At the leading-edge of genomic science, data analysis is getting complicated. Knowing what analysis to perform, how to wield the available analytical tools and how to visualize and interpret results are critical.

Majority of the Genomics work generates huge data with difficult to analyze and interpretation. Transform your research data into a captivating discovery story and narrate it with visually stunning plots and graphics! Our team provides diverse types of bioinformatics insights to support discovery and translational research. Talk to us, analyse your data and get greater biological insights.

When your assays are performed at theraCUES, raw and normalised data are always included and advanced analysis is performed on request.

If you cannot find the bioinformatics service you need, contact us to discuss your project!

1. Nanostring® Data Analysis
What can nCounter® quantified mRNA provide you?
Targeted Gene expression-Genes involved in core panel specific pathways along with optimized Housekeeping genes.
Cell Type Profiling- Estimation of abundance of > 13 different Immune / Cancer-Immune cell types.
Data Visualization- Visualize the gene expression results ranging from QC plots to pathway level regulation

Advanced analysis
Gene Deregulation- Fold change in Up/ Downregulation of any gene against Control.
Pathway Level Expression- Condense each sample's gene expression profile into a small set of pathway scores.

Drug efficacy studies
Drug resistance specific gene identification using multiOMICS
Drug mechanism of action via Gene expression analysis
Pathways targeted by drugs and their expression regulation
Identification of genes modulated by Dose and Time of drug treatment
Signature gene identification based on multiple drug treatment

Figure 1: Timepoint wise modulations for selected targets at selected dose

Figure 2: Dose wise modulations for selected targets at selected time-point

2. Spatial Data Analysis
We provide Digital spatial profiling services through GeoMx® platform, and normalised gene expression data is always included with the run. Data from other spatial platforms (10x Visium) will also be accepted for analysis and insights.

Sample clustering plots-
  1. Dimension reduction: PCA, tSNE, UMAP plots
  2. Unsupervised hierarchical clustering of samples: Heatmap
Differential expression analysis:
  1. Statistical test – T-test/LMM-test results along with statistical significance (p-value)
  2. Binary ratio test – Comparison of Tumor vs TME from same ROI (Region of interest) (TME analysis)
Pathway analysis:
  1. GSEA (gene set enrichment analysis): List of pathways upregulated/downregulated
  2. ssGSEA (single sample GSEA): Pathway expression for each AOI/Segment
  3. ORA (Over representation analysis): Pathways enriched within the Upregulated genes/ Downregulated genes analyzed separately
  4. Visualization of pathway analysis: Color gradient Bar plots, Volcano plot
Spatial Deconvolution:
  1. Cell type abundance for each AOI/Segment
  2. Visualization of cell type abundance using Bar plot and Heatmap
High quality image of the ROI/AOI selected from tissue

While above mentioned are the standard deliverables, analysis at theraCUES are often customized based on the study and additional requirements of the customer.
3. RNA Seq Analysis
Sample clustering
Differential gene expression
Functional enrichment reports (Gene ontology – Biological process, Cellular Component, Molecular Function & KEGG/REACTOME pathways)
Supporting visualization at each step (PCA/UMAP/tSNE plots, Heatmaps, Volcano plots, Functional enrichment gradient plots, KEGG pathview maps and many more..!)
4. Whole genome sequencing
Raw & QC Trimmed data (.fastq files) and QC reports per sample
Mapped data (.BAM) files per sample and related QC reports
Variant call results per sample and combined matrix – per sample VCF and merged VCF file.
Annotated Variant call file (xlsx/ .csv format) - Functional as well as Pathogenic effect annotation included; per variant type (INDEL/SNP)
7. Metagenomics (16S rRNA/18S/ ITS )
OTU detection table and abundance profile for each samples
Taxonomic assignment and abundance table
Diversity analysis
  1. Alpha diversity (per sample analysis) for each sample and related rarefaction plots
  2. Beta diversity (comparative analysis) across samples and related PCoA plots - (ONLY IF MORE THAN 3 SAMPLES)
  3. Functional annotation table
  4. Phylogenetic analysis of the top abundant OTUs
  5. Visualizations - Heatmap, Barplot, Piechart and Krona chart.
6. Single cell sequencing
Gene expression matrix : Matrix, Barcodes and Feature files
QC Reports per tissue/sample
Cell clustering (UMAP/ tSNE)
Report for Markers/ DEGs per cluster
Cell type assignment report
Single cell trajectory report
Functional enrichment analysis report
5. Multi-Omics Analysis
Combination of assays for studying the different aspects of a disease can often help us to understand the complete picture of the study of interest. For example, combining Exome-Seq (DNA Mutation) with Gene Expression data can often provide significant insights on details on Drug resistance causality, Downstream effects of gene variation reflected in the expression of the targets etc.

At theraCUES the Drug resistance causality can be unravelled through Multi-Omics studies where a combined approach of Exome-Seq where the key genes known to be the target of the drug & their interactors would be profiled for loss of function variants. Further the expression of the drug targets would be cross validated by a targeted approach of NanoString® Gene Expression Assay.

We can also perform Spatial transcriptomics and proteomics approach to get insights regarding micro-environment, immunotherapy possibilities, etc with multi-omics approach.

8. Custom Analysis
Our Bioinformatics team and subject matter experts can work with you to understand your data better, customize analysis and help uncover insights that were previously unknown. For more details click here.