Our team can curate data sets from a range of publicly available sources and databases. We can also assist in identifying suitable sources as starting points for dataset identification. In many instances, we can automate this to, for example, quickly search for co-occurrences of specific search terms in journal abstracts, or relevant metadata from GEO datasets to assist in identifying specific datasets of interest.
Data Landscaping
There are now vast amounts of bio data available in the public domain that can be effectively mined for specific biological questions of interest. Since public domain data can be used for hypothesis generation, it can dramatically reduce the time and costs associated with wet-lab experimentation and data generation. Moreover, in many cases, public datasets provide a great resource for validation of in-house findings. While public datasets provide a rich source of data, harbouring data generated from thousands or tens of thousands of samples then accessing this data and harmonising the various sources available is a technical challenge from both a computing and scientific perspective.
Data Mining
Once suitable data sets are identified, Fios Genomics can apply robust quality controls. This way we can provide the best starting point for downstream analysis and investigation. We can perform bio data mining by using standard or bespoke workflows. Our team also has experience with meta-analyses where data and outcomes from several studies are combined to increase the overall statistical power.
What We Offer
Our team can curate data sets from a range of publicly available sources and databases. We can also assist in identifying suitable sources as starting points for dataset identification. In many instances, we can automate this to, for example, quickly search for co-occurrences of specific search terms in journal abstracts, or relevant metadata from GEO datasets to assist in identifying specific datasets of interest.
Our Bio Data Mining Experience:
We have previously mined the below public datasets on behalf of clients:
- The Cancer Genome Atlas (TCGA)
- Cancer Dependency Map (DepMap)
- Cancer Cell Line Encyclopaedia (CCLE)
- Gene Expression Omnibus (GEO)
- European Nucleotide Archive (ENA)
- Expression Atlas
- Database of Immune Cell EQTLs, Expression, Epigenomics (DICE)
- cBioPortal for Cancer Genomics
Below you can view an example bioinformatics report we created using data we mined from the Cancer Cell Line Encyclopedia:
We have utilized the Bioinformatics team at FIOS Genomics for many of our drug discovery projects, as they provide expertise in the analysis of complex bioinformatic datasets. This includes large scale datasets from public sources as well as internally generated datasets. In many instances, at the start of a project, we have planned our large scale transcriptomic/proteomic studies with the FIOS team, to ensure that the data generated would provide the information we need, and that our projects had the highest chance of success. We have been consistently impressed with the rigor of FIOS’ work, their communication throughout the projects, and the rapid speed at which they complete their analyses.
Every time our clients work with us, they benefit from:
- A dedicated analyst backed by an experienced team to curate all data, identify the most appropriate statistical approach to take and provide a biological interpretation of results.
- An interactive data analysis report, internally peer-reviewed, including all analysis methods and results.
- Post-report follow ups: upon receipt of our data analysis report, we arrange a teleconference so that our lead analyst can talk through the results.
- Access to large capacity computing and secure data storage facilities.
WHAT YOU WILL GET
Transparency
All methods and analysis tools utilised are detailed in the final report. This means no blackbox of analysis.
Fast Turnaround
We help you to achieve your research goals in a quick and timely manner.
Rigorous QC
We always perform Quality Control as part of an analysis project.
Getting Your Data Ready For Analysis
We can analyse:
- Recent data, generated within your own laboratory or that of a 3rd party provider
- In-house historic data
- Data sourced from the public domain.
While we prefer to receive data in the raw format (eg .CEL files) we can also receive pre-normalised files.
However, if you have yet to generate the data, we can help by arranging for the generation of your data through one of our preferred laboratory service partners. Otherwise, we can source and mine bio data from available databases. We are happy to work with you at every stage of your study to ensure the best outcome for your research.
Our Reports
Once complete, we provide our analysis reports via an HTML link hosted on our secure server. The secure link leads the user to a password-protected HTML document which is clickable, searchable and dynamic. This format allows you to easily interrogate and explore your data. Additionally, we fully document all methods, tools and thresholds within the report.
We offer a wide range of services:
Discovery
Selecting the correct targets and/or the correct indication is essential for development success. We help support the process with robust analysis of historic or new data.
Preclinical Research
We help in experimental design and statistical analysis and guide our clients in making informed decisions during the preclinical stage.
Clinical
Research
We offer a comprehensive analysis approach for augmenting clinical trial outcomes, ensuring you get the most information out of your research.
Drug Repurposing
We have strong experience with identifying in silico new potential indications for existing drugs, reducing the cost and time of downstream wet lab validation.
