Data Analysis

The Genomics Center mission is to provide knowledge-based genomics, biostatistical and bioinformatics service. Every new project starts with a kick-off meeting where research question is clarified, bioinformatics data analysis pipeline suggested, and statistical analysis tools proposed. Using our extensive genomics knowhow we offer an assortment of solutions, from basic to cutting-edge projects, using tools from the public domain as well as in-house customized scripts.

 

Below is a list of different types of analyses we recently performed:

  • Gene expression, microRNA and alternative RNA splicing profile (RNAseq)
  • Single base and structural variant detection (DNAseq, exome sequencing)
  • Low frequency variant detection (Cancer samples)
  • DNA methylation profile (Bisulfite DNAseq)
  • Identification of novel transcripts (De-novo RNAseq assembly)
  • 16S rRNA profiling (Microbiome sequencing)
  • DNA-protein interaction analysis (ChIP-seq and more)
  • RNA-protein interaction analysis (RIP-seq, CLIP, etc)
  • DNA conformation profile (Hi-C, ATAC-seq, etc)
  • Novel motif discovery (ChIP-seq and RNAseq)
  • Data mining – analyzing and combining datasets from the public domain
  • Pathway analysis – meaningful interpretation of gene lists using several tools such as Ingenuity Pathway Analysis (IPA), FGNet and iPathwayGuide

 

Figures from recent analyses:

Heat Map

heatmap

 

Principle component analysis (PCA)

PCA

 

Volcano plot

vulcano

 

 

 

 

 

 

 

 

 

 

vulcano1

 

Venn diagram

ForLiat_VennDiagram

 

 

Sequence motif

 

motif3.logo

 

 

Canonical pathway

Cannonical Pathway

 

Enrichment analysis

IPA

 

 

Regulator effect

RegulatorEffect

 

 

Functional network analysis

nwFunctionalNetwork

 

nwIntersection_kk

 

Genetic and physical interactions

genemania

 

 

Integrative genomics viewer (IGV)

SNP

 

Weighted correlation network analysis (WGCNA)

wgcna

 

clustering

 

cluster dendogram

 

Softwares that we use for pathway and network analysis

 

Pathway and network analysis copy