Introduction to Bioinformatics - Tutorial no. 13

Probe Design

Gene Networks

Probe design problem

Given a genome with a set of genes. Recall that each gene is represented by a

probe (a short segment) of the corresponding cDNA.

The length of a probe can be 20, 50, 70! The probe design problem tries to identify a

probe for every gene.

Probe design problem (Informal definition)

Given a genome, for every cDNA (or mRNA) Xi, a probe pi is identified such that

pi is a substring of Xi; and pi does not cross-hybridize with other mRNAs

Probe design problem creates a probe pi for every mRNA Xi

X2 X3 X4X1

p1 p1 p1p1 X X X

Primer3 Input

Sequence

5’ PCR primer

Oligo probe

3’ PCR primer

Include in PCR primerExclude from

PCR primer

Repeats library

Primer3 Output

mRNA position

Length

Hybrid Tm

% GC Self complementarity

3’ complementarity

Sequence

Product

5’ PCR primer Oligo

probe

3’ PCR primer

OligoDB

Sequence name to find

OligoDB Input

Oligonucleotide lengthNumber for each mRNA

Background database

Ensembl Gene IDEnsembl

mRNA ID

OligoDB Output

mRNA position

Tm of hybrid

Probe stability

Background matches

Oligo probe

Biochemical Pathway Visualization Tools

BioCarta EXPASY KEGG WIT MetaCyc

BioCarta

Main focus: Pathways and tools to study them.

Pathway tool is web-based. http://www.biocarta.com/genes/index.asp

Static pages of pathways. Metabolic and regulatory pathways.

Need licence to add/edit pathways.

BioCarta Homepage

BioCarta Metabolic Pathway Example Glycolysis. Compounds shown in

chemical and textual form.

Enzymes above arrows with legend at bottom.

Only enzymes are clickable.

BioCarta Regulatory Pathway Example ATM signalling

pathway. All genes are clickable.

ExPASy “Expert Protein Analysis System”. Main focus: Analysis of protein sequences and

structures. Pathway tool is web-based.

http://www.expasy.org/cgi-bin/search-biochem-index Static pages of pathways.

Metabolic and Regulatory pathways. Scanned in version of the Boehringer Mannheim

“Biochemical Pathways” map. Map partitioned into 115 pieces. Keywords matched against entries in map.

Cannot add/edit pathways.

ExPASy Homepage

ExPASy Metabolic Pathway Example Glycolysis. Color convention based on

Michal’s “Biochemical Pathways”. Color of compounds

depends on compound type. Color of arrows depend on

species (plant, animal, yeast, prokaryotes).

Only enzymes and arrows outside diagram are clickable.

ExPASy Regulatory Pathway Example Insulin receptors. Only enzymes and

arrows outside diagram are clickable.

KEGG

“Kyoto Encyclopedia of Genes and Genomes”. Main focus: Biochemical pathway visualization. Pathway tool is web-based.

http://www.kegg.com/kegg/kegg2.html Static pages of pathways.

Metabolic and Regulatory pathways. Different organisms.

KEGG Homepage

KEGG Metabolic Pathway Example Glycolysis. Substrates and products

are drawn in circles. Enzymes, represented by

EC number, are drawn in rectangles.

Adjacent pathways are drawn in semi-rectangles.

Enzymes found in the gene catalog of a specific organism are marked green.

All items are clickable.

KEGG Metabolic Pathway Example Select specific species

Link to other pathway

Link to compound

Link to enzyme

KEGG Regulatory Pathway Example MAPK signaling

pathway (Homo Sapiens).

WIT

“What is There”. Main focus: Produce metabolic

reconstructions for sequenced (or partially sequenced) genomes.

Pathway tool is Web-based.http://wit.mcs.anl.gov/WIT2/

Static pages of pathways. Only metabolic pathways.

WIT Homepage

WIT Metabolic Pathway Example Glycolysis. Enzymes.

Substrates, and products are clickable.

MetaCyc

Electronic encyclopedia of over 450 metabolic pathways from over 150 different organisms.

Software: Implemented in COMMON LISP; AI techniques

incorporated to allow inference, such as pathway prediction from sequenced genomes.

Need a licence to obtain software. Free for academic purposes only.

Graph layout algorithm for drawing metabolic pathways dynamically at run-time.

Need to manipulate database to add/edit pathways.

MetaCyc Software

MetaCyc Metabolic Pathway Example Glycolysis. Everything

(Substrates, products, adjacent pathways, and arrows) is clickable.

Question

Do the enzymes form the same pathway share a common regulation?

Inspect Lysine Biosynthesis pathway. Use the following tools:

KEGG: http://www.genome.jp/kegg/ UCSC Genome Browser: genome.ucsc.edu TransFac database or alternative search tools like

TESS: http://www.cbil.upenn.edu/tess/