Custom DNA Microarray Data Analysis

Creative Biolabs provides expert custom services for microarray data mining, analysis and management with a focus on gene expression profiling. DNA microarray is the leading technology in the field of functional genomics for simultaneous analysis of the expression patterns of thousands of genes. DNA microarray has been widely used in gene expression profiling, genomic instability monitoring, gene discovery, and genotyping and pathway analysis. Robotic technologies for source DNA processing, array fabrication, probe preparation, hybridization, image signal acquisition and data output have been fully developed; however, huge amounts of data generated by this high-throughput technology present a tremendous challenge for both academic laboratories and industry due to the lack of well trained personnel in this field. 

Featured Services:
     o Gene Expression Index Calculation
          • We use a suite of software algorithms including but not limited to GCOS, dCHIP, RMA, GCRMA and PDNN.
     o Differential Gene Expression Detection 
          • We use GCOS Change algorithm to compare gene expression between two samples;
          • We use statistical algorithm dChip, RMA, PDNN to find differently expressed genes. Result will be further examined by 
            SAM program to eliminate the false positive data.
     o Hierarchical Clustering 
          • We use various gene-clustering algorithms to create subsets of genes that have similar expression patterns;
          • We group genes that share a biological context, e.g. co-regulated genes, genes involved in the same pathway, or genes 
            correlated with the same disease;
          • We group samples of biological relevance to discover subclasses of clinical phenotypes or find genealogical relationship 
            of different microorganism strains.
     o Gene Filtering and Gene List Creation
          • We filter genes according to various criteria such as GO terms; 
          • We build Gene Lists with detailed annotations. 
     o Pathway Analysis
          • We integrate gene expression data with metabolic or signal-transduction pathway information extracted from KEGG 
            pathway database;
          • We infer gene transcription network and present its entire topology as graphics. The interaction among genes and their 
            protein products can be visualized.
     o Advanced Statistical Graphics
          • We provide Advanced Statistical Graphics in high-resolution publication quality and in diverse formats such as PNG, PDF, 
            EPS, TIFF, JPG, etc.

Creative Biolabs handles raw data generated from all current DNA microarray platforms that use different databases, arrays, signal scanning systems and image analysis tools. For Affymetrix GeneChip® microarray expression profiling projects, the minimum requirement is the CEL file of the microarray data. Further information describing the sample's biological properties is optional; but supplying that information will help generation of MIAME formatted reports and interpretation of the results. Clients will receive summary reports with lists of differentially expressed genes. The lists show probe sets of significant p-values, corresponding gene names and detailed function annotations. We also provide a file showing expression index, p-values and fold-change for all probe sets for each comparison. Advanced statistical analysis including cluster analysis, disciminant analysis and pathway analysis can be performed upon request. Our deliverables also include other publishable presentations if requested.