Center for Genome Dynamics Mouse SNPDatabase

User Documentation

This help document answers the following questions:

• What type of information can I get from CGD SNPdatabase?
• what search terms are acceptable in the search engine?
• How do I use this search engine?

What type of information can I get from CGD SNPdatabase?

• SNP-gene association (nearest genes,gene type)
• SNP-transcript association
• SNP-EXON association (exon rank,terminal exons,internal exons,...)
• SNP-functional implication (stop gained,stop lost, coding synonymous,...)
• SNP-type (Transition, Transversion)
• SNP-CpG site association
• SNP-Amino-Acid characteristics (Symbol, Chemical Characteristics, Hydropathy Index, Structure)
• SNP- Amino-Acid substitution frequency(Conservative, or not Conservative, NCBI Blosum62 score)
• SNP location (Intergenic,Intron,Exon,UTRs,...)
• SNP quality (conflict between sources,bad cluster windows,..)
• SNP minor allele frequency

What search terms are acceptable in the search engine?

Our Mouse SNP Search Engine takes the following terms:

• SNPaccession ID
• Ensembl Genes i.e ENSMUSG00000053211
• Ensembl Transcripts i.e ENSMUST00000065545
• MGI gene_accessions i.e MGI:99213
• MGI gene_symbols i.e Zfy1
• Single base pair SNP(chromosome:bp_position) i.e 4:20266796
• Base pair range SNPquery i.e 4:20231103-20575856
• Perlegen SNP IDs i.e NES08626062
• Broad SNP IDs i.e mm33-2-87850569
• GNF SNP IDs i.e GNF3-011603
• dbSNPrs IDs i.e rs13476298
• SS IDs i.e 38506440

How do I use this search engine?

Simple query

Input data	Data Description	Data format
Single/multiple SNPAccession ID	SNPSubmitter Id(s) . Consecutive entries are separated by a semicolon character	Perlegen IDs : NES15244502,NES15244487 Broad IDs : mm33-10-7389447, mm33-10-7392281 GNF IDs : GNF3-078615, GNF3-078614 SS IDs : 38506440 , 38506439 rs IDs
Single/Multiple base pair positions (Format: chromosome:bp_position)	Multiple base pair position on same chromosome or on different chromosomes. Consecutive entries are separated by a semicolon(;) character	Single positon on chromosome 10 :10:7458402 Multiple positions on chromosome 10 :10:7458402; 10:7471201; 10:7471222 Multiple positions on different chromosomes: 10:7458402 ; 1:7407367; x:7402193 Single Range query on chromosome X :x:7400000-7500000 Multiple Range queries on different chromosomes : x:7400000-7500000;10:7400000-7500000 Mixed : x:7400000-7500000; 1:7407367 ; 10:7400000-7500000
Single/multiple Gene ID, or Symbol	Ensembl geneid ; MGI gene symbol. Consecutive entries are separated by a commas character	Single Ensembl Gene Id :ENSMUSG00000031171 Multiple Ensembl Gene Ids :ENSMUSG00000031171; ENSMUSG00000031170 Single MGI Gene Symbol : Slc38a5 Multiple MGI Gene Symbol : Ftsj1;Slc38a5 Single/Multiple MGI Gene Id(s) Single/Multiple Entrez Gene Id(s) : Coming soon
Single/multiple Ensembl transcript ID(s)	Using Ensembl transcript(s) to query for SNPs. Consecutive entries are separated by commas character	Single Ensembl Transcript Id :ENSMUST00000033513 Multiple Ensembl Transcript Ids :ENSMUST00000033513; ENSMUST00000033512
What additional features should we implement?
Single/multiple Ensembl protein ID(s)	Using Ensembl protein ID(s) to query for SNPs	Consecutive entries are separated by a semicolon character
Single/multiple MGI phenotype term ID(s)	Using MGI phenotype term ID(s) to query for SNPs	Consecutive entries are separated by a semicolon character
Single/multiple MGI phenotype term(s)	Using MGI phenotype term(s) to query for SNPs	Consecutive entries are separated by a ";" character
Single/multiple GO term ID(s)	Using GO term ID(s) to query for SNPs	Consecutive entries are separated by a semicolon character
Single/multiple GO term(s)	Using GO term(s) to query for SNPs	Consecutive entries are separated by a ";" character

File upload

Input data	Data Description	Data format
A list of single SNP IDs	A file containing a list of single base pair position on the genome. One entry per line	chromosome:bp_position
A list of Ensembl Gene IDs	A file containing a list of Ensembl geneids	One entry per line
A list of Entrez Gene IDs	A file containing a list of Entrez geneids	One entry per line
A list of MGI Gene IDs	A file containing a list of MGI geneids	One entry per line
A list of MGI Gene symbols	A file containing a list of MGI Gene symbols	One entry per line
A list of MGI phenotype term IDs	A file containing a list of MGI phenotype term IDs	One entry per line
A list of MGI phenotype terms	A file containing a list of MGI phenotype terms	One entry per line
A list of GO term IDs	A file containing a list of GO term IDs	One entry per line
A list of GO terms	A file containing a list of GO terms	One entry per line