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geneXplain GmbH
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We can explain your genes and put bricks together.
We can explain your genes and put bricks together.

62 followers
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Watch this video about the SysmedIBD project, where geneXplain is a part of the scientific team.

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On 29 April Alexander Kel (CSO) and Olga Kel-Margoulis (Director Applied Life Science Informatics) carried out a hands-on training in handling the geneXplain platform. The training course took place within the framework of the project "Unlocking infectious diseases research potential at Rīga Stradiņš University". The training programme provided theoretical functionalities and practical application for the identification of #drug #targets and #biomarkers with the geneXplain platform.
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#Release 3.0 of the geneXplain platform is available now with new tools in expression data analysis, statistical analysis, binding site analysis, with several new and enhanced workflows, and with the integrated latest releases of TRANSFAC® and TRANSPATH® databases (2013.3 and 2013.4), and many additional enhancements.
Follow your key topics on our new start page.
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Expression Mapping on the geneXplain platform
 
This function enables highlighting of up-regulated and down-regulated genes in the network diagrams.
 
First, open a network in the work area. You might be interested to use the table with identified differentially expressed genes and calculated fold change values for #expression #mapping. After the table with expression data is dragged and dropped, the up- and down-regulated #genes are automatically highlighted.
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Find master regulators in networks
This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.
This workflow is designed to find important #master #regulators in #signal #transduction pathways. The search is done based on the network of the TRANSPATH® database.
Red = Master regulatory molecule
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Analyze promoters on the geneXplain platform

This workflow is designed to search for putative transcription factor binding sites (#TFBS) on the promoters of an input gene set.

As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set (1).

At the first step, the input table is converted into a table with Ensembl Gene IDs (2).
At the next step, #promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 relative to the transcription start sites.
Site search is done with the help of the #TRANSFAC® library of the positional weight matrices (#PWMs).
At the same step, frequencies of putative TFBSs are compared between Yes set and No set to identify sites overrepresented in Yes set versus No set. Default No set in the workflow is a set of housekeeping genes for the corresponding species.
The result of this step is a list of PWMs the hits of which are overrepresented in Yes set versus No set. Default No set in the workflow is a set of housekeeping genes for the corresponding species.

Next, the list of PWMs is converted into a table of transcription factors (3).

The output is a new folder with several tables, including a summary of the predicted TFBSs, genomic tracks of the Yes and No promoters and sites, as well as the tables with transcription factors potentially regulating the genes in the Yes set.

It is possible to get a #visualization of TFBS for individual genes (4).
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The geneXplain team wish you a peaceful #Christmas time!

Hope to see you on the platform in 2014...
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#Organization of the geneXplain platform

When you login into the geneXplain platform for the first time, a window opens that contains the following areas:

A - The Work Space, which is the main part of the window. The Start page presents a couple of predefined workflows/pipelines, which are chains of ready-to-start methods.

B- The Tree Area (to the left of the Work Space), where you find the collection of Databases, the uploaded data files and the available analyses methods under the corresponding tabs, organized in a hierarchical tree structure.

C - The Info Box (in the lower left part), where you can select the data resource to search in, or where you will get Information about the data file or analysis method that you select with a single click in the Tree Area.

D - The Operations Field (lower right part), providing a number of options under the different tabs in a context-dependent manner.

E - The general Control Panel, on top of the different areas, showing a context-dependent set of icons for the available operations.

Register here for a #free #account of the geneXplain platform!
http://www.genexplain.com/genexplain-platform-registration
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...or you should use the geneXplain platform!
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