AHM 2002

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AHM 2002

• Tutorial on Scientific Data Mediation
• Example 1

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SCENARIO_Genome-scale Modeling of Low-Dose
Irradiation Responses Using Microarray Based Gene
Networks

• Hypotheses Genes that show similar expression
  patterns in response to low-dose irradiation are
  components of coordinated expression groups
  (called synexpression groups) and that
  understanding the differential regulation of
  these synexpression groups will (a) provide
  DNA-sequenced-based understanding of the complex
  biological processes associated with low-dose
  radiation and (b) identify determinants of
  radiation dose and genetic susceptibility to
  radiation damage.

Database search for common promoter elements to
link new candidate genes
Statistical Clustering of genes
Microarray analysis
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SPECIFIC AIMS

• 1. Develop a web-accessible database resource to
  assemble microarray transcription profiles of
  radiation responsive genes and to link these
  genes to genomic and cDNA sequence information.
• 2. Apply statistical and bioinformatic tools to
  identify novel synergistic gene expression groups
  of radiation responsive genes.
• 3. Apply the model to the analysis of
  gene/pathway responses to low-dose IR.

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Clusfavor
http//mbcr.bcm.tmc.edu/genepi/
wrap1
Accession Number
wrap2.xml
NCBI GeneBank
pwrap1
http//www.ncbi.nlm.nih.gov/
wrap2
Sequence to search
wrap3.xml
BLAST
pwrap2
http//www.ncbi.nlm.nih.gov/blast/
wrap3
The top match
wrap4.xml
http//transfac.gbf.de/cgi- bin/matSearch/matsearc
h.pl
MatInspector
pwrap3
Resulting sequences similarity scores
wrap4

• an external program to build a model or
• back to blast to find additional matches, or
• to clustal to determine a consensus sequence
  which is then sent to blast.

SCENARIO WORKFLOW
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CLUSFAVOR
NCBI GeneBank
Database search for promoter identification
Microarray analysis
cDNA Cluster
BLAST
Promoter model
Common promoter alignment
Promoter sequences
TRANSFAC


- New candidate target genes



Database search
Adapted from Thomas Werner Biomolecular
Engineering, 17 87-94 (2001)
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CLUSFAVOR

• CLUSFAVOR- CLUSter and Factor Analysis with
  Varimax Orthogonal Rotation
• A standalone program whose output consists of
  several clusters of named sequences that have
  similar expression characteristics in the current
  experiment.
• GOAL Given a gene expression data, to end up
  with another set of related sequences from which
  to build a model.
• INPUT gene expression data
• OUTPUT collection of clustered cDNA fragments

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NCBI GeneBank

• GOAL Given the name (or, better, the accession
  number) of a cDNA string from the clusfavor
  results, do a name lookup in GenBank to obtain
  the cDNA sequence.
• INPUT The accession number or the name of a cDNA
  string
• OUTPUT cDNA sequence for the input cDNA string

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BLAST

• Basic Local Alignment Search Tool_ BLAST
• A set of similarity search programs designed to
  explore all of the available sequence databases
  regardless of whether the query is protein or
  DNA.
• INPUT Output cDNA sequence from GeneBank.
• OUPUT A set of similar sequences.

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MatInspector V2.2 based on TRANSFAC

• MatInspector - Matrix Inspector
• TRANSFAC - The Transcription Factor Database
• Search for potential transcription factor binding
  sites in your own sequences and detect consensus
  matches in nucleotide sequence data using the
  TRANSFAC 4.0 matrices.

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GENEBANK MEDIATION DEMO