RESOURCES

Function Assessment Tools and Databases

Category	Resource [Reference]	Prediction Target
Protein Coding	PolyPhen [1]	deleterious missense SNP
	SIFT [2]
	SNPeffect [3]
	SNPs3D [4]
	LS-SNP [5]
	Ensembl [6]	nonsense SNPs, missense SNPs
Splicing Regulation	ESEfinder [7]	exonic splice sites
	RescueESE [8]
	ESRSearch [9]
	PESX [10]
	Ensembl [6]	intronic splice sites
Transcriptional Regulation	TFSearch [11]	transcription factor binding sites
	Consite [12]	transcription factor binding sites
	GoldenPath [13]	microRNA targets, cpgIslands, and other potential regulatory regions
	Ensembl [6]	regulatory regions
Post Translation	KinasePhos [14]	phosphorylation sites
	OGPET [15]	O-glycosylation sites
	Sulfinator [16]	tyrosine sulfination sites
Conserved	GoldenPath [13]	conserved genomic regions between multiple species

SNP/Gene/Disease Annotation Databases

Resource [Reference]	Downloaded Dataset (Downloaded Date)
dbSNP [17]	dbSNP Build 126 (Apr. 2007) SNP to Entrez mapping (Mar. 2007)
Ensembl [6]	Ensembl Homo Sapiencs Core, Variation 45_36 (Mar. 2007)
Genes and Disease [18]	Disease Category, Disease Info (Jul. 2007)
OMIM [19]	OMIM Gene Map (June, 2007)

Cross-Referenced Databases / Web Services

Resource [Reference]	Web URL
dbSNP [17]	http://www.ncbi.nlm.nih.gov/projects/SNP/
NCBI Map View	http://www.ncbi.nlm.nih.gov/mapview/
Ensembl SNP	http://www.ensembl.org/
Ensembl Contig	http://www.ensembl.org/Homo_sapiens/
USCS Genome Browser [20]	http://genome.ucsc.edu/
HapMap [21]	http://www.hapmap.org/
GeneCard [22]	http://www.genecards.org/
OMIM [19]	http://www.ncbi.nlm.nih.gov/omim/

References

[1]	Ramensky, V. and Sunyaev, S. (2002) Human nonsynonymous SNPs: server and survey. Nucleic Acid Research, 30, 3894–3900.
[2]	Ng, P. and Henikoff, S. (2001) Predicting deleterious amino acid substitutions. Genome Research, 11, 863–874.
[3]	Reumers, J., Schymkowitz, J., Ferkinghoff-Borg, J., Stricher, F., Serrano, L., and Rousseau, F. (2005) SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acid Research., 33 (Database issue), D527–532.
[4]	Yue, P., Melamud, E., and Moult, J. (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics, 7, 166.
[5]	Karchin, R. et al. (2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics, 21(12), 2814–2820.
[6]	Hubbard, T. J. P., Aken, B. L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., et al. (2007) Ensembl 2007. Nucleic Acids Research, 35(Database issue).
[7]	Cartegni, L., Wang, J., Zhu, Z., Zhang, M. Q., and Krainer, A. R. (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Research, 31(13), 3568–3571.
[8]	Yeo, G. and Burge, C. B. (2004) Variation in sequence and organization of splicing regulatory elements in vertebrate genes. In the Proceeding of Proc. Natl. Acad. Sci., 101(44), 15700–15705. 5
[9]	Fairbrother, W. G., Yeh, R. F., Sharp, P. A., and Burge, C. B. (2002) Predictive identification of exonic splicing enhancers in human genes.. Science, 297, 1007–1013.
[10]	Zhang et al. (2005) Exon inclusion is dependent on predictable exonic splicing enhancers. Molecular and Cellular Biology, 25(16), 7323–7332.
[11]	Akiyama, Y. (1998) TFSEARCH: Searching Transcription Factor Binding Sites. WEB URL: http://www.rwcp.or.jp/papia/,. /td>
[12]	Sandelin, A., Wasserman, W. W., and Lenhard, B. (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Research, 32(Web Server issue), W249–252.
[13]	Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J. and others. The UCSC Genome Browser Database. Nuclelic Acids Research, 31(1), 51-54.
[14]	Huang, H., Lee, T., Tseng, S., and Horng, J. (2005) Kinasephos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Research, 33(Web server issue), W226–229
[15]	Gerken, T., Tep, C., and Rarick, J. (2004) The role of peptide sequence and neighboring residue glycosylation on the substrate specificity of the uridine 5’-diphosphate-alpha-n-acetylgalactosamine:polypeptide n-acetylgalactosaminyl transferases t1 and t2: kinetic modeling of the porcine and canine submaxillary gland mucin tandem repeats. Biochemistry, 43, 9888–9900.
[16]	Monigatti, F., Gasteiger, E., Bairoch, A., and Jung, E. (2002) The sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics, 18, 769– 770.
[17]	Sherry, S., Ward, M., Kholodov, M., Baker, J., Phan, L., Smigielski, E., and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29, 308–311.
[18]	National Library ofMedicine, N. C. f. B. I. (2002) The NCBI handbook - genes and disease. World Wide Web URL: http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html Bethesda, MD, USA .
[19]	McKusick-Nathans Institute ofGenetic Medicine, J. H. U. and National Center forBiotechnology Information, N. L. o. M. Online Mendelian Inheritance in Man, OMIM (TM). WEB URL: http://www.ncbi.nlm.nih.gov/omim/,.
[20]	Kuhn, R., Karolchik, D., Zweig, A., Trumbower, H., Thomas, D., Thakkapallayil, A., Sugnet, C., Stanke, M., Smith, K., Siepel, A., et al. (Jan, 2007) The ucsc genome browser database: update 2007. Nucleic Acids Research, 35(Database issue), D668–73.
[21]	The International HapMap Consortium. (2003) The International HapMap Project. Nature, 426, 789–796.
[22]	Rebhan, M., Chalifa-Caspi, V., Prilusky, J., and Lancet, D. (1997) Genecards: encyclopedia for genes, proteins and diseases. World Wide Web URL: http://www.genecards.org/ Weizmann Institute of Science, Bioinformatics Unit and Genome Center, Rehovot, Israel.