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PhD Program in Computational Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, April 29-May 2, 2008
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Cell-cycle microarray analysis
Lars Juhl JensenEMBL Heidelberg
microarrays 101
RNA levels
all genes at once
two technologies
mechanical spotting
cDNAs
ESTs
oligomer probes
photolithography
Affymetrix
two types of data
one-channel
two-channel
normalization
noise vs. bias
real-world example
DownloadedSMD data
After intensitynormalization
Spatial biasestimate
After spatialnormalization
cell-cycle expression
cell cultures
synchronization
isolate mRNA
microarrays
time courses
expression profiles
Cho et al.
visual inspection
Spellman et al.
Fourier score
Zhao et al.
single-pulse model
Johansson et al.
partial least squares
Langmead et al.
rhythmic analysis
Wichert et al.
Fisher’s G-statistic
Luan et al.
Luan et al.
cubic-splines model
Lu et al.
periodic-normal mixture
de Lichtenberg et al.
dual permutation test
Willbrand et al.
up-down patterns
Ahdesmäki et al.
Fisher’s G-statistic
Chen
Fisher’s G-statistic
Qiu et al.
resynchronization
Glynn et al.
Lomb-Scargle periodogram
Andersson et al.
Bayesian detector
Ahnert et al.
low entropy patterns
Xu et al.
partial energy ratio
Lu et al.
homology transfer
Liew et al.
Fisher’s G-statistic
Morton et al.
cyclohedron test
Rowicka et al.
correlation to known genes
things to consider
change
periodicity
shape
loss of synchrony
stress response
uneven sampling
missing data points
multiple experiments
one (ranked) list