Bioinformatics support at School of Biological Sciences

University of Essex

Igor ChernukhinSteven Yates

Bioinformatics support

NGS transcriptome analysisChip-seqMicroarray analysis

Bioinformatics support

NGS transcriptome analysis Fast sequence-aligning tools working in parallel

computing environment Static software for transcriptome analysis and R or Matlab workframe Network analysis & Graphical presentation

Chip-seqMicroarray analysis

Transcriptomics RNA-seqWorkflow (example)

Filtering illumina reads from contaminating bacterial sequences

Transcriptome assembly

Counting reads

NGS transcriptomics

Transcriptome annotationTypically 60 - 70% transcripts should

be annotated with Uniprot

Analysisof Differentially Expressed Genes

Clustering analysisof expression data

GO enrichmentanalysis

DEG analysis in R::edgeR (example)NGS transcriptomics

Dispersions

Gene Ontology - enrichment analysis

NGS transcriptomics

R::topGO:Evaluates overrepresentation of GO

terms in DEG using several statistical models

Revigo: Updating/removing redundant GO terms

Cytoscape: building network of activated biological processes

GO - enrichment network(example)

NGS transcriptomics

Data clustering analysisfor time-series datasets:

finding similar expression profile

NGS transcriptomics

Matlab or R workspace:Choosing clustering algorithm

Analysis of individual clusters

Data clustering analysis (example)

NGS transcriptomics

Finding similar expression profile

Data clustering:analysis of individual clusters (example)

NGS transcriptomics

Response to salt

967, 7728, 12711: Iron starvation induced protein (Ferritin)

NGS transcriptomics

5628, 11741, 21761: Protein heat shock protein Hsp7015404: Eukaryotic translation initiation factor

Response to salt & cold

Data clustering:analysis of individual clusters (example)

NGS transcriptomics

Biological data modelling

Inferring gene networkwith Variational Bayesian State Space

Modelling

VBSSM will generate a network of gene interactions from time series expression data by treating the data as linear dynamical system, also known as a state-space model.

Plant bioinformatics

Online tools

http://bsproteomics/PlantBinfo/

Plant bioinformatics

Room 5.41

Igor Chernukhin (igorc)Steven Yates (sayates)

Bioinformatics support at School of Biological Sciences

University of Essex