Investigator Resources

Next Generation Whole Transcriptome Sequencing: In-silico and In vitro collaborative venues

1. Analytical pipelines

  • Absolute and comparative abundance of expression (FPKM)
  • Splicing: Novel Isoforms, absolute and comparative abundance of novel and known isoforms
  • Variations: Novel and known variants

2. Post-analytical pipelines

  • Integration of Variation, Expression, and Splicing in search for novel regulatory networks
  • Comparative expression and variation analysis with population and cancer-centered public datasets
  • Extraction of cancer related features: Loss-of-heterozygosity, Allele-preferential Expression, RNA editing, Disease-driving somatic changes
  • Noncoding transcriptome
  • Selected gene or pathway focused analyses: alignment of within user’s dataset info with the public sources on specific genes and pathways of interest
  • Custom user-generated analyses and queries
  • Advise for wet-lab validation

3. Epigenomic pipelines

  • Mapping of ChIP-seq reads to reference genome - coding and non-coding regions
  • Peak calling
  • Linking with histone marks
  • Analysis of Peak co-ordinates and associated gene-annotation
  • MOTIF analysis

4. Proteome-wide analysis of effects of non-synonymous variation

  • Analysis of functional impact of variation on active site, binding sites, pathways and domains
  • Analysis of effects of variation on Post-translational modifications

5. Metagenomic analysis

Analysis of short-reads from metagenomes to determine taxonomic distribution

6. Phylogentic analysis using SNP data

Create phylogenetic trees from SNP data to classify samples

7. Software

MGPC currently subscribes to the following software licenses: