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GeneGo Services
Need to outsource projects? GeneGo can help. Over the last ten years, we have built a multi-disciplinary team of computational and wet lab biologists, bioinformaticians, chemists and
medical doctors that can handle a broad range of projects. As a company, we have published over 60 peer-reviewed articles in leading journals, have been awarded 15 research grants and have
participated in multiple international research projects and FDA-led consortia. Most importantly, we have successfully completed dozens of commercial research projects for our customers
from industry, academia and government.
Services Case Studies
Driving ROI of a top 10 pharmaceutical company by improving data management systems
Good response biomarkers secure success of Phase III trial
CONTRACT RESEARCH
Figure 1: Tropical Disease project. Using several methods of functional and statistical analysis in MetaCore, GeneGo experts helped to identify two sets of prognostic expression
“candidate biomarkers” for prediction of severity of Dengue fever.
Functional Analysis of OMICs data: Best-in-class pathway analysis from best-in-class pathway software providers.
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Starting from a variety of data types (gene lists, SNP arrays, sequence data, expression chips, metabolic profiles and more) GeneGo scientists can help to recognize perturbed pathways,
find biomarkers, model pathways leading to/from altered genes and proteins, reconstruct mechanisms for knock-out organisms, characterize cellular responses to different perturbations,
identify changes between patients, time points, dosages or treatments, and more.
Questions
- What are my top genes and what are they interacting with?
- What are the most important processes, pathways, disease genes, biomarkers in my data?
- What are the most likely drug targets in my study and what biological effects might their inhibition cause?
- Which genes can be easily assayed and used as biomarkers?
- How does impact on an organism change at different time points of treatment?
- I have a list of SNPs and expression profiles from patients that do not intersect - how should I proceed with my analysis?
- What transcriptional factors are responsible for expression changes in the animal model?
- My analysis prioritizes well-known hubs like p53 - are they really significant for my data?
Benefits
- Increase efficiency of research efforts
- Reduce cost of research
- Improve understanding of diseases and MOA
- Support of key decision making
- Access to a team of data analysis professionals
- Provide access to new algorithms and features not available in standard off-the-shelf products
Biomarker Discovery: Join the growing list of successful customers who entrusted biomarker discovery to GeneGo scientists.
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Our team uses all available statistical and functional methods of analysis to provide accuracy and reproducibility for your biomarker discovery. GeneGo can combine a variety of data
types (gene lists, SNP arrays, sequence data, expression chips, metabolic profiles and more) to help you develop diagnostics, make progress in predictive toxicology, classify patients and
provide functional validation and underlying biological mechanisms for already derived signatures.
Questions
- Which genes from my data can be easily assayed and used as biomarkers?
- What are the biomarkers of disease A?
- I have expression data of responders and nonresponders to a treatment - can I use the data to select patients for clinical trials?
- How can I measure drug effectiveness in an animal model or patients?
- I derived an expression signature - how can I validate its robustness?
- My signature works well in an animal model, but will it work in humans?
Benefits
- Increase efficiency of research efforts
- Reduce cost of research and clinical trials using prediction opportunities
- Improve understanding of diseases and MOA
- Support of key decision making
- Access to a team of data analysis professionals
- Provide access to new algorithms and features not available in standard off-the-shelf products
Patient Stratification: Make a step towards personalized medicine with patient stratification services from GeneGo.
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To define the optimal genetic profile of patients, GeneGo will help you to find markers that predict disease susceptibility traits, drug tolerance (metabolism and clearance) and
efficacy (drug targets and transport proteins). By understanding drug response in all phenotypic subgroups, GeneGo will enable identification of the exclusion criteria to eliminate
nonresponder phenotypes and reduce the cost of drug development, providing expedited and more focused clinical trials.
Questions
- I have expression data for a large patient cohort; can I use it to distinguish several disease subtypes and find treatments for them?
- I have expression data for treatment responders and non-responders - can I use the data to select patients for clinical trials?
- My drug is ineffective in some patients, can I explain why?
Benefits
- Shorten clinical trials
- Reduce cost of research and clinical trials
- Improve understanding of diseases and MOA
- Support of key decision making
- Access to a team of data analysis professionals
- Provide access to new algorithms and features not available in standard off-the-shelf products
Statistical Analysis: Get the most out of your data with GeneGo statisticians.
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By creating data repositories for our customers and ourselves, we have adjusted and polished our data processing algorithms to get the most out of any data. We have used gene signature
analysis in categorization of patients, predictive toxicogenomics and other applications. Participation in FDA-led consortia to develop a set of recommended best practices for microarray
data analysis and microarray-based predictive models has brought our experience to a new level. It also allowed us to develop a new concept of functional descriptors, leveraging the power
of statistics with the comprehensiveness and biological understanding provided by GeneGo’s knowledgebase.
Questions
- I have expression data for a large patient cohort; can I use it to distinguish several disease subtypes?
- I have expression data for treatment responders and non-responders - can I use the data to select patients for clinical trials?
- I derived an expression signature - how can I validate its robustness?
- My signature works well in an animal model, but will it work in humans?
Benefits
- Reduce cost of research due to predictive opportunities
- Facilitate biomarker discovery
- Facilitate patient stratification
- Improve understanding of diseases and MOA
- Support of key decision making
- Access to a team of data analysis professionals
- Provide access to new algorithms and features not available in standard off-the-shelf products
Translational Research: Remove barriers to multi-disciplinary collaboration by driving the advancement of medical research with GeneGo.
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GeneGo’s knowledgebase, one of the most comprehensive manually curated databases of mammalian biology and medicinal chemistry data, is an excellent example of combining different
types of data, protein interactions, curated pathways, compound activity, toxicity information and more, into one integrated environment. It allows us to translate findings obtained in
bacteria and animal models to humans, facilitating research and saving time and money by maximizing the value of research done using model organisms.
Questions
- My compound causes a side effect in mice, will it cause the same effect in humans?
- I obtained my data in Organism A, can I extrapolate my findings to humans?
- My signature works well in an animal model, but will it work in humans?
Benefits
- Reduce cost of research
- Facilitate biomarker discovery
- Improve understanding of diseases and MOA
- Support of key decision making
- Access to a team of data analysis professionals
- Provide access to new algorithms and features not available in standard off-the-shelf products
Pharmacological Analysis: Leverage the power of a comprehensive compound database, sophisticated algorithms and systems biology solutions to learn more about your compounds.
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GeneGo can provide known and predicted in silico information on aspects of compound safety and activity including metabolic fate, ADME properties, therapeutic area, toxicity issues,
protein targets, and affected pathways. GeneGo’s systems pharmacology approaches can help you with drug repositioning, compound profiling and prioritization, target identification, solving
compound mechanisms of action and more using compound structure and/or OMICs data.
Questions
- What are the diseases my new compound may treat?
- I have four drug candidates but can move only one into clinical trials. Which one to choose?
- My new compound seems safe in rats. How likely is it to cause problems in clinical trials, and which problems? What are the risk factors?
- My compound induces osteogenesis, but I don’t know its molecular target and mechanism of action.
- What compounds from my virtual library should I synthesize and assay first?
- How is my compound metabolized? Are any of its metabolites toxic?
Benefits
- Reduce cost of chemical synthesis, wet lab and animal experiments, clinical trials and drug development in general
- Support “go” or “no-go” decisions on specific alternative drug candidates
- Support decisions for potential combinations of developmental and existing drugs, or drugs with activity at multiple targets
- Provide mechanisms of action for laboratory results that can be used to support patent applications and to gain regulatory approval
- Provide access to new algorithms and features not available in standard off-the-shelf products
Toxicity Assessment: Assess safety liabilities of drugs, environmental contaminants and other xenobiotics with GeneGo.
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A comprehensive database of gene, protein and metabolite associations to chemical toxicity, toxicity-related pathway maps and tools for visualization and filtering of systems toxicology
information allows us to investigate mechanisms of toxicity, identify safety biomarkers, design experiments to model specific pathologies and more starting from compound structure and/or
OMICs data.
