Boris Steipe

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ACGCThe Applied Computational Genomics Course -
Winnipeg, June 2004Day 4 - Introduction

• Boris Steipe

Department of Biochemistry, Department of Medical
Genetics and Microbiology, Program in Proteomics
and Bioinformatics
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Biology - Layers of self-organized complexity
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cis/TF algorithm and resources

• Find potential cis element patterns in upstream
  regions by automated pattern discovery.
• Prepare composite expression patterns from genes
  with shared potential cis regulatory regions.
• Calculate correlation of known trans-cription
  factor expression patterns with composite target
  gene patterns.
• Output ranked correlations, potential binding
  sites, regulated genes, and their cognate
  transcription factors.

• Organize results

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Bioinformatics
Inheritable information is a substance.
Holley Khorana Nirenberg
Avery
Analyse as substance - Molecular Biology Analyse
as information - Bioinformatics
Crick Watson
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Transcription factor search from expression
profiles

• Gene expression is controlled by transcription
  factors.
• Thus transcription levels of genes and their
  regulating TFs should correlate.
• Group genes according to expression patterns and
  search for shared regulatory motifs in their
  upstream region.

An algorithm to discover transcription factor
binding sites and their regulated genes from
expression profiles.
Birnbaum K, Benfey PN Shasha DE (2001) cis
Element/Transcription Factor Analysis (cis/TF) A
Method for Discovering Transcription Factor / cis
Element Relationships. Genome Research
111567-1573 (http//www.genome.org/cgi/doi/10.110
1/gr.158301)
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... but in practice ?

• The post genomic era is here ...
• ... and where are we ?

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(Gen) omic Bioinformatics

• Industrial scale (Data intensive)
• Multiple genes (Cross-sectional)
• Model Organisms (Inference by analogy)
• Complete, exhaustive description (Missing
  entities are important)
• Discovery Science (Association, not Hypothesis)

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Post-Genomic Bioinformatics

• Genomes available (complete information )
• Systems concepts (Function, not existence)
• Complex objects ( Coregulated sets, interactions,
  complexes, pathways ... )
• Dynamic datasets ( re-query )

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Post-Genomic Bioinformatics

• Data overload
• Service overload
• Poor integration
• Peer review and expert opinions lacking
• Cultural gap between life- and computer sciences

The question becomes less what can you do but
what should you do !
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ACGC Day 4

• Discuss the process of making data computable
  from observations to goal oriented processes of
  enquiry. Discuss two strategies to transform
  correlations into causalties - significance test
  and biological interactions.

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ACGC Day 4

• Recognize "Cargo Cult Bioinformatics"

... In the South Seas there is a cargo cult of
people. During the war they saw airplanes land
with lots of good materials, and they want the
same thing to happen now. So they've arranged to
imitate things like runways, to put fires along
the sides of the runways, to make a wooden hut
for a man to sit in, with two wooden pieces on
his head like headphones and bars of bamboo
sticking out like antennas--he's the
controller--and they wait for the airplanes to
land. They're doing everything right. The form is
perfect. It looks exactly the way it looked
before. But it doesn't work. No airplanes land.
So I call these things cargo cult science,
because they follow all the apparent precepts and
forms of scientific investigation, but they're
missing something essential, because the planes
don't land. Now it behooves me, of course, to
tell you what they're missing. But it would be
just about as difficult to explain to the South
Sea Islanders how they have to arrange things so
that they get some wealth in their system. It is
not something simple like telling them how to
improve the shapes of the earphones. But there is
one feature I notice that is generally missing in
cargo cult science. ... It's a kind of
scientific integrity, a principle of scientific
thought that corresponds to a kind of utter
honesty ....
Richard Feynman
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ACGC Day 4

• Data modeling
• Processes
• Statistics
• Interaction Databases

Abstractions in bioinformatics Relational
datamodels
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ACGC Day 4

• Data modeling
• Processes
• Statistics
• Interaction Databases

Combining data and procedures Goal oriented
processes
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ACGC Day 4

• Data modeling
• Processes
• Statistics
• Interaction Databases

The importance of "significance" Confidence Simu
lation tests
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ACGC Day 4

• Data modeling
• Processes
• Statistics
• Interaction Databases

Biological Context BIND