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1. Functional genomics, sequencing and micrioarray technologies, October 18th, 2007
2. Design of microarray experiments, November 1st, 2007
3. Microarray data QC, normalization, and data correction, November 15th, 2007
4. Unsupervised (hypothesis-free) analysis of microarray experiments, November 29th, 2007
5. Types of hypothesis and hypothesis based analysis of microarray experiments, December 13th, 2007
6. Full genome (tiling) arrays and identification of induced genome elements, December 27th, 2007
7. Analysis of CHIP-on-chip array experiments, January 10th, 2008
8. Association of physiological/clinical measurements and microarray data, January 24th, 2008
9. Static networks of gene expression regulation, February 7th, 2008
10. Dynamic network simulation for gene expression regulation, February 21st, 2008
11. Functional genomics through high-throughput sequencing; QC of reads/flowgrams, March 6, 2008
12. Methods of genome assembly from short reads/flowgrams, March 20th, 2008
13. Methods of automatic genome annotation, April 3d, 2008
14. Comparative analysis of genomes, April 17th, 2008
15. Drugs, chemical libraries, library diversification, and clustering of small molecules, May 1st, 2008
16. High-throuput screening and dose response activity of a small molecule, May 15th, 2008
17. Pharmacophor identification and library screening, May 29th, 2008
18. Identification of protein 3D structure active sites, June 12th, 2008
19. Docking of a ligand into protein's active site, June 26th, 2008
Array designs
Uses of tiling array
Ru-Fang Yeh: Lectures on statistical methods in bioinformatics, lecture7: Tiling Arrays, UCSF, BMI209 fall07
Probe signals across gene region
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AS
Discovery of novel transcription sites using whole-genome tiling microarrays
Tiling microarrays could be successfully applied for discovery of novel sitesof active transcription that lie within the ‘dark matter’ in genomes.
• Sequence-based computational gene prediction - not sufficient for accurate gene structuredetermination and/or identification of all transcription units of an organism.
• Cloning and sequencing of cDNA molecules corresponding to expressed gene products -misses very low abundance and non-polyadenylated (polyA) transcripts.
• cDNA collections are often biased to transcripts that are expressed in response to a specific physiological or environmental condition(s).
• Tiling array expression studies in Arabidopsis identified a large number of novel sites of active gene expression missed by computational gene prediction algorithms and cDNAcollections (Yamada et al, Science 2003, 302:842-846 ).
• This tiling array study was able to capture a number of novel transcripts originating in centromeric regions, which were previously thought to be mostly devoid of active gene expression.
• Tiling array indica rice studies (Li et al, Nat Genet 2006, 38:124-129) identified a large number of novel sites of active gene expression never before annotated in this model crop genome.
Yazaki et al, Mapping the genome landscape using tiling array technology, Curr Opin Plant Biol. 2007
Non-coding RNAs (ncRNAs) in intergenic regionsIdentification of their expression by tiling array hybridizations
Transcription of the ncRNA, which is located in the
promoter region of an ORF blocks the binding of transcription factors and/or RNAPII necessary for proper gene expression from this locus.
A number of ncRNAs increase expression in the absence of DNA methylation. Thus, the over-expression of these ncRNAs
may be a biproduct of the loss of DNA methylation, which when present would silence expression from these loci.
Yazaki et al, Mapping the genome landscape using tiling array technology, Curr Opin Plant Biol. 2007
Small interfering RNA (siRNA)Anti-sense transcripts can regulate neighboring genes
through formation of regions of dsRNA that subsequently recruit various RNA silencing pathways
Over-lapping anti-sense gene productsregulate P5CDH levels during response to salt stress in Arabidopsis.
•Salt stress conditions induce expression of SRO5, a gene of unknown function.
•The 3’ ends of the SRO5 and P5CDH transcripts overlap, thereby forming a region of dsRNA.
•This dsRNA region initiates a series of siRNAprocessing steps that ultimately result in the downregulation of P5CDH in response to salt stress.
P5CDH is expressed under normal Arabidopsis growth conditions.
