SUPPLEMENTARY MATERIALS
Figure S1 Process Diagram of Semi-auto Data Retrieval from External Data Sources
Table S1. Integrated external databases
Integrated Databases
NCBI Genbank
NCBI Homologene
NCBI PubMed
Gene Ontology
UniProt
PDB
Ensembl
BIND
Description
Gene information
Collection of groups of homolog sequences
Collection of biomedical literature citations and
abstracts
Gene annotations
Protein information
Protein structure
Annotation of large eukaryotic genomes
Molecular interactions
Literature cited
[1]
[2]
[2]
[3]
[4]
[5]
[6]
[7]
[1] Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2006) GenBank. Nucleic Acids Res., 34,
D16-D20.
[2] Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R.,
Federhen,S. et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids
Res., 34, D173-D180.
[3] Gene Ontology Consortium. (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11,
1425-1433.
[4] Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H.,
Lopez,R. et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic Acids Res., 34, D187-D191.
[5] Deshpande,N., Addess,K.J., Bluhm,W.F., Merino-Ott,J.C., Townsend-Merino,W., Zhang,Q., Knezevich,C., Xie,L.,
Chen,L. Feng,Z. et al. (2005) The RCSB Protein Data Bank: a redesigned query system and relational database based
on the mmCIF schema. Nucleic Acids Res., 33, D233-D237.
[6] Birney,E., Andrews,D., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cox,T., Cunningham,F., Curwen,V., Cutts,T. et al.
(2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
[7] Alfarano,C., Andrade,C.E., Anthony,K., Bahroos,N., Bajec,M., Bantoft,K., Betel,D., Bobechko,B., Boutilier,K.,
Burgess,E. et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids
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Figure S2 Animated TLR Signaling Pathways
Descriptions of labels in the Figure S2 are listed in the below:
Steps to run the animated signaling pathway
1 Choose the ligands
2 Click here to show the pathway components
3 Click here to start the simulation
Description of functionality of the buttons
A Click one of the button to set status of the selected pathway component.
 WT: set the status of the component as wild type
 M: set the status of the component as mutant
 KO: set the status of the component as knockout
B Click to view details of mutant/knockout phenotype
C Click to view description of the selected pathway component