SPIKE

1
SPIKE

• Signaling Pathway Integrated Knowledge Engine

Rita Vesterman Nira Amit Igor Ulitsky
Jackie Assa Rani Elkon Ron Shamir Yossi Shiloh
2
SPIKE - Modules

• Database for regulatory interactions
• Visualization module
• Constructs graphical pathway maps based on the
  information stored in the database
• Algorithmic Engine
• Analyze the networks to gain new functional links

3
(No Transcript)
4
(No Transcript)
5
(No Transcript)
6
SPIKE Visualization Module
7
ATM Map
8
p53 Map
9
MAPK Map
10
TLR Map
11
G2-M network
12
SPIKE - Data

• Three main sources
• Regulatory interactions manually curated and
  uploaded by SPIKEs users ( 800 high quality
  regulations)
• External signaling pathway DBs (KEGG, Reactome)
• Protein-protein interactions derived from
  high-throughput proteomic screens (2-Hyb, CoIP
  etc. 15K interactions, noisy data, low
  integrity)
• The user set the minimal integrity level to be
  included in the analysis (default only high
  integrity)

13
SPIKE Data (II)

• Curated data currently focus on interactions
  related to DNA damage, cell cycle and stress
  responses.
• Human
• Populating the DB - collaborative effort in order
  to keep the DB up-to-date and comprehensive
• contributed by SPIKE users
• supervised by SPIKE curators

14
(No Transcript)
15
(No Transcript)
16
(No Transcript)
17
(No Transcript)
18
(No Transcript)
19
(No Transcript)
20
(No Transcript)
21
(No Transcript)
22
(No Transcript)
23
(No Transcript)
24
Algorithmic Engine

• Designed to include advanced graph-theory and
  statistical algorithms for network analysis
• Currently implemented
• Path Finding
• Interconnections within a set of proteins
• Enriched Maps

25
SPIKE Create New Regulation
26
(No Transcript)
27
(No Transcript)
28
(No Transcript)