Bioinformatics

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Bioinformatics
One of many definitions Computer assisted use of
large databases for
biomedical purposes
I. Data structures data mining use of
web-based environments
II. Sequence analyses genomics and proteomics
III. Pathways and networks information
retrieval flux analyses
IV. Statistics maximum likelihood and
probabilistic methods
AS APPLIED TO BIOLOGY-DRIVEN QUESTIONS
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THE LIFE CYCLE OF DICTYOSTELIUM DISCOIDEUM
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K-means clustering 5 groups
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Clustering of developmentally regulated genes
Early genes
Middle genes
Late genes
Downers
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Curve fitting
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EXPRESSION PERIODS FOR MARKER GENES
KP
BOTH
AX4
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Prestalk cells
Dependent Sequence in Dictyostelium
Development
ecmA
tagB
Stalk cells
tagC
yakA
Gbg
pufA
GBF
ecmB
acrA
carA
Prespore cells
acaA
pkaC
spiA
LagC
mybC
stkA
csaA
CRAC
cotA
Spores
CAR3
csbA
Pia
cotB
RegA
ZAK1
ERK2
cotC
GSK3
Ga2
PKA
PKA
Precocious cessation of transcription
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Genes induced by cAMPbut not by PKA
SLK857
Prespore specific genes
SSL490
mybC
cAMP acting independently of
PKA
SLE837
acbA
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MybC Dependent Prespore Genes
gadA
SSA273
wacA
SSJ886
SLK857
SSB695
SSL490
SLD184
cAMP
mybC
SSG693
acbA
SLB103
spiA
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Bioinformatics
AS APPLIED TO THE GENETICS AND CELL BIOLOGY OF
DICTYOSTELIUM
I. Data structures-gt mapping and genomic
sequencing
II. Sequence analyses-gt annotation
III. Pathways and networks-gt microarray gene
expression
IV. Statistics-gt curve-fitting
Challenges for the future 1) apply to other
complex systems 2) predict experimental
outcomes 3) recognize higher order complexity
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QUESTIONS
ANSWERS
Many but not all are shared cAMP and peptide
signals A few genes recognized so
far Bioinformatics may not tell