Bioinformatics support at School of Biological Sciences University of Essex Igor Chernukhin Steven Yates.

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