be visualized by GraphVis with varying depth-cutOff. Genes from hierarchical regulations are included by default. Additionally, the regulatory network can be extended using any gene as starting point ("Extend Graph" button). The visualization is achieved by using the Java graph library yFiles. For detailed documentation on yFiles see: yWorks products documentation.

Legend and color codes:

red node repressor
red line repressing regulatory interaction
green node activator
green line activating regulatory interaction
blue node dual regulator
blue line sigma factor interaction
gray node regulated target gene preceded by a transcription factor binding site
gray box regulated target gene that is part of an operon and not preceded by a transcription factor binding site
black line homology (sequence based similarity)




Web Service server

An explicit documentation on the BacRegNet Web Service server can be found here.