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SNP Mining from Feature Enrichment

Genes

 
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GENES
Insert gene symbols in the textbox.
The format must be comma separated values.
The text box is case insensitive.

 

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BIOLOGICAL PROCESSES
An autocompletion feature is provided to support the search: user can digit the process he is interested into and suggestions will be visualized.
The input can be part of the process name. Example: "DNA double-strand break processing" can be retrieved by inserting just some letters as "stra", and by scrolling down the input list
Once the process is selected, the system extracts each gene annotated with the related GO term.
 
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SNPS
Insert SNP names in the textbox.
The format must be comma separated values.
The text box is case insensitive.

 

       
Use Ontological Expansion
Similarity Score Threshold
Similarity Measure
   
       
Gene Flanking region  

Features Enrichment

 
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SNPs and Genes Section

Info
Available Feature Feature Properties and specific weights Feature Weight
MAF
Localization
intron
frameshift
missense
coding-synonymous
near-gene 3'
near-gene 5'
nonsense
untranslated 3'
untranslated 5'
unknown
Essential Genes  
Phylo  
Lamina associated domains  
         

Epigenetics and Transcriptional Regulations Section

Info
Available Feature Feature Properties and specific weights Feature Weight
Open Chromatin hint
Hint.
   
If you want select multiple values, press CRT and click on the value that you want to add.  
To select ALL values, select the first value and then press CRT + SHIFT + END.  
Chromatin Structure hint
Hint.
   
If you want select multiple values, press CRT and click on the value that you want to add.  
To select ALL values, select the first value and then press CRT + SHIFT + END.  
Methylation (seq regions) hint
Hint.
   
If you want select multiple values, press CRT and click on the value that you want to add.  
To select ALL values, select the first value and then press CRT + SHIFT + END.  
Methylation hint
Hint.
   
If you want select multiple values, press CRT and click on the value that you want to add.  
To select ALL values, select the first value and then press CRT + SHIFT + END.  
CPG Island  
DNase clusters  
TSS (eponine)  
CpG islands, promoters, first exons (firstEF)
FOX2 CLIP-seq  
TAF1 binding sites  
Intergenic regulatory elements
TSS (SwitchGear)  
Regulatory regions (OregAnno)
TFBS (TRANSFAC)  
TXN factor ChIP-Seq  
Enhancers (VISTA)  
       

Translation Regulations Section

Info
Available Feature Feature Properties and specific weights Feature Weight
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KNOWN ALTERNATIVE
Description of the function and values.
Alternate Promoter (altPromoter) - Transcription starts at multiple places. The altPromoter extends from 100 bases before to 50 bases after transcription start.
Alternate Finish Site (altFinish) - Transcription ends at multiple places.
Cassette Exon (cassetteExon) - Exon is present in some transcripts but not others. These are found by looking for exons that overlap an intron in the same transcript.
Retained Intron (retainedIntron) - Introns are spliced out in some transcripts but not others. In some cases, particularly when the intron is near the 3' end, this can reflect an incompletely processed transcript rather than a true alt-splicing event.
Overlapping Exon (bleedingExon) - Initial or terminal exons overlap in an intron in another transcript. These often are associated with incompletely processed transcripts.
Alternate 3' End (altThreePrime) - Variations on the 3' end of an intron.
Alternate 5' End (altFivePrime) - Variations on the 5' end of an intron.
Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends rather than the usual GT/AG. These are associated with the minor spliceosome.
Strange Intron Ends (strangeSplice) - An intron with ends that are not GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to sequencing error or polymorphism.
Known Alternative Splicing
cassetteExon
bleedingExon
altPromoter
strangeSplice
retainedIntron
altThreePrime
altFivePrime
altFinish
atacIntron
miRNA binding regions  
       

Proteins Section

Info
Available Feature Feature Properties and specific weights Feature Weight
Hub Protein min Num of Interactions
Protein Domain  
PolyPhen  
SNPs 3D  
LS-SNP  
Protein Interactions  
PTM  
         

Diseases Section

Scoring Function  
       

SNP

 
DbSNP release  
Threshold Rank % of SNPs to keep
Output File Name  
   

NOTE: Running Time may be slow, depending on the number of features and genes.

   

 

 

Last modified 17/02/2014
Report Bugs and Contacts : andrea.calabria {A-T} unimi.it; ivan.merelli {A-T} itb.cnr.it