Difference between revisions of "Mapping SNPs HEXA"
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== Statistical comparison of HGMD and SNP-DB == |
== Statistical comparison of HGMD and SNP-DB == |
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+ | [[Image:barplot.png|center|500px|Figure 1: Barplot of the Mutationposition for the differen tables]] |
Revision as of 16:05, 17 June 2011
Contents
Methods
First of all, we had to parse the HGMD database and the DB-SNP database.
HGMD
We logged us in and searched for Tay-Sachs diseases and chose one entry of HEXA. In our case there were two entries with identical content. We only looked at the missense/nonsense mutations, which are 68 annotated in HGMD. We just copied the webpage in a textfile and than wrote a short parser, which parse the codon change, amino acid change and codon number.
DBSNP
It was more complicated to parse the DBSNP output, than the output of HGMD. First of all, we search for HEXA in this database and chose only the SNPs which occur in human. We used the grapical output and again copied and pasted the page in a textfile. An entry in DBSNP has following structure: First of all there is the name of the SNP. Next the sequence and the graphical representation of the sequence. In the next line, there are the allel origin, the clinical relevance and last the annotations of the mutation. TBA...
Comparison of mutations in HGMD and SNP-DB
Mutations annotated in both databases
mutations which are not silent and cause a phenotype
SNP-DB Identifier | Codonposition | Mutationposition | Amino Acids | Codons |
rs121907964 | 26 | 3 | Trp -> TER | TGGc -> TGA |
rs121907979 | 39 | 2 | Leu -> Arg | CTT -> CGT |
rs121907975 | 127 | 1 | Leu -> Phe | aCTC -> TTC |
2 | Leu -> Arg | CTC -> CGC | ||
rs121907962 | 137 | 1 | Arg -> TER | cCGA -> TGA |
rs121907972 | 170 | 1 | Arg -> Trp | cCGG -> TGG |
rs121907957 | 2 | Arg -> Gln | CGG -> CAG | |
rs28941770 | 178 | 2 | Arg -> His | CGC -> CAC |
2 | Arg -> Leu | CGC -> CTC | ||
rs121907953 | 1 | Arg -> Cys | tCGC -> TGC | |
rs121907969 | 180 | 3 | Tyr -> TER | TACc -> TAG |
rs28941771 | 1 | Tyr -> His | tTAC -> CAC | |
rs121907973 | 197 | 2 | Lys -> Thr | AAA -> ACA |
rs1800429 | 200 | 1 | Val -> Met | cGTG -> ATG |
rs121907976 | 204 | 2 | His -> Arg | CAT -> CGT |
rs121907961 | 210 | 2 | Ser -> Phe | TCC -> TTC |
rs121907974 | 211 | 2 | Phe -> Ser | TTC -> TCC |
rs121907970 | 247 | 1 | Arg -> Trp | aCGG -> TGG |
rs121907959 | 250 | 1 | Gly -> Ser | gGGT -> AGT |
2 | Gly -> Asp | GGT -> GAT | ||
2 | Gly -> Val | GGT -> GTT | ||
rs121907971 | 258 | 1 | Asp -> His | tGAC -> CAC |
rs121907954 | 269 | 1 | Gly -> Ser | aGGT -> AGT |
2 | Gly -> Asp | GGT -> GAT | ||
rs121907977 | 301 | 2 | Met -> Arg | ATG -> AGG |
rs121907967 | 329 | 2 | Trp -> TER | TGG -> TAG |
rs121907963 | 393 | 1 | Arg -> TER | gCGA -> TGA |
rs121907958 | 420 | 3 | Trp -> Cys | TGGt -> TGC |
3 | Trp -> Cys | TGGt -> TGT | ||
rs28940871 | 451 | 1 | Leu -> Val | tCTG -> GTG |
rs121907978 | 454 | 2 | Gly -> Asp | GGT -> GAT |
1 | Gly -> Ser | tGGT -> AGT | ||
rs121907981 | 474 | 3 | Trp -> Cys | TGGc -> TGC |
rs121907952 | 482 | 1 | Glu -> Lys | cGAA -> AAA |
rs121907968 | 485 | 1 | Trp -> Arg | gTGG -> CGG |
rs121907966 | 499 | 1 | Arg -> Cys | aCGT -> TGT |
rs121907956 | 2 | Arg -> His | CGT -> CAT | |
rs28942071 | 504 | 1 | Arg -> Cys | cCGC -> TGC |
rs121907955 | 2 | Arg -> His | CGC -> CAC | |
rs4777502 | 506 | 3 | Glu -> Asp | GAA -> GAC |
3 | Glu -> Asp | GAA -> GAT |
Graphical representation:
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
MTSSRLWFSLLLAAAFAGRATALWP!PQNFQTSDQRYVRYPNNFQFQYDVSSAAQPGCSVLD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLS
QCLFLSETVWGAL!GLETFSQLVWKSAEGTFFINKTEIEDFPRFPHWGLLLDTSHH!LPLS
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
SILDTLDVMAYNTLNMFHWRLVDDPFSPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFL
AWLRSIRVLAEFHTPGHTLSWGPSIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFRSTFFL
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
EVSSVFPDFYLHLGGDEVDFTC!KSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYG
KGYVVWQEVFDNKVKIQPDTIIQVW!EDIPVNYMKELELVTKAGFRALLSAPCYLNRISYG
PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
PDWKDFYIVEPLAFEGTPEQKAVVIDGEACMWGEYVDNTNLVPRLCPRAGAVAKRLRSNKL
TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT TSDLTFAYECLSHFCCDLLRRGVQAQPLNVGFCEQEFEQT Non-silent mutation Silent mutation Wrong AA in mutation annotation
Mutations annotated only in HGMD
not found
Mutations annotated only in SNP-DB
mutations annotated only in SNP-DB and not silent (pos in codon ist annotiert und sicher):
Here we list all mutations which are annotated in the SNP-DB, not silent and not annotated in the HGMD database. Some of these mutations have a really detailed NP annotation, other mutations do not have a very detailed annotation and therefore we had to map these mutations. The detail list of the mutations, which are mapped by us can be found [here].
