SNPInspector: Identify TF sites affected by SNPs

[Introduction] [Sequence Selection] [Parameters] [Output]

Introduction

SNPInspector analyses the potential effects of a single nucleotide polymorphism (SNP) associated with your sequence. For each SNP allele the transcription factor binding sites either deleted or generated by the nucleotide exchange are determined. The analysis is based on MatInspector and Genomatix' library of matrix descriptions for transcription factor binding sites.

Sequence Selection

Sequence Selection
Choose from your previously uploaded sequences	Select a sequence file from the list of your personal sequence files. Please note that only sequences can be analyzed for which the alleles of the SNP are provided in a format supported by SNPInspector.
or enter the formatted DNA sequence	Enter your correctly formatted sequence(s) directly into the form, e.g. with copy and paste.
or upload a file containing sequence(s)	If your browser supports this option, a sequence file can be uploaded. If you use this option, the file should contain the sequence(s) in one of the supported formats.
or enter accession number(s)	Enter a dbSNP identifier as accession number (e.g.rs2230036). Please note that other accession numbers will also be accepted, but SNPInspector will probably not find a SNP description in these sequences.

There are two different formats supported by SNPInspector:

dbSNP format:
The information about the alleles of the SNP and its position in the sequence are provided in the description line of a FASTA sequence e.g.
```
>gnl|dbSNP|rs2230037|allelePos=151|totalLen=301|taxid=9606|snpclass=1|alleles='C/T'|mol=cDNA|build=11
```
This is the same format as used in dbSNP (NCBI). SNPInspector requires the two fields "allelePos=151" and "alleles='C/T'" to extract the position of the SNP and the alleles described for this position. The fields in the description line have to be separated by "|" .
IUPAC format:
The information about the SNP (position, alleles) can also be provided within the sequence. Both, position and alleles, are indicated by the usage of an ambiguous nucleotide. Therefore, the sequence may only contain one ambiguous nucleotide. Otherwise the position of the SNP can't be identified clearly.
As the information about the SNP is not extracted from the annotation, the sequence may be provided in any of the sequence formats supported by Genomatix.

The two formats cannot be mixed. If there is a SNP description detected in the FASTA description line the sequence is not analyzed for ambiguous nucleotides.
There should be only IUPAC characters in the sequence, any other characters will be skipped!

Parameters

The matrix library is divided into the subsections/groups

Fungi
Insects
Plants
Vertebrates
Miscellaneous (e.g. Bacteria)
Other Functional Elements (e.g. PolyA signal)

You can select one or more of the available matrix groups for analysis.

Program Output

The result page contains a table for each of the nucleotide exchanges analyzed. It lists the transcription factor binding sites either lost or generated due to this exchange.

Additional values in the table like RE, opt. and the similarities all refer to the lost/found matrix and are explained in the matrix help page.

Inspecting sequence rs2230036 (1 - 301):

SNP	Position:	151
	Allele:	A -> T

	Name of family/matrix	RE	Opt.	Position	Strand	Core sim.	Matrix sim.
Lost Sites	V$CHOP/CHOP.01	1.10	0.90	144-156	+	1.000	0.911
Lost Sites	V$HNF6/HNF6.01	0.05	0.82	145-158	+	0.833	0.838
New Sites	V$OCT1/OCT1.04	0.03	0.80	146-159	-	0.846	0.868
	V$BCL6/BCL6.02	0.01	0.77	147-162	-	0.800	0.780
	V$STAT/STAT3.01	0.00	0.74	147-165	+	1.000	0.760

In this example the substitution of a adenine (A) by a thymine (T) results in the loss of two transcription factor binding sites (CHOP, HNF6). On the other side transcription factor binding sites for OCT1, BCL6, and STAT are generated due to the exchange.

The results can be exported to an Excel formatted file by pressing the button "Export in EXCEL format".