Questions
- My new compound seems safe in rats. How likely is it to cause problems in clinical trials, and which problems? What are the risk factors?
- What biomarkers can be measured to identify lipid accumulation in lungs?
- My compound was safe in dogs but caused side effects in humans. What is the mechanism of the toxicity, and how can I identify it in animals in the future?
- What toxicity-related pathways are affected at different compound dosage regimens?
Benefits
- Reduce cost of chemical synthesis, wet lab and animal experiments, clinical trials and drug development in general
- Support “go” or “no-go” decisions on specific alternative drug candidates
- Improve understanding of mechanisms of toxicity
- Provide access to new algorithms and features not available in standard off-the-shelf products
Collaboration on Grants and Publications: GeneGo’s innovative science has resulted in many successful grant applications and a strong publication record.
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Our scientists are eager to collaborate and offer assistance in writing grants and articles with partners in academia, industry, and elsewhere.
Questions
- My lab does not have bioinformaticians to analyze the data generated for my article. Could GeneGo help?
- I used GeneGo’s software for my publication - how can I best describe the data analysis in the Methods section?
- I need to be persuasive in my grant application - maybe GeneGo’s experience could help me?
Benefits
- Branch out into new areas of systems biology research via collaborations with GeneGo scientists
- Obtain assistance in conceptualizing and writing grants and publications
KNOWLEDGE MANAGEMENT
Figure 2: Clinical data project. GeneGo scientists manually curated and pre-processed clinical data
(OMICs data, clinical parameters, patient details etc), and contributed to the development of internal applications that search and analyze the data.
Data Management: Increase the value and availability of your data with GeneGo’s customized solutions for efficient data flow within your institution.
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Our systematic approach can facilitate integration of external and internal data, and current and historical information to create a multi-domain knowledge base. Experienced knowledge
engineers from GeneGo will help you in development of internal data management software, terminology (ontologies, controlled vocabularies), annotation interfaces and curation procedures
designed for your specific environment.
Questions
- How can we capture our experimental results in a more searchable, re-usable system?
- What in-house compounds do we have that inhibit Pathway X?
- What assay technologies have been used to study Protein A? Using which cell lines?
- Should Receptor B be avoided for safety reasons? Were inhibitors of this receptor tested in animal safety models at our company?
- What cell lines do we have internally that contain mutations in Gene Z?
Benefits
- Save time by improving data accessibility and search efficiency
- Increase the ROI on experiments by reusing data to avoid repetition and leverage prior experience
- Answer multi-disciplinary questions by integrating data from multiple domains (chemical, biological, toxicological, demographic, etc.)
- Provide more efficient data analysis through integration of external and internal data
- Save time and money through improved management of biological reagents
Curation and Annotation: Improve the quality of your data analysis and hypothesis generation by using manually-curated content. Trust your internal data curation to professionals.
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GeneGo has extensive experience in manual curation and annotation of many types of information:
- interactions (e.g. compound-target, protein-protein, nucleic acid-protein)
- associations (e.g. biomarker-disease, compound-disease)
- biological dossiers (cell line attributes, target CV)
- clinical data (study parameters and patient information)
- OMICs data
- pathway map construction
Questions
- What biomarkers of disease N are described in the literature?
- Have any knock-out models of my target been described?
- What cell lines derived from fibroblasts are available?
- What are the changes in signaling pathways for disease N?
- Find all expression profiles of patients treated with drug A.
- How many smoking patients responded to treatment?
Benefits
- Save time and resources on literature search
- Provide access to high-quality manually-collected information
- Provide a basis for internal curation and registration systems
- Gain access to GeneGo terminologies
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“We outsourced prioritization of three compounds to GeneGo. While we understood the effect of these drugs, we needed to prioritize them with respect to biologic potency and possible toxicity. GeneGo's software was able to confirm the biologic activity that we expected and highlighted functional processes and key drug targets that allowed us to focus our testing by suggesting biological activities that could be critical to the success of the candidates, saving us time and money.”