Biooinformatic tools for detecting regulatory elements shared by ....ppt

Caratterizzazione funzionale di trascritti attraverso l'individuazione di elementi di controllo post-trascrizionale
Graziano PESOLE
Università di Milano
7 Marzo 2002
graziano.******@
Microarray Experiment Result
Functional classification
Gene characterization problem
Gene classification problem
Gene characterization problem
ESTs
mRNA
5’
3’
3’
CDS
known gene
gene identification through database searching (. BLASTX)
gene identification by aa pattern discovery (. Pfam, etc.)
gene identification by nt pattern discovery ( patterns)
EST assembling
Gene characterization problem
mRNA
5’
3’
CDS
CDS
DNA
protein
Eventual alternatively spliced mRNAs
Gene characterization problem
3’ EST
5’
3’
CDS
?
mRNA 3’UTR
post-transcriptional regulation of gene expression
STABILITY
TRANSLATION
SUBCELLULAR
LOCALIZATION
CDS
3’UTR
3’UTR
5’UTR
mRNA
Biological role of mRNA UTRs
nuclear export
polyadenylation status
mRNA cellular localization
Control of mRNA stability
Control of mRNA translation
Function
mediated by
oligonucleotide patterns
stem-loop structures
Patterns known to play some regulatory
activity (experimental assay, ic
footprinting)
Pattern discovery in biosequences
Novel patterns candidate of functional activity
(Statistical analyses carried out on
non-redundant databases)
UTRdb - release (January 2001)