Introduction to Bioinformatics - Tutorial no. 13

1
Introduction to Bioinformatics - Tutorial no. 13

• Probe Design
• Gene Networks

2
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.

3
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

4
Primer3 Input
Repeats library
Sequence
5 PCR primer
Oligo probe
3 PCR primer
Include in PCR primer
Exclude from PCR primer
5
Primer3 Output
Length
GC
Self complementarity
Product
mRNA position
Hybrid Tm
Sequence
3 complementarity
5 PCR primer
Oligo probe
3 PCR primer
6
OligoDB
Sequence name to find
7
OligoDB Input
Oligonucleotide length
Number for each mRNA
Background database
Ensembl Gene ID
Ensembl mRNA ID
8
OligoDB Output
mRNA position
Tm of hybrid
Probe stability
Background matches
Oligo probe
9
Biochemical Pathway Visualization Tools

• BioCarta
• EXPASY
• KEGG
• WIT
• MetaCyc

10
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.

11
BioCarta Homepage
12
BioCarta Metabolic Pathway Example

• Glycolysis.
• Compounds shown in chemical and textual form.
• Enzymes above arrows with legend at bottom.
• Only enzymes are clickable.

13
BioCarta Regulatory Pathway Example

• ATM signalling pathway.
• All genes are clickable.

14
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-inde
  x
• 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.

15
ExPASy Homepage
16
ExPASy Metabolic Pathway Example

• Glycolysis.
• Color convention based on Michals 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.

17
ExPASy Regulatory Pathway Example

• Insulin receptors.
• Only enzymes and arrows outside diagram are
  clickable.

18
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.

19
KEGG Homepage
20
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.

21
KEGG Metabolic Pathway Example
Select specific species
Link to compound
Link to other pathway
Link to enzyme
22
KEGG Regulatory Pathway Example

• MAPK signaling pathway (Homo Sapiens).

23
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.

24
WIT Homepage
25
WIT Metabolic Pathway Example

• Glycolysis.
• Enzymes. Substrates, and products are clickable.

26
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.

27
MetaCyc Software
28
MetaCyc Metabolic Pathway Example

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

29
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/