spot.cgsmd.isi.edu

SNP Prioritization submit

For help. Please contact us. If you have any comments or suggestions. You can watch the video. Of SPOT in action. SNPs only, no p. Maximum SNPs to output:. Prioritization of specific genes and other genomic regions. Linkage Disequilibrium (LD) options. Do not use LD proxies:. CEU: European American (CEPH). ASW: African American (Southwest USA). CHB: Chinese (Beijing, China). CHD: Chinese (Denver, Colorado). GIH: Gujarati Indians (Houston, Texas). JPT: Japanese (Tokyo, Japan). LWK: Luhya (Webuye, Kenya).

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SNP Prioritization submit | spot.cgsmd.isi.edu Reviews

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For help. Please contact us. If you have any comments or suggestions. You can watch the video. Of SPOT in action. SNPs only, no p. Maximum SNPs to output:. Prioritization of specific genes and other genomic regions. Linkage Disequilibrium (LD) options. Do not use LD proxies:. CEU: European American (CEPH). ASW: African American (Southwest USA). CHB: Chinese (Beijing, China). CHD: Chinese (Denver, Colorado). GIH: Gujarati Indians (Houston, Texas). JPT: Japanese (Tokyo, Japan). LWK: Luhya (Webuye, Kenya).

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1 quick run

2 user's guide

3 click

4 snp prioritization project

5 snps and p

6 values

7 upload method

8 file

9 enter manually

10 options

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quick run,user's guide,click,snp prioritization project,snps and p,values,upload method,file,enter manually,options,value threshold,use all snps,hapmap sample,threshold,additional options,ecr factor,frameshift,nonsense,5' splice,3' splice,missense,5' utr

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SNP Prioritization submit | spot.cgsmd.isi.edu Reviews

https://spot.cgsmd.isi.edu

For help. Please contact us. If you have any comments or suggestions. You can watch the video. Of SPOT in action. SNPs only, no p. Maximum SNPs to output:. Prioritization of specific genes and other genomic regions. Linkage Disequilibrium (LD) options. Do not use LD proxies:. CEU: European American (CEPH). ASW: African American (Southwest USA). CHB: Chinese (Beijing, China). CHD: Chinese (Denver, Colorado). GIH: Gujarati Indians (Houston, Texas). JPT: Japanese (Tokyo, Japan). LWK: Luhya (Webuye, Kenya).

INTERNAL PAGES

spot.cgsmd.isi.edu

1

ECR node scoring parameters

https://spot.cgsmd.isi.edu/doc/ecr_scoring.html

2

Maximum SNPs to output documentation

https://spot.cgsmd.isi.edu/doc/snp_output_threshold.html

Only this number of SNPs will be used in the output table. The top SNPs ranked by weighted p-value (or GIN prioritization score if the option Do not use p-values is selected) will be selected for the output table. Reducing this number will decrease processing time as well as the size of the downloadable SNP output file. The value must be a number greater than 0.

3

Custom Gene documentation

https://spot.cgsmd.isi.edu/doc/custom_gene.html

Here you can tell SPOT to how to prioritize specific genes. Genes are entered using an exact symbol or numeric ID, or by using various types of queries that retrieve multiple genes. In addition to genes, you may prioritize genomic regions and specific SNPs. See the user's guide for more information.

4

SNPs and p-values documentation

https://spot.cgsmd.isi.edu/doc/snp_pValues.html

Enter a list of SNP IDs and (optionally) p. Values from a genetic association study. SPOT will prioritize these by combining evidence of association with information from biological databases. NOTE: there must be no duplicate SNP IDs in this list.

5

No p-values

https://spot.cgsmd.isi.edu/doc/no_pvalues.html

When this option is selected p-values are ignored (and can be omitted) and the SNPs are ranked by the GIN prioritization instead of the weighted p-value.

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SNP Prioritization submit

For help. Please contact us. If you have any comments or suggestions. You can watch the video. Of SPOT in action. SNPs only, no p. Maximum SNPs to output:. Prioritization of specific genes and other genomic regions. Linkage Disequilibrium (LD) options. Do not use LD proxies:. CEU: European American (CEPH). ASW: African American (Southwest USA). CHB: Chinese (Beijing, China). CHD: Chinese (Denver, Colorado). GIH: Gujarati Indians (Houston, Texas). JPT: Japanese (Tokyo, Japan). LWK: Luhya (Webuye, Kenya).

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