Business (Service) Purpose and Target
The goal is to identify the action point 1 the actional mechanism 2 and the biomarker 3 through reinterpretation of genomic data (genomic data(Microarray & NGS data), stored in each lab PC, to provide basic data for securing intellectual property rights.
1Molecular target: it is interpreted as a molecular target, and can be used as a biomarker through validation study.
2Mode-of-action: it is to understand the function of each molecule in networks of various molecules, and the interaction and role of activation.
3Biomarker: a market that can assess a normal/pathological condition or a degree of reaction to a drug from the objective perspective.
Especially, biomarkers are used as an important evaluation indicator in the clinical trial stage for drug development, and also for diagnosis and risk assessment of disease. According to the 2006~2015 clinical trail success rate of the US, the success rate of development of a new biomarker-based drug from the clinical phase 1 to approval was more than three times higher (source: the result of an analysis of Biomedtracker data, a clinical trial monitoring service by the American Bio Association).
* The identification of drug mode-of-action might suggest the possibility of repositioning of existing drugs.Provision/Analysis and Example
1. Raw data QC: box plot, PCA(Principal Components Analysis, Principal Component Analysis), hierarchical clustering, Volcano plot, and Venn diagram
- - box plot :
- It can be used to evaluate whether the distribution of data among samples is similar (patterning), to grasp the average and median values of all data in the sample, and to use it to evaluate whether normalization of data (adequacy of normalization) is necessary (QC of samples) (it can also be used as a QC standard for QC of samples or analytical methods)
- - PCA :
- Check the spatial distribution of entire data among samples, and use it for the access base of supervised (predictive or directed) or unsupervised (descriptive or undirected) data mining
- - hierarchical clustering :
- Used to identify the correlation of data among samples
- - Volcano plot :
- Used to select the genes satisfying the statistical significance upon the selection of genes with different expression (activity)
- - Venn diagram :
- Used to extract common or differentiated sub-groups among groups.
2. Supervised (predictive or directed) and unsupervised (descriptive or undirected) data mining
- - Supervised data mining :
- Set the experimental groups and the control groups in advance and then, select the candidate gene group.
- - unsupervised data mining :
- Select the candidate gene group without setting the experimental groups and the control groups in advance.
3. Specific gene selection (biomarker discovery)
Selection of candidate gene groups using functional and statistical techniques (Student's t-test , ANOVA) =4. GeneOntology and pathway analysis: using DAVID and KEGG Mapper
- - GeneOntology :
- dividing it into GO biological process, GO molecular function, and GO cellular component to provide, and being used to predict the action point or action mechanism.
- - pathway analysis :
- Used for functional prediction researches on interaction and correlation between selected genes, which are based on existing research results (public BD)
5. Network analysis (IPA, Ingenuity Pathway Analysis: upstream regulator, regulator effects, etc.)
- - IPA :
- A paid data mining tool provided by QIAGEN Bioinformatics, and it is used for various data analysis or to provide results for such analysis (http://www.ingenuity.com). In particular, it could play a significant role in the research of action points and action mechanisms by referring the analysis results such as 'Upstream Regulator Analysis', 'Mechanistic Networks', 'Causal Network Analysis', 'Downstream Effects Analysis', etc.
6. [Opt] mRNA and miRNA interaction analysis
7. [Opt] DNA methylation biomarker discovery
: Metylation Data Analysis Support8. Discussion and writing a manuscript
: Discuss the purpose and result of an analysis through communication with researchers, and preparation of thesis and presentation materials in the field9. Etc.
: Other Data Analysis Support/Cost and PeriodCostand Period
1. Cost: pricing upon the no. of samples, purpose, and requirements (two installment payment), possible to determine a price after preliminary analysis
2. Period: determined considering requirements (~1week)