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

2. NGS transcriptome analysis Chip-seq Microarray analysis
Bioinformatics support
NGS transcriptome analysis
Chip-seq
Microarray analysis

3. NGS transcriptome 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-seq
Microarray analysis

4. Transcriptome assembly
NGS transcriptomics
Transcriptomics RNA-seq
Workflow (example)
Filtering illumina reads from contaminating bacterial sequences
Transcriptome assembly
Transcriptome annotation
Typically % transcripts should
be annotated with Uniprot
Counting reads
Analysis
of Differentially Expressed Genes
GO enrichment
analysis
Clustering analysis
of expression data

5. DEG analysis in R::edgeR (example)
NGS transcriptomics
DEG analysis in R::edgeR (example)
Dispersions

6. Gene Ontology - enrichment analysis
NGS transcriptomics
Gene Ontology - enrichment analysis
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

7. GO - enrichment network
NGS transcriptomics
GO - enrichment network
(example)

8. Data clustering analysis for time-series datasets:
NGS transcriptomics
Data clustering analysis
for time-series datasets:
finding similar expression profile
Matlab or R workspace:
Choosing clustering algorithm
Analysis of individual clusters

9. Data clustering analysis (example)
NGS transcriptomics
Data clustering analysis (example)
Finding similar expression profile

10. analysis of individual clusters (example)
NGS transcriptomics
Data clustering:
analysis of individual clusters (example)
Response to salt
967, 7728, 12711: Iron starvation induced protein (Ferritin)

11. analysis of individual clusters (example)
NGS transcriptomics
Data clustering:
analysis of individual clusters (example)
Response to salt & cold
5628, 11741, 21761: Protein heat shock protein Hsp70
15404: Eukaryotic translation initiation factor

12. Biological data modelling
NGS transcriptomics
Biological data modelling
Inferring gene network
with 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.

13. Plant bioinformatics
Online tools

14. Room 5.41 Bioinformatics support at School of Biological Sciences
Plant bioinformatics
Bioinformatics support at
School of Biological Sciences
University of Essex
Igor Chernukhin (igorc)
Steven Yates (sayates)
Room 5.41