How can you benefit from the Bioinformatics Resource

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How can you benefit from the Bioinformatics
Resource?

• Can (John) Bruce, Ph.D.
• Associate Director
• Bioinformatics Resource
• Keck Biotechnology Laboratory

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The Bioinformatics Core

• Created within Keck Lab upon request from Yale
  School of Medicine, July 2007.
• Director Hongyu Zhao Ph.D Associate Directors
  Can Bruce, Ph.D. Yong Kong , Ph.D.
• The facility is located at Sterling Hall of
  Medicine.
• Commercial software packages provided free by the
  Core are available to Yale researchers 24/7.

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Services

• Access to large number of widely used commercial
  and open source bioinformatics programs.
• Fee-based consultation services for well defined
  bioinformatics analyses.
• Collaborative projects requiring longer-term
  commitment of time and effort

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Available programs

• DNA/protein sequence analysis Lasergene and
  Gene Construction Kit.
• Pathway Analysis Ingenuity Pathway Analysis and
  MetaCore.
• Protein structure modeling Sybyl, a protein
  structure modeling and visualization program.
• Mass spectrometry data analysis GPMAW.
• Pipelining programs Pipeline Pilot and VIBE

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Examples of Current Collaborations

• Pathway analysis on proteomics data (Yale/NIDA
  Proteomics Center Project and Yale/NHLBI
  Proteomics Center Project investigators)
• Development of an algorithm for identification of
  phosphorylation sites from tandem spectrometry
  data (E. Gulcicek in Keck Proteomics )
• Molecular modeling of MAP Kinase ligand
  interactions (B. Turk in Pharmacology)
• Sequence analysis for defining invention claim
  for Office of Collaborative Research

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Microarray analysis software

• GeneSpring GX, provides visualization and
  advanced statistical analysis for gene expression
  data.
• Partek Genomics Suite, provides advanced
  statistics and interactive data visualization
  designed for gene expression analysis, exon
  expression analysis, promoter tiling array
  analysis, chromosomal copy number analysis, and
  SNP analysis.

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Sequence Analysis Software

• DNASTAR Lasergene, a comprehensive suite of
  programs for analysis of DNA/RNA/protein
  sequences including sequence editing, sequence
  assembly, sequence alignment, primer design,
  protein structure prediction, and gene detection
  and annotation.
• Gene Construction Kit 2.5, a tool for designing,
  drawing, and annotating DNA sequences especially
  plasmid constructs.

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PIPELINING PROGRAMS
This pipeline from Pipeline Pilot takes a
Swiss-Prot sequence, from a Web portal, then
generates a results page with four tabs, giving
summary data, sequence features map, chemical
structures of substrates and blast results.
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PATHWAY ANALYSIS

• MetaCore (from GeneGo),
• Ingenuity Pathways Analysis 3.1 (from Ingenuity
  Systems).
• Both are integrated software suite for functional
  analysis.
• Based on a proprietary manually curated database
  of human protein-protein, protein-DNA and protein
  compound interactions, metabolic and signaling
  pathways and the effects of bioactive molecules.
• Metacore can be integrated with other software
  packages such as Genespring, Resolver,
  Expressionist etc. , Pipeline Pilot, EndNote,
  Cytoscape.
• Ingenuity can be integrated with Genespring,
  Partek genomics, SAS-Jump Genomics, Spotfire.

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Why Pathway Analysis?
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Pathway Creation Algorithms in MetaCore (1)
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Direct Interactions Algorithm
Draws direct interactions between selected
objects.No additional objects are added to the
network
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Self regulatory Networks
Finds the shortest directed paths containing
transcription factors between your genes in the
gene list. (better used for small number of
targets)
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Expand by one(not suitable for large collections
of targets)
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Auto expand
Draws sub-networks around the selected objects,
stopping the expansion when the sub-networks
intersect
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Pathway Creation Algorithms in MetaCore (2)

• Analyze Network Creates a list of possible
  networks, ranked according to how many objects in
  the network correspond to the user's list of
  genes, how many nodes are in the network, how
  many nodes are in each smaller network.
• Analyze Transcription Network similar to above,
  sub-networks created are centered on TFs.
• Analyze Networks (Transcription Factors) focusses
  on presence of TFs at end notes.
• Analyze Networks (Receptors) focusses on presence
  on Receptors at end point of a network.

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Analyze Network Algorithm
Generates sub-networks highly saturated with
selected objects. Sub-networks are ranked by a
P-value andG-Score and interpreted in terms of
Gene Ontology
A proteomics experiment. Effect of drug
infusion on plasma proteins
Plt1e-18
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Analyze Networks (Transcription Factors)
Algorithm- an example -
Favors netwok construction where the end-nodes of
transcriptionally regulated pathways are present
in the original gene list.
Example from an mRNA expression analysis data set
comparing healthy and lesion skin.
P7.2e-46
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Analyze Network (Receptors) Algorithm- an
example -
Favors network construction where the end-point
of a pathway leads to a receptor (through
receptor binding) and the starting point of
a pathway (a transcription factor, or ligands,
etc) is present in the original gene list,
regardless of the presence of the end-point
receptor in the list.
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Transcription Regulation Algorithm
Generates sub-networks centered on transcription
factors. Sub-networks are ranked by a P-value and
interpreted in terms of Gene Ontology
13 targets/14 nodes P7.3e-31
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Immune response Histamine H1 receptor signaling
in immune response (p1e-4)
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GeneGo process networks
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WNT signaling (p1e-5)
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Disease biomarker enrichment
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Network-disease associations
1) Carcinoma (72 coverage, p3.3e-10) 2)
Neoplasms, connective and soft tissue. (42
coverage, p8e-10)
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Use of Pathway Analysis in Candidate Gene
Identification
FGF2, WNT5A, Tenascin-C, EGF, ILI1RN, BDNF,
TGF-beta2, FGF2, OSF-2, CSPG4(NG2), IL-8,
ENA-78, GCP2, SLIT2, SLIT3, Activin beta A,
Annexin I
1061 genes are located to mapped region for
disease
Other up- or down- regulated genes
360 genes up- or down- regulated by gt2x
17 receptor ligand genes are important input
nodes to pathways formed by genes with changed
expression.
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Pathway analysis narrows down number of candidate
genes for disease
ErbB2 PECAM1 DDX5 BCAS3 microRNA1 RARalpha MUL
VHR WIP ErbB2 NIK Plakoglobin HEXIM1
Prohibitin STAT5A STAT3 Clathrin PSME3 PSMC5 Er
bB2
FGF2, ILI1RN, ErbB2
Other up- or down- regulated genes
360 genes up- or down- regulated by gt2x
These genes, from mapped region of interest, are
able to form interaction pathways going through
these receptor ligands identified by first
analysis.
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A caveat
Not every gene belongs to a pathway in the
database
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Why Pathway Analysis Software?

• A learning tool
• Study a group of gene products.
• A data analysis tool.
• Which pathways are particularly affected?
• What disease has similar biomarkers?
• A hypothesis generation tool
• Can provide insight into mechanism of regulation
  of your genes. Which is the likely causative
  agent for the observed changes? What is likely to
  happen as a result of these changes?
• Suggest effects of gene knock-in or knock-outs.
• Suggest side-effects of drugs.
• Can highlight new phenomena that needs further
  investigation. What does the program not explain?

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Thank you.