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Lars Juhl Jensen
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SEMM, IFOM, Milan, Italy, June 15-16, 2006
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Protein networks as a scaffold for structuring other data
1.
Protein networks as
a scaffold for structuring other data Lars Juhl Jensen EMBL Heidelberg
2.
cell cycle regulation
3.
4.
Chapter 1
5.
interaction networks
6.
what is an
interaction?
7.
functional interactions
8.
physical interactions
9.
yeast two-hybrid
10.
complex pull-down
11.
12.
high-throughput
13.
S. cerevisiae
14.
Uetz et al.
15.
Ito et al.
16.
Gavin et al.
17.
Ho et al.
18.
Gavin et al.
19.
Krogan et al.
20.
C. elegans
21.
Li et al.
22.
D. melanogaster
23.
Giot et al.
24.
H. sapiens
25.
Stelzl et al.
26.
Rual et al.
27.
28.
yeehaa!
29.
network topology
30.
degree distribution
31.
32.
scale-free
33.
34.
hubs
35.
essentiality
36.
network robustness
37.
targeted attacks
38.
artefacts
39.
self-activating baits
40.
highly expressed proteins
41.
Han et al.
42.
43.
can we trust
this data?
44.
the human interactome
45.
(incomplete)
46.
yeast two-hybrid
47.
1936 13 4
4 1385 65 18465 Stelzl et al. Rual et al. Small-scale studies
48.
32 0 3
4 18 4 23 Stelzl et al. Rual et al. Small-scale studies
49.
62 8 39
Small-scale studies Stelzl et al. Rual et al. 852 17 473 432 69 260
50.
3.5% and 21%
sensitivity
51.
the yeast interactome
52.
five years ago
53.
yeast two-hybrid
54.
1150 117 117
72 4053 118 4469 Uetz et al. Ito et al. Small-scale studies
55.
162 53 34
72 180 29 338 Uetz et al. Ito et al. Small-scale studies
56.
511 189 616
Small-scale studies Uetz et al. Ito et al. 439 178 759 897 190 1347
57.
19% and 12%
sensitivity
58.
three years ago
59.
complex pull-down
60.
14186 784 1178
287 19492 230 3475 Gavin et al. Ho et al. Small-scale studies
61.
2341 125 656
287 2725 42 149 Gavin et al. Ho et al. Small-scale studies
62.
4431 1465 5041
Small-scale studies Gavin et al. Ho et al. 14913 1071 632 8047 517 746
63.
63% and 41%
sensitivity
64.
what about accuracy?
65.
66.
67.
30–50% specificity
68.
what can we
do about it?
69.
topology-based scoring
70.
complex pull-down
71.
log[(N 12 ·
N)/((N 1 +1) · (N 2 +1))]
72.
yeast two-hybrid
73.
-log((N 1 +1)
· (N 2 +1))
74.
calibrate against KEGG
75.
76.
subcellular localization
77.
78.
filtering
79.
high-throughput
80.
81.
high-confidence
82.
Chapter 2
83.
expression data
84.
S. cerevisiae
85.
86.
synchronized cell culture
87.
microarray time series
88.
89.
periodically expressed genes
90.
91.
S. cerevisiae
92.
Cho et al.
93.
Spellman et al.
94.
yeehaa!
95.
Zhao et al.
96.
Langmead et al.
97.
Johansson et al.
98.
Wichert et al.
99.
Luan and Li
100.
Lu et al.
101.
Ahdesm äki et
al.
102.
Willbrand et al.
103.
Chen et al.
104.
Qiu et al.
105.
Ahnert et al.
106.
Andersson et al.
107.
no benchmarking
108.
reanalysis
109.
benchmarking
110.
111.
no progress
112.
no benchmarking
113.
114.
Chapter 3
115.
1+2 = 3
116.
expression data
117.
118.
protein interactions
119.
120.
temporal network
121.
122.
benchmarking
123.
124.
125.
very low error
rate
126.
discovery tool
127.
128.
30+ uncharacterized proteins
129.
detailed function prediction
130.
novel module
131.
132.
global statements
133.
dynamic and static
134.
135.
136.
CDK–cyclin complexes
137.
138.
consistent timing
139.
140.
141.
pre-replication complex
142.
143.
just-in-time assembly
144.
145.
how can we
test this?
146.
evolutionary conservation
147.
Chapter 4
148.
more expression data
149.
S. cerevisiae
150.
microarray time series
151.
152.
periodically expressed genes
153.
154.
S. pombe
155.
Rustici et al.
156.
(good job)
157.
Peng et al.
158.
Oliva et al.
159.
no benchmarking
160.
no integration
161.
reanalysis
162.
benchmarking
163.
164.
no progress
165.
no benchmarking
166.
no integration
167.
168.
H. sapiens
169.
Whitfield et al.
170.
reanalysis
171.
benchmarking
172.
173.
A. thaliana
174.
Menges et al.
175.
reanalysis
176.
benchmarking
177.
178.
list of genes
179.
peak times
180.
Chapter 5
181.
cross-species comparison
182.
orthology assignment
183.
peak times
184.
not comparable
185.
time warping
186.
187.
188.
not conserved
189.
individual genes
190.
just-in-time assembly
191.
protein complexes
192.
DNA polymerases
193.
194.
pre-replication complex
195.
196.
chromatid cohesion
197.
198.
reproduces what is
known
199.
known differences
200.
timing has changed
201.
identity has changed
202.
self-consistent
203.
make sense
204.
protein complexes
205.
individual genes
206.
broader perspective
207.
protein networks
208.
context
209.
understanding
210.
Acknowledgments Ulrik de
Lichtenberg Thomas Skøt Jensen Christian von Mering Søren Brunak Peer Bork
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