Computational Functional Genomics
(26-BE-790)
(Statistical Models in Computational
Biology)
Instructor:
Mario Medvedovic, [email protected]
Teaching Assistants:
Johannes Freudenberg (Bioinformatics),
Junhai Guo (Biostatistics),
http://eh3.uc.edu/ComputationalFunctionalGenomics.html
1-3-2004
1
Course Outline
•
Everything will be posted on the web-site
– lecture slides, links to the papers to read, syllabus, computer programs, data,
homework, etc
•
The course will start from very beginning in three different areas:
– Molecular genetics
– Statistics and probability
– Programming
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•
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•
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People with different backgrounds will need to focus their efforts differently
Independent readings and practice is expected
Access to a reasonably good PC computer with ability to install additional
software is absolutely necessary
The focus of the course is analysis of microarray data: experimental design,
normalization, identification of differentially expressed genes, cluster analysis and
microarray data base classification.
Towards the end, statistical models for regulatory motifs will also be discussed
If time permits, applications of general graphical models will also be discussed
1-3-2004
2
Course Outline
•
Everything will be posted on the web-site
–
•
The course will start from very beginning in three different areas:
–
–
–
•
•
•
•
•
•
•
lecture slides, links to the papers to read, syllabus, computer programs, data, homework, etc
Molecular genetics
Statistics and probability
Programming
People with different backgrounds will need to focus their efforts differently
Independent readings and practice is expected
Access to a reasonably good PC computer with ability to install additional software is
absolutely necessary
Those without an access to a decent computer need to send me an email right away
The focus of the course is analysis of microarray data: experimental design, normalization,
identification of differentially expressed genes, cluster analysis and microarray data base
classification.
Getting to actual practical microarray data analysis very quickly – next lecture
Filling in gaps as we go
1-3-2004
3
Course Outline
•
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Basic concepts of molecular genetics, microarray technology, sources of variability, motivation of the
need for statistical analysis
Introduction to programming and data analysis using R and Bioconductor.
Basics of probability theory (random events, probability, random variables, probability distributions,
conditional probability)
Basics of statistical inference (statistical models, random sample, parameter estimation, hypothesis
testing, p-value)
Identifying differentially expressed genes (normalization approaches, t-test, multiple comparison
adjustments)
Cluster analysis and post-hoc analyses
Mid-term exam (in-class)
Elements of Experimental design as applied to microarray data (Random block design, Confounding,
Analysis of Variance, Elements of optimal design)
Basics of Bayesian statistical inference (Bayes theorem, Beta-Binomial and Gamma-Normal models,
Empirical Bayes approach, Hierarchical models)
Statistical models in cluster analysis (hierarchical approaches, partitioning approaches, mixture model
based clustering, EM algorithm, Gibbs sampling)
Statistical models and computational tools for identifying genomic regulatory elements
Bayesian graphical models in functional genomics
Final Project
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4
References
No single universal reference textbook
 Peter Delgraad. Introductory Statistics with R. SpringerVerlag, NY, 2002.
 Statistical Analysis of Gene Expression Microarray Data.
Speed T.
 The Analysis of Gene Expression Data: Methods and
Software. Parmigiani, G., Garrett, E.S., Irizarry, R.A., Zeger,
S.L.
 Statistical methods in bioinformatics: an introduction /
Warren J. Ewens, Gregory R. Grant
 Bioinformatics: The machine learning approach/ Baldi, P.,
Brunak, S.
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Lecture Outline
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•
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Molecular genetics – “The Central Dogma”
Functional Genomics – assigning function to genes
Gene Expression
– Functional Genomics Data – Microarrays
– Transcription and Regulatory motifs
– Computational Functional Genomics
• Very wide area
• Computational analysis of functional genomics data
• Computational methods just a “front” of underlying statistical methods
•
Stochasticity of functional genomics data and molecular biology in
general
– Measurement error
– “Biologic variability”
– Stochasticity of underlying molecular processes
•
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Results in “noisy” data with significant stochastic components
(microarray data, transcription factor binding motifs, protein folds, etc)
6
DNA
• In the nucleus of Eukaryotic cells
• A linear polymer of 4 nucleotides (A,C,G,T)
• Two strands of DNA for double helix by specific
pairing of their nucleotides (A-T,C-G)
…AGCTGGCGGT…
…TCGACCGCCA…
• The specificity of pairings is used for preserving
genetic information during the cell division –
individual strands of the double helix are separated
and two identical copies are created by filling in
appropriate nucleotides
• Genes are portions of DNA coding for proteins
• Proteins are the functional molecules in a living
system
• Proteins are linear polymers of 20 amino acids
• DNA encodes different proteins through the “genetic
code” – each three letters code for one amino acid
…AGCTGGCGGT…
…-Ser - Trp –Arg-…
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DNA Replication
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The Central Dogma – From Information to Function
1-3-2004
• Translating Information stored in the
DNA into function – protein production
• mRNA carries the information from the
nucleus to cytoplasm where proteins are
produced
• Transcription is the process of
“copying” the genetic information from
DNA into mRNA
• Translation is the process of protein
synthesis based by decoding the mRNA
sequence
• Genome of the cell is the DNA - static
• Transcriptome of a cell are all mRNA
molecules in the cell – dynamic
• Proteome of a cell are all proteins in
the cell – dynamic
• Cell maintains proper functioning by
regulating its protein levels
• A major mechanism for regulating
protein levels is regulation of mRNA
levels
9
Functional Genomics
• n : the branch of genomics that determines the
biological function of the genes and their products
– Source: WordNet ® 2.0, © 2003 Princeton University
• Functional genomics data
– Data that facilitates assigning function to genes or is directly
assessing gene function (DNA/Protein sequence, 3D protein
structure, mRNA levels measurements, etc.)
