Gene Expression, RNA-Seq, SAGE Data Analysis

  • Consulting for Experimental Design
  • Normalization and Gene Expression Analysis
  • Identification of Differentially expressed genes
  • Knowledge Extraction
  • Pathway Analysis
  • Regulation in Transcriptional Factor Activities and Network Analysis
  • Integration of your data in public databases such as GEO or ArrayExpress
  • Identification of significant biomarker by large scale data mining and correlation with clinical data (survival, stage, etc.)

Copy Number Data Analysis

Core personnel have developed a CGH array (Agilent and Affymetrix) normalization and segmentation pipeline. The input to this pipeline is raw Agilent CGH array or Affymetrix SNP 6.0 array data from the Genomics Core Lab, and the output is genomic segments annotated with copy-number data. Procedures for integration with gene expression and methylation can alo be provided. The output of the analysis is the list of segmented regions sample by sample, recurrent altered genes on all the samples (with q-val), functional copy number genes, Go analysis and Pathway analysis of the selected genes.

Consulting on Bioinformatics Scripting and Databases Integration

Members of the Bioinformatics Core provide consultation services on a large variety of topics including the following: microarray data analysis, automated functional and pathway analyses of high-throughput data, and protein and nucleotide sequence analysis. Core members have participated in numerous internal and external proposals, and have also contributed to the development of bioinformatics analysis methods and results.

All  services are provided at a cost of $100/hour for any work exceeding an hour. Cost estimates are given before work begins. Please contact Fulvio D’Angelo Ph.D. for further information and for a pricing estimate.

Computational Infrastructure

more info at Bioinformatics Computational Infrastructure