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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