• Computational functional genomics (as assumed in
this course)
– Computational methods that facilitate application of
appropriate mathematical/statistical models for analysis and
interpretation of functional genomics data
– In a broader sense, computational approaches to functional
genomics
1-3-2004
10
Reading Materials
Online Reading (in the suggested order):
•
An Introduction to biocomputing
•
Kimball’s Biology Pages – an online hypertext “textbook”
– http://www.techfak.uni-bielefeld.de/bcd/Curric/Introd/ch0.html
– http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/
– http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
– http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
Traditional References
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Lodish, H. et al. Molecular Cell Biology. (Ch1),Ch2, (Ch3), Ch4
Lewin, B. Genes. Ch1-Ch3
Courses to Take
•
Introduction to Molecular Genetics
1-3-2004
11
Microarray Technology – Measuring levels of all
mRNA species in parallel
• Base-pairing or hybridization is the underlining
principle of DNA microarray.
– Identify a representative fragment of a gene’s coding
sequence (e.g. TCGACCGCCA)
– Synthesize corresponding DNA fragments
– Place the such “probes” on the glass slide
– Repeat the process for all gene genes you want to include on
the microarray and place each on a pre-defined position on
the glass slide
– Some fancy technology is used to actually place up to 40k
spots of DNA on a microscope slide
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TCGACCGCCA
12
“Single-channel” Microarrays – Experimental
Protocol
Biological Sample
• mRNA is extracted from the biological
sample of interest
• mRNA is labeled by using a fluorescence dye
• Microarray is “hybridized” with labeled
mRNA
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Extracted mRNA
Labeled mRNA
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Hybridization Reaction
• Labeled mRNA fragments are floating
around in search of its complementary
DNA fragments immobilized on the
microarray slide
• The amount of the labeled mRNA that
“sticks” to a “spot” representing a gene is
proportional to the “copy” number of the
corresponding mRNA
• The amount of labeled mRNA “stuck” to
each spot is quantitated by measuring the
fluorescence intensity of each spot
• The real-world dynamics of this process
is complex and there is no simple
relationship between the quantitative
measurement of fluorescence and the
actual number of copies of each mRNA
1-3-2004
14
“Two-channel” Microarrays – Experimental Protocol
• Direct assessment of relative
abundance of different mRNA
species
• mRNA extracted from two
different biological samples is
labeled with different
fluorescence dies (usually Cy3 and Cy-5)
• Two pools of labeled mRNA
are “co-hybridized” on a
single microarray
• After quantitating individual
dye intensities, the results are
can be represented using
almost notorious shades of
green and red
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15
Color Coding of Intensity Ratios
Scanning the “Green Channel”
(XG)
Scanning the “Red Channel”
(XR)
XR
XG
1-3-2004
log(X R )  log(X G )
• The particular shade for each pixel of
a spot on a microarray is calculated
by a computer program based on the
(log)ratio of the two intensity
measurements
• The process of quantitating
fluorescence intensities consists of
several semi-automated steps:
• Identification of the position of all
spots on the microarray
• Determination of the “foreground”
and the “background” area for each
spot
• Segmentation of the “spots” –
measuring intensity of all pixels in
the area
• Summarizing the intensity of
individual pixels (mean or median,
variability measures, etc)
16
Graphical Presentation of Data From a Single Microarray
•Scatter plot of fluorescence intensity
(>6000 genes)
•Row measurement plotted on the
“logarithmic axes” – equivalent to
plotting log-transformed data using
regular “linear axes”
•Points close to the 45o line represent
genes with similar expression in the
two samples
•Points far away from the 45o line
suggest differentially expressed genes
•In this experiment same sample was
split in two and labeled with two
different dyes – we don’t expect any
differentially expressed genes
•Red dots represent “spiked” control
RNA species that should be
1-3-2004
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Two Technical Replicates
•What happens if we measure
the same thing twice?
•The original
•Do we expect to get the same
log-expression ratios?
•What does “same” really
mean?
