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Genomatix: Gene-TF Analysis


[Introduction] [Parameters] [Output]

Introduction

The Gene-TF Analysis determines for each gene and each transcription factor (TF) from the input gene list if the transcription factor has a validated or predicted binding site (+) on the gene's promoter or not (-). In addition, it determines for each pair of genes if there are sufficient interaction evidences from the literature and uses different colors to highlight such interactions. The minimum number of evidences from the literature and from validated interactions can be set as a parameter. The program will automatically detect which of the input Gene IDs are transcription factors and which are not.

Definitions:


Parameters

Input
Type of Input The Gene-TF analysis accepts various types of gene keywords. The following gene keywords are supported:
  • Entrez Gene IDs (e.g. 30818) and/or Ensembl Gene IDs (e.g. ENSG00000115041)
  • Gene Symbols/Names (e.g. KCNIP3)
  • Transcript Accession Numbers (e.g. NM_001034914, ENST00000360990 or AK315437)
  • Affymetrix Probe Set IDs (e.g. 231774_at)
Input keywords

List of gene keywords for the Gene-TF analysis. The gene list has to contain at least one transcription factor, otherwise no result will be generated.

You can either paste the gene keywords into the input field or upload a file with gene keywords (separated by blanks or commas). Gene keywords containing commas or blanks have to be put in double quotes.

Organism Please select from which organism the input genes are.
Evidence level You can choose between five different evidence levels for the Gene - TF correlations:
  • The abstract level counts two genes as co-cited if they occur in the same abstract.
  • The sentence level counts two genes as co-cited if they occur in the same sentence (in an abstract).
  • The function word level requires additionally a function word between the two genes in the sentence.
  • The validated regulatory level contains only experimentally validated regulatory interactions (ENCODE Project: TF-Gene and TF-miRNA correlations).
  • The expert level, which contains only interactions curated by (NetPro and Genomatix) experts, based on literature analysis.
The selected evidence level is a minimum evidence level, i.e. the interactions are based on the number of evidences in all evidence levels above the selected evidence level. For example, if you set the evidence level to "function word level", gene - TF interactions based on the function word level, validated regulatory level (if not excluded) and the expert level are shown.
The default evidence level is sentence level and the validated regulatory evidences are excluded by default.
Minimum evidence number

The evidence filter specifies the minimum number of evidences for the gene - TF interactions. For example, if the number of evidences is set to 10 and the evidence level is set to sentence level, only gene - TF interactions with at least 10 evidences in the sentence level or a higher level (function word, validated regulatory and expert level) are shown in the output.

Evidence types are:

  • The sentence and function word level count a sentence as evidence.
  • The abstract and expert level count an abstract as evidence.
  • The validated regulatory level counts an interaction in a cell type as evidence.

Result
Result Here, you can edit the default name of the result file.
Email address Here you can choose between two methods for receiving the results:
  • Show result directly in browser window
    In this option the URL of the result is directly shown in your browser window.

    Warning: Please use this option only for analyses which can be performed in a short time.
    If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to".

  • Send the URL of the result via email
    In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished.

The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management!

We recommend to use the email option for more than ca. 500 input genes.


Output

The result is represented in a table where each column is labeled with a TF and each row is labeled with one of the genes. In each cell there are three values:

Furthermore, each cell represents these values with a different background color:

The second line in each cells shows the number of evidences that are available for the various levels and provides links to the corresponding literature.

A click on a row header in the table will start a MatInspector analysis on the gene's promoter(s).
A click on the column header within the table will get detailed information on the transcription factor from MatBase.

The Gene-TF Analysis allows to export the table as Excel and as TSV file. The content of the Excel file is identical to the HTML output except for the order of genes. A TSV file contains just tab-separated values and no background colors. The additional information on the number of evidences for the various levels is not exported to Excel and TSV files.


Example output:

Gene-TF Analysis started with the human genes ARHGEF7, CREBBP, NFKBIA, RELA and STAT5A (gene IDs: 8874, 1387, 4792, 5970, 6776).
Each column is labeled with a TF (CREBBP, STAT5A and RELA) and each row is labeled with one of the five genes.

Gene-TF Analysis Example Output


ENCODE project data