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Prediction of
interactions
Gene fusion
Gene neighbours
Gene co-ocurrence
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human
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drosophila
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elegans
mouse
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phylogenies
Proteína B
Proteína A
Profiles
(phylogeny)
Expand interactions:
Using “interologs”
DIP
COG members
Predicción basada en estructura
Step 1: Building a grid for a molecule
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Surface and core regions
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CORE
VOLUME
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Convolution function:
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C ( x, y)   Score_ mobile(i  x, j )  Score_ static(i, j  y)
j 1 i 1
0 outside

Score _ m obile(i )  1 surface
4 core

0 outside
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Score _ static( j )  1 surface
- 4 core

Obtain the maximum C
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Convolution function by Fourier Transform
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C ( x, y )   Score_ m obile(i  x, j )  Score_ static(i, j  y )
j 1 i 1
F ( x)  ( Score_ m obile)
G ( y )  ( Score_ static)
F ( x)  G ( y )  (C ( x, y ))
C ( x, y )  1 ( F ( x)  G ( y ))
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Baldomero Oliva Miguel
STRING
use of database
http://string.embl.de
Gene fusion
Gene neighborhood
Gene co-expression
Text Mining
Gene co-ocurrence
GRAPH
GRAPH
Depth 2
Prediction of
metabolic
pathways
4.2.1.2
1.1.1.37
Oxalo-acetato
Malato
A-B
Fumarato
Pathway based
in common
substrates and
products
(except water)
Applications
in
proteomics
Reference
sample
RNA
extraction
Test
sample
mRNA
Reverse
transcription
Cy3-dCTP
Cy3-
cDNA-Cy3
Cy5-dCTP
Cy5-
cDNA-Cy5
-
cDNA or oligo microarray
Dr. L. Sumoy
(CRG)
Block Column Row
1
1
1
1
2
1
1
3
1
1
4
1
1
5
1
1
6
1
1
7
1
1
8
1
1
9
1
1
10
1
1
11
1
1
12
1
1
13
1
1
14
1
1
15
1
1
16
1
...
...
...
ID
F649 Median B649 Mean
gen 1
5356
240
gen 1
5472
298
gen 2
8986
279
gen 2
6729
300
gen 3
8981
318
gen 3
9287
391
gen 4
5138
358
gen 4
5438
332
gen 5
7634
356
gen 5
9056
405
gen 6
12181
701
gen 6
15159
552
gen 7
6805
243
gen 7
6715
261
gen 8
6073
319
gen 8
5041
355
...
...
...
F550 Median B550 Mean
11532
256
12293
221
12788
295
10520
364
18099
276
20459
308
11082
434
9594
257
13316
363
14402
291
16383
433
18793
263
14445
298
13874
199
12385
439
9371
335
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
metastasis
pH
4
tumor
7
tumor
metastasis
Mw
68.8
7505
4511
8401
6405
8301
28.4
2303
5201
8204
2202
7202
21.7
8201
5203
7201
7109
7004
16.8
9.1
7115
5004
Dra. A. Sierra (IRO)
Spec #1=>BC=>NR(2.00)[BP = 1211.7, 1206]
1211.6717
100
1206.4
90
80
% Int e ns it y
70
60
1906.0343
50
40
1194.6158
862.4662
1929.9591
1348.8247
30
1476.7584
20
10
0
799.0
843.5174
870.5190
1307.7049
1112.1055
1523.7867
1092.5729 1297.0594 1494.4012
1289.7267
1339.4
1863.0635
2296.0478
1939.0241
1734.9791
2265.0709
1972.0282
1718.8513
2333.0787
1944.0422
1730.9145
2138.1660 2320.5267
1919.9480
1879.8
2420.2
2718.0768
2632.7978
2642.1528
2873.6527
2951.7657
3173.1839
3112.6114 3305.1839
2901.5867
2960.6
0
3501.0
Mass (m/z )
Dr. D. Andreu (UPF)
SPOTS
aSpot
Protein Identity
Acc. No.
pI
Mr
(kDa)
Function
2202
Multicatalytic endopeptidase
complex zeta chain
P28066
4.7
26.58
Proteolysis
2303
Tyrosine3/tryptophan5
NP_006752
4.6
29.33
Transduction
4511
ATP synthase beta chain
P06576
5.3
56.53
Synthesis of ATP
Chen et al, 2001
5004
Beta-tubulin cofactor A
O75347
5.3
12.90
Complex Assembly
Perou et al., 1999
5201
Ran-BP1 (Ran binding
protein 1)
P34022
5.2
23.74
GTPase activating
____________
5203
My 032 protein
AF061735
6.6
15.82
___________
____________
6405
F-actin capping protein alpha-1
subunit
P52907
5.5
33.07
Complex Assembly
Su et al., 2001 ; Ross et al., 2000
7004
Stathmin 1
P16949
5.8
17.29
Transcription
Perou et al, 1999 ; Curmi et al, 2000 ;
Brattsand G., 2000 ; Bieche et al, 1998
7109
Familial Als mutant G37r
IAZV_A
5.9
16.12
Redox
Chandel, 2000
7115
Non-metastatic cells 1 protein
nm-23
P15531
5.8
17.31
Transcription
Su et al., 2001 ; Nakopoulou et al 1999 ;
Kapranos, 1996
7201
Thioredoxin peroxidase B
1QMV_A
5.4
21.91
Redox
Su et al., 2001 ; Perou et al., 1999; Ross et al, 2000 ;
Husbeck et al ,2001 ; Berggren 2001 et al. ;
Harvey et al , 2001
7202
Glutathione transferase
P09211
5.4
23.57
Glut. transferase
Perou et al., 1999 ; Ross et al, 2000
Dialyna et al, 2001; Ghalia et al, 2000;
Huang et al, 2000
7505
Aminoacylase 1
Q03154
5.8
46.08
Hydrolysis
Su et al., 2001 ; Perou et al., 1999 ;
Ross et al, 2000
8201
Hypothetical protein MGC15429
NP_116139
5.9
22.45
___________
_____________
8204
Peroxiredoxin3
P30048
7.1
28.05
Redox
Su et al., 2001 ; Perou et al., 1999 ;
Ross et al, 2000
8301
Carbonyl reductase 3
O75828
5.8
31.23
Redox
_____________
8401
Enolase 1
P06733
7.1
47.78
Transcription
Su et al., 2001 ; Perou et al., 1999 ;
Ross et al , 2000
No.
Differential expression
in breast cancer
Su et al., 2001 ; Perou et al., 1999 ;
Ross et al ,2000
Galectin
Tubulin  5
HSP27
STRING database
DIP database
Predicción estructural
Cathepsin D
Prdx 4
ATP synthase
Laminin R
Glyoxalase
Proteinas identificadas
Proteinas propuestas
Help to
solve 2D
page gels
Apply on
the graph
Filtering by
weight &
isoelectric
point
Explaining
biological
processes
Functional
interest
FUNCIONAL
GROUP
(GO cluster)
A
FUNCIONAL
GROUP
(GO cluster)
B