•Scatter plots of all gene
expression values seem pretty
similar…
9
LR1=TE1-CE1
Treatment - Experiment 2
Treatment - Experiment 1
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7
5
LR2=TE2-CE2
7
5
3
3
1
2
3
4
5
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7
Control - Experiment 1
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2
3
4
5
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Control - Experiment 2
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10
Experimental Variability – Histogram describing the
“distribution” of differences in Log-ratios between two replicated
experiments
•Differences between two replicated
measurements of expression ratios can be
up-to 4-fold!
•What is the “correct” ratio for a given
gene?
•Expression measurements have a
stochastic component
•The expression ratio can be characterized
by a statistical model (i.e. probability
distribution) that defines the “probability”
of an outcome
•Probability of an outcome in a experiment
can be defined as the proportion of times
that this particular outcome would occur in
a very large (“infinite”) number of
replicated experiments
•The appropriate statistical model for a
particular experiment can be postulated by
considering the nature of the experiment,
the underlying physical nature of the
experiment, and by exploratory data
analysis
1-3-2004
LR = LR1- LR2
M axim um C hange = 4 fold
4
2
2
Log2 Fold C hanges in R eplicated Experim ents
•The Histogram can be used as an “empirical” model by
assuming that the probability of the outcome occurring within a
specific interval is equal to the observed proportion of
measurements in this interval
•Various re-sampling and randomization approaches for
establishing statistical significance are based on this assumption
•Sometimes (wrongly) considered inherently superior to
“parametric” method
19
4
(Parametric) Statistical Model for Log Gene
Expression Ratio Measurements
LR ~ N (μ, σ 2 )
1
f N ( LR | μ , σ ) 
e
2πσ
2
(LR μ) 2
2σ 2
4
P(3  LR  4)   f N (LR | μ, σ 2 )
3
• LR=Log expression ratio (observed)
• =Mean expression ratio (assumed fixed – represents
the signal of interest). This value is also the
“expectation” of the LR, or the average of a very large
(infinitely many) observations

-2
0
2

4
6
LR
• =Standard Deviation – quantifying the variability of
observations.
• fN =The probability distribution function (pdf) – the probability of any observed LR being in a
given interval is the area under the curve defined by the pdf above this interval. The total area
under the whole curve is equal to 1. Pdf can be interpreted as the histogram for a very large
number of measurements (infinite) when the width of boxes is made very small (very close to
zero)
1-3-2004
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Transcription and Transcriptional
Regulation – Grossly Over-Simplified
• Transcription of a gene is initiated
by a transcription factor that
specifically binds to a “regulatory
motif” in the gene’s regulatory
region
• A number of other proteins
(general transcription factors) are
recruited and bind to DNA in the
proximity of the transcription start
site
• Finally, the RNA Polymerase, the
protein that performs the synthesis
of mRNA is recruited and the
transcription is initiated
RNA
Transcription General Transcription
Polymerase
Factor
Factors
ACGCGTAA
TATAAA
Regulatory Motif
Tata Box
Coding Region
• Transcriptional regulation one of the most important mechanism for a cell to respond to
external stimuli, and the cell-type specific gene expression defines the nature of different cells
in a multicellular organism
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Statistical Model of TF-Binding Motifs
1 -8 1 -7 12
; p A  ; p A  ...
12
12
12
2
2
0
pC-9  ; pC-8  ; p A-7  ...
12
12
12
1
0
0
pG-9  ; pG-8  ; pG-7  ...
12
12
12
8
9
0
pT-9  ; pT-8  ; pT-7  ...
12
12
12
p A-9 
•If you identify a portion of the promoter region that is bound by these
two TF’s, the identity of different nucleotides at different positions
within the motif will be to some extend random
•For a specific position in the motif, multinomial model for
probability of occurrence of a specific nucleotide is:
p( N 9 )  pN9 ~ MULT( p A9 , p A9 , p A9 , p A9 ,1)
• The product-multinomial model for probability of a whole sequence
recognized by these TFs (assuming the independence between
different positions in the motif) is:
9
8
8
9
p( N N ... N N ) 
9
p
i  9
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i
Ni
22
Stochasticity of Protein Folds
• 3D Protein structure is often considered as the ultimate determinant of its function
• It turns out that a more accurate description of the 3D protein structure is a probability distribution over different possible
confirmations. In some cases major features of the structure are preserved across a whole set of highly probably
conformation. However, in some cases the
• The differences and the uncertainties related to the 3D protein structure are due to thermodynamic fluctuations which are
themselves inherently stochastic
1MBA
1-3-2004
1AEY
1B8Q
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Estimating Model Parameters from Data
LR ~ N (μ, σ 2 )
• Model parameters represent “population” properties
of our measurements.
• The conclusions about the phenomenon under
investigation are made in terms of (unknown)
population parameters
• Example: is the log-ratio of expression measurements
for a gene between two different types of biological
samples on average greater than zero? (i.e. >0)

-2
0
2

4
6
LR
• Actual measurements (sample) are used to calculate sample-parameters that are used as
estimates of population parameters
• Example: if we have n replicated microarray experiment, the average of observed log-ratios can
be used to estimate the underlying population mean
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