X-Services

With the help of the geneXplain platform plus a number of proprietary programs and data collections, we offer to share our expertise with you to get the very best out of your data. Please, contact us for further details under info(at)genexplain.com!
 
What we can do for you:
Organizing, analyzing and providing a biological interpretation of your high-throughput data
 
Microarray data
For data generated with Affymetrix, Illumina or Agilent expression arrays, we provide:
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A platform for data collection and systematization
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Normalization
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Affymetrix CEL files: MAS4, MAS5, RMA, GCRMA, background correction, PM correction
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Illumina normalization
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Agilent normalization
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Statistical analysis
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Fold change and P-value
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Correlation analysis
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Hypergeometric analysis
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Polynomial regression analysis
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CRC clustering
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Numerous other clustering methods
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Meta-analysis
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Mapping to ontology terms: Gene Ontology and more
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Gene set enrichment analysis (GSEA)
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Transcriptional regulation
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Extracting promoters as well as other regulatory regions of the required length
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Mapping transcription factor binding sites (TFBSs)
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Comparison with background sequences
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Identifying TFBSs that characterize sets of co-regulated genes
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Composition of co-regulated promoters
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Suggesting transcription factors acting on co-expressed genes
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Network and pathway analysis
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Mapping expression data onto pathways
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Upstream search for master regulators
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Downstream search for effector molecules
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Expanding networks around specific molecules of interest
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Identifying potential biomarkers and drug-targets
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Visualization in several layouts
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Analysis of multi-conditional data series, e.g.:
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Treated vs. non-treated individuals
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Time series data
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Treatment with a number of different compounds
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Series of treatments and concentrations
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Series of patients, treatments and concentrations
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Series of species, tissues, or cell lines
 
Proteomics data
Starting from a list of already identified proteins/peptides, we can provide:

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A platform for data collection and systematization
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Mapping to ontology terms: Gene Ontology and more
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Gene set enrichment analysis (GSEA)
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Network and pathway analysis
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Mapping expression data onto pathways
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Upstream search for master regulators
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Downstream search for effector molecules
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Expanding networks around molecules of interest
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Identifying potential biomarkers and drug-targets
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Visualization in several layouts
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Combined proteomics and transcriptomics analysis

 
Using PASS and PharmaExpert, and backed up by the expert teams that have developed these unique software tools, we offer our assistance in evaluating the potential biological activities of chemical substances.
 
This is what we can provide you with:
Prognosis of biological activities for drug-like compounds
 
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Basic prognosis of biological activities for drug-like compounds
For a list of organic compounds, we provide a set of biological activities accompanied by estimated mathematical probability. Prognosis is done for about 4000 activity terms that are grouped into four major categories:
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Therapeutic effects
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Molecular mechanisms
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Metabolic regulation
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Toxicity and adverse effects
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Further expert interpretation of the basic prognosis, which includes:
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Selecting compounds with desirable therapeutic effects and without adverse effects
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Selecting compounds with multiple mechanisms of action
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Suggesting drug-drug interactions with regard to their pharmacokinetic, pharmacodynamic, and adverse effects.
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Search for compounds with required activities in public and proprietary databases of chemical structures
Compounds can be suggested that act as inhibitors for drug target molecules identified by analysis of microarray, proteomics, or RT-PCR data (see above, geneXplain platform-based services).
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Customized training of the PASS program to generate a specific version of the software
Customized training of PASS can be done on user data or, alternatively, on our manually collected database. The latter option involves topic-oriented literature-based data collection.