PMID- 23282018
OWN - NLM
STAT- MEDLINE
DCOM- 20130612
LR  - 20211021
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 13 Suppl 7
IP  - Suppl 7
DP  - 2012
TI  - Discovering pathway cross-talks based on functional relations between pathways.
PG  - S25
LID - 10.1186/1471-2164-13-S7-S25 [doi]
AB  - BACKGROUND: In biological systems, pathways coordinate or interact with one 
      another to achieve a complex biological process. Studying how they influence each 
      other is essential for understanding the intricacies of a biological system. 
      However, current methods rely on statistical tests to determine pathway 
      relations, and may lose numerous biologically significant relations. RESULTS: 
      This study proposes a method that identifies the pathway relations by measuring 
      the functional relations between pathways based on the Gene Ontology (GO) 
      annotations. This approach identified 4,661 pathway relations among 166 pathways 
      from Pathway Interaction Database (PID). Using 143 pathway interactions from PID 
      as testing data, the function-based approach (FBA) is able to identify 93% of 
      pathway interactions, better than the existing methods based on the shared 
      components and protein-protein interactions. Many well-known pathway cross-talks 
      are only identified by FBA. In addition, the false positive rate of FBA is 
      significantly lower than others via pathway co-expression analysis. CONCLUSIONS: 
      This function-based approach appears to be more sensitive and able to infer more 
      biologically significant and explainable pathway relations.
FAU - Hsu, Chia-Lang
AU  - Hsu CL
AD  - Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 
      Taiwan.
FAU - Yang, Ueng-Cheng
AU  - Yang UC
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20121213
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (Receptors, Lysosphingolipid)
RN  - EC 3.6.5.2 (rhoA GTP-Binding Protein)
SB  - IM
MH  - *Algorithms
MH  - Computational Biology
MH  - Databases, Factual
MH  - Humans
MH  - Metabolic Networks and Pathways
MH  - Protein Interaction Maps
MH  - Receptors, Lysosphingolipid/metabolism
MH  - Signal Transduction
MH  - rhoA GTP-Binding Protein/metabolism
PMC - PMC3521217
EDAT- 2013/01/11 06:00
MHDA- 2013/06/13 06:00
PMCR- 2012/12/07
CRDT- 2013/01/04 06:00
PHST- 2013/01/04 06:00 [entrez]
PHST- 2013/01/11 06:00 [pubmed]
PHST- 2013/06/13 06:00 [medline]
PHST- 2012/12/07 00:00 [pmc-release]
AID - 1471-2164-13-S7-S25 [pii]
AID - 10.1186/1471-2164-13-S7-S25 [doi]
PST - ppublish
SO  - BMC Genomics. 2012;13 Suppl 7(Suppl 7):S25. doi: 10.1186/1471-2164-13-S7-S25. 
      Epub 2012 Dec 13.