SNP-DB Identifier | Codonposition | Mutationposition | Amino Acids | Codons |
rs4777505 | 29 | 2 | Asn -> Ser | AAC -> AGC |
rs61731240 | 179 | 1 | His -> Asp | CAT -> GAT |
rs3743230 | 208 | 1 | Asn -> Asp | AAC -> GAC |
rs61747114 | 248 | 1 | Leu -> Phe | CTT -> TTT |
rs1054374 | 293 | 2 | Ser -> Ile | AGT -> ATT |
rs1800430 | 399 | 1 | Asn -> Asp | AAC -> GAC |
rs1800431 | 436 | 1 | Ile -> Val | ATA -> GTA |
rs121907982 | 456 | 2 | Tyr -> Ser | TAT -> TCT |
Graphical representation:
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
MTSSRLWFSLLLAAAFAGRATALWPWPQSFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLS
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRDYLPLS
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFL
ARFRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPILNNTYEFMSTFFL
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVDYMKELELVTKAGFRALLSAPWYLNRISYG
PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
PDWKDFYVVEPLAFEGTPEQKALVIGGSACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT Non-silent mutation Silent mutation Wrong AA in mutation annotation
silent mutation
Because this mutations are not annotated in the HGMD database, the mutations have to be silent and do not lead to a phenotype.
This mutations are badly annotated in the SNP-DB. Therefore we rotated the found codons, because the original codon has to code for the amino acid which occur in the protein sequence.
Therefore we used the codon with the mutation at position one, position two and position three. Next we also reverse it and made the complemetary sequence of both.
The detailed result can be seen [here]
If we found more than one nucleotide combination which code for the amino acid in the protein sequence, we list all of them in the following table, if they are silent mutations. Otherwise, we also listed all mutations which are not silent, if there do not exist any other possible mutation for this postition.
Here is the result, which combinations are possible:
SPN-DB Identifier | Codonposition | Mutationposition | Amino Acids | Codons | translation |
rs1800428 | 3 | 3 | Ser -> Ser | AGC -> AGT | Forward |
rs11551324 | 109 | 3 | Thr -> Thr | ACC -> ACT | forward |
rs28942072 | 324 | 3 | Val -> Val | GTT -> GGA | Forward |
rs28942072 | Val -> Val | GTC -> GTT | Forward | ||
rs34085965 | 446 | 1 | Pro -> Pro | CCT -> CCC | complemantry reverse |
rs4777502 | 506 | 3 | Glu -> Glu | GAG -> GAA | Forward |
Graphical representation:
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLS
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLS
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFL
ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFL
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYG
PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT Non-silent mutation Silent mutation Wrong AA in mutation annotation
Summary
Graphical representation:
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLD
MTSSRLWFSLLLAAAFAGRATALWP!PQSFQTSDQRYVRYPNNFQFQYDVSSAAQPGCSVLD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
EAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDD
QCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLS
QCLFLSETVWGAL!GLETFSQLVWKSAEGTFFINKTEIEDFPRFPHWGLLLDTSHD!LPLS
SILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
SILDTLDVMAYNTLNMFHWRLVDDPFSPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEY
ARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEFMSTFFL
AWFRSIRVLAEFHTPGHTLSWGPSIPGLLTPCYSGSEPSGTFGPVNPILNNTYEFRSTFFL
EVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
EVSSVFPDFYLHLGGDEVDFTC!KSNPEIQDFMRKKGFGEDFKQLESFYIQTLLDIVSSYG
KGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPWYLNRISYG
KGYVVWQEVFDNKVKIQPDTIIQVW!EDIPVDYMKELELVTKAGFRALLSAPCYLNRISYG
PDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKL
PDWKDFYVVEPLAFEGTPEQKAVVIDGSACMWGEYVDNTNLVPRLCPRAGAVAKRLRSNKL
TSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT TSDLTFAYECLSHFCCELLRRGVQAQPLNVGFCEQEFEQT Non-silent mutation Silent mutation Wrong AA in mutation annotation