Bioinformatics

Validated workflows for Bioinformatics include:

	Supported Platforms	Workflows	Data-analysis Tools and Software
Experimental design	Affymetrix, DNA arrays, next-gen sequencing, protein arrays, iTraq/ICAT workflows	Study design issues such as replication, sample numbers, balancing and analysis considerations	As applicable
RNA expression	All existing microarray applications	Data Quality assessment, normalization, data filtering, outlier identification; Differentially expressed annotated genes, clustering, gene set enrichment (GSE) analysis, classification	Partek Genomics Suite, R/Bioconductor
SNP genotyping	All existing microarray and PCR-based applications	SNP calls, single/multiple SNP association tests performed on allele, genotype, and dominant/recessive models.	Partek Genomics, R/Bioconductor
Copy-number variation (CNV) analysis	All suitable array-based applications	Copy number variation (CNV) Allele Specific Copy Num LOH analysis Disequilibrium analysis	Partek Genomics, R/Bioconductor and other open source tools
DNA sequencing	Standard Sanger and next-generation sequencing (454, SOLID, Illumina)	Large-scale raw cDNA sequence analysis, sequence clean-up, sequence contigs SignalP analysis, BLAST analysis De-novo sequencing,re-sequencing, targeted re-sequencing, micro-RNA, RNA-seq	CLC Genomics, dCAS, Galaxy
Protein arrays	Native; rec protein,peptide, and antibody arrays; bead-based suspension arrays (Luminex)	Data acquisition, data quality assessment and outlier detection Pin to pin and array to array normalisation using proprietary algorithms Data Quality assessment, normalization, data filtering, outlier identificationData Quality assessment, normalization, data filtering, outlier identification Data interpretation via cross-referenced databases, e.g. pdb for protein structures	Custom analysis pipelines
Mass spectrometry	MALDI-ToF/ToF, LC-MS/MS, iTraq, ICAT	Peptide and protein identification Peptide and protein quantitation Protein expression profilingProtein expression profiling De-novo peptide sequencing	Protein Pilot v 4.0, Mascot,Trans Proteomic Pipeline (TPP).
Biological pathway analysis	IPA-Tox, IPA-Metabolomics IPA-Biomarker	Cross-platform data integration Network relationship analysis Gene Ontology (GO)analysis, OMIM links, GEO Cross literature analysis from PubMedGene Ontology (GO)analysis, OMIM links, GEO Cross literature analysis from PubMed Biomarker discovery	Ingenuity Pathway, custom pipelines

Sample Prep Genomics Proteomics Bioinformatics Cell Culture Recombinant Protein Forms