Yazaki et al, Mapping the genome landscape using tiling array technology, Curr Opin Plant Biol. 2007
The probe signals along genome: How to identify significantly upregulated fragments (exons )?
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AS-signal
The probe signals along genome: How to detect if a portion of antisense RNA is significantly upregulated?
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A_antisense_RNA
Repetitive probe measurements
MAT: GCRMA-like sequence dependent non-specific probe affinityA regression of the log-signal against probe sequence and probe repetitiveness
W. Evan Johnson et al, Model-based analysis of tiling arrays (MAT), PNAS, 2006
Royce et al, Assessing the need for sequence based normalization in tiling microarray experiments, Bioinformatics,2007
MAT: Expected non-specific probe affinity
W. Evan Johnson et al, Model-based analysis of tiling arrays (MAT), PNAS, 2006
MAT: Standardization of probe signals
W. Evan Johnson et al, Model-based analysis of tiling arrays (MAT), PNAS, 2006
MAT: Detection of activated regions
W. Evan Johnson et al, Model-based analysis of tiling arrays (MAT), PNAS, 2006
MAT: Detection of activated regions by sliding window
Sliding window
MAT: FDR approved score for windows
1.Cover the genome by non-overlaping windows (600 bp)
and get distribution of scores
2. Reflect left part of the distribution over it’s median
3. Ratio of two tails beyond the cutoff is the False
Discovery Rate the for given cutoff
Tail of the real distribution
Tail of the “null” distribution
cutoffmedian
The window-free approach:
Instead of covering the genome by windows …….
Best score fragment Third best score fragmentSecond best score fragment
Best score fragmentSecond best score fragment
The sorted by score series of non-intersecting fragments of different lengths is detected :
)( LnNNO ⋅
Leontovich AM, Brodsky LI, Gorbalenya AE (1993) Construction of the full local similarity map for two biopolymers, Biosystems, 30(1-3): 57-63.
Ricotia in Evolution CanyonRicotia vs. Arabidopsis under normoxia and
temperature stress(PhD project of O. Kossover, The Institute of Evolution, University of Haifa)
Genome fragments with significant activation:
• Arabidopsis seedling ---- 180%
• Arabidopsis adult ----------100%
• Ricotia (A-slope) ----------- 40%
• Ricotia (E-slope) ----------- 30%
Exon structure of probe activations as
detected by the window-free approach
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Chr1: E vs A significant differentiation, transposons
Ch1: Transposons
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spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
tran
spo
son
E-power
A-power
A > EE > A
Ch1: photosynthesis related genes
0
10
20
30
40
50
60
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
t
ligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
t
ph
oto
ph
oto
ph
oto
ligh
tligh
t
ligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
t
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
t
ele
ctr
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ele
ctr
ele
ctr
ligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
tligh
t
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ele
ctr
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
ph
oto
E-power
A-power
0
10
20
30
40
50
60
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
light
light
light
light
light
light
photo
photo
ele
ctr
on
ele
ctr
on
ele
ctr
on
photo
light
light
light
light
light
light
light
light
light
light
light
light
light
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
photo
photo
photo
photo
photo
light
light
light
light
light
light
light
light
light
light
light
light
light
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
photo
photo
photo
photo
photo
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
ele
ctr
on
photo
photo
photo
photo
photo
photo
photo
photo
photo
photo
photo
photo
photo
E-power
A-power
A > EE > A
Chromosome2:Selection of active fragments based on power(A) > 5
Ricotia project (Evolution Canyon)
Highly upregulated GO categories
• ATP biosysnthesis
• carbon utilization
• chlorophyll related processes
• chloroplast protein translation
• electron transport
• photosynthesis
• photosystem assembly
• response to light stimulus
• RNA elongation
• Transposons (17)
• abscisic acid mediated signaling
• actin filament-based movement
• glucose related processes
• lipid metabolic process
• phosphate transport and phosphorylation
• protein amino acid phosphorylation
• heat shock proteins
• multiple responses to stresses
• multiple negative regulations
• Transposons (43)
