Cancer research in geneXplain
As a deeply rooted biomedical research company, geneXplain GmbH is proud to share with you our latest news, recent and upcoming events, and breakthrough solutions for the cancer research field.
Check out reports on transcription factors playing important roles in cancers at our Transcription Factors in Cancer page >>>
Check out the open calls for cancer research grants at our Research Collaboration page >>>
Check our recent cancer-related webseminars, including the lectures from World Cancer Research Day at geneXplain:
You will find the full list of our recent webseminars and their recordings on this page.
It is out honour to assist the cancer research community by providing access to the best-in-class tools for gene regulation studies, prospective drug targets and biomarkers identification, and personalised treatment selection on the basis of full reconstruction of the molecular mechanism of the studied pathology. Below we provide some of the application examples of our geneXplain platform and Genome Enhancer tools, coupled with the TRANSFAC®, TRANSPATH® and HumanPSD™ databases, for identification of prospective master-regulators of the studied tumours.
geneXplain platform applications in cancer research
The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications.
You can log in to the geneXplain platform with your Genome Enhancer account or register a new account to check out the functionality of the free basic account of this comprehensive bioinformatics solution. For details on the difference between the basic and the professional accounts, please visit this page.
For the example of geneXplain platform application in cancer research, we have selected the analysis of RNA-seq data retrieved from triple negative breast cancer (FASTQ files were taken from Gene Expression Omnibus, GSE188914). The aim of the analysis was to identify master regulatory molecules in triple negative breast cancer as well as the regulatory transcription factors that might serve as biomarkers and putative drug targets.
The detailed explanation of the performed analysis and the obtained results can be viewed on this page or in the document below:
The explanatory videos, showing the performed analysis, can be viewed on our YouTube channel inside the respective playlist.
Genome Enhancer applications in cancer research
Genome Enhancer is a fully automatised pipeline for patient omics data analysis, which identifies prospective drug targets and corresponding treatments by reconstructing the molecular mechanism of the studied pathology. Genome Enhancer can be launched from raw or pre-processed patient genomics, transcriptomics, epigenomics, metabolomics, and proteomics data.
Key benefits for cancer research:
- Identifies activated targets in the examined patient data and suggests known and re-purposing drugs
- Can be used for both: personalised medicine and cohort patient studies (identification of molecular mechanisms of various cancers)
- Is based on information from widely accepted databases TRANSFAC® (transcription factor binding sites), TRANSPATH® (signalling and metabolic pathways), HumanPSD™ (gene-drug-disease assignments)
- Applies unique algorithms developed in-house by renown gene regulation experts
- Can be used by researches and medical doctors with no bioinformatics skills required
- Analyses all types of omics data starting either with raw or pre-processed data
- Integration of promoter and pathway analysis gives unrivalled disease molecular mechanism modeling accuracy
- Generates a comprehensive report on the identified drug targets and prospective therapies
- Generates MTB (Molecular Tumor Board) report on patient’s genomics data for a number of pathologies
Demo reports examples:
- Full report (Personalized patient data) — Genomics, VCF
- MTB (Molecular Tumor Board) report — Genomics, VCF
Esophageal squamous cell carcinoma:
Osteosarcoma, neoplasm metastasis:
Non-Small Cell Lung Carcinoma:
Below we provide the preview of the full report text generated by Genome Enhancer for the colorectal cancer patient case (VCF file taken as input):
The results of Genome Enhancer analysis, contained in any of the reports produced by this pipeline, are intended for research use only and should not be used for medical or professional advice. GeneXplain GmbH makes no guarantee of the comprehensiveness, reliability or accuracy of the information contained in the reports generated by Genome Enhancer.
Decisions regarding care and treatment of patients should be fully made by attending doctors. The predicted chemical compounds listed in the reports are given only for doctor’s consideration and they cannot be treated as prescribed medication. It is the physician’s responsibility to independently decide whether any, none or all of the predicted compounds can be used solely or in combination for patient treatment purposes, taking into account all applicable information regarding FDA prescribing recommendations for any therapeutic and the patient’s condition, including, but not limited to, the patient’s and family’s medical history, physical examinations, information from various diagnostic tests, and patient preferences in accordance with the current standard of care. Whether or not a particular patient will benefit from a selected therapy is based on many factors and can vary significantly.
The compounds predicted to be active against the identified drug targets in the reports are not guaranteed to be active against any particular patient’s condition. GeneXplain GmbH does not give any assurances or guarantees regarding the treatment information and conclusions given in the reports. There is no guarantee that any third party will provide a refund for any of the treatment decisions made based on these results. None of the listed compounds was checked by Genome Enhancer for adverse side-effects or even toxic effects.
The analysis reports contain information about chemical drug compounds, clinical trials and disease biomarkers retrieved from the HumanPSD™ database of gene-disease assignments maintained and exclusively distributed worldwide by geneXplain GmbH. The information contained in this database is collected from scientific literature and public clinical trials resources. It is updated to the best of geneXplain’s knowledge however we do not guarantee completeness and reliability of this information leaving the final checkup and consideration of the predicted therapies to the medical doctor. In all cases, the end user (including researchers and medical doctors) accepts full responsibility for all risks associated with using of information, contained in the reports generated by Genome Enhancer.
The scientific analysis underlying the Genome Enhancer reports employs a complex analysis pipeline which uses geneXplain’s proprietary Upstream Analysis approach, integrated with TRANSFAC® and TRANSPATH® databases maintained and exclusively distributed worldwide by geneXplain GmbH. The pipeline and the databases are updated to the best of geneXplain’s knowledge and belief, however, geneXplain GmbH shall not give a warranty as to the characteristics or to the content and any of the results produced by Genome Enhancer. Moreover, any warranty concerning the completeness, up-to-dateness, correctness and usability of Genome Enhancer information and results produced by it, shall be excluded.
The results produced by Genome Enhancer, including the analysis reports, severely depend on the quality of input data used for the analysis. It is the responsibility of Genome Enhancer users to check the input data quality and parameters used for running the Genome Enhancer pipeline.
Note that the text given in the reports is not unique and can be fully or partially repeated in other Genome Enhancer analysis reports, including reports of other users. This should be considered when publishing any results or excerpts from the reports. This restriction refers only to the general description of analysis methods used for generating the reports. All data and graphics referring to the concrete set of input data, including lists of mutated genes, differentially expressed genes/proteins/metabolites, functional classifications, identified transcription factors and master regulators, constructed molecular networks, lists of chemical compounds and reconstructed model of molecular mechanisms of the studied pathology are unique in respect to the used input data set and Genome Enhancer pipeline parameters used for the current run.