Difference between revisions of "Sequence-based mutation analysis Gaucher Disease"

From Bioinformatikpedia
(→‎Substitution scores)
Line 171: Line 171:
   
 
<figtable id="tab:subst_blosum">
  
<figtable id="tab:subst_blosum">
−
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:center" width="450px"
 +
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:center" width="350px"
 
|- style="background-color: lightgrey"
  
|- style="background-color: lightgrey"
−
! Nr !! Mutation !! Score mutation !! Score min !! Score max
 +
! Nr !! Mutation !! Score<br/>mutation !! Score<br/>min !! Score<br/>max
 
|-
  
|-
 
| colspan=5 style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 1px 0 0 0"|
  
| colspan=5 style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 1px 0 0 0"|
Line 197: Line 197:
 
| 10 || R83S || -1 || -3 || 5
  
| 10 || R83S || -1 || -3 || 5
 
|}
  
|}
−
<caption>BLOSUM62 scores of the selected mutations</caption>
 +
<caption>BLOSUM62 scores of the selected mutations.</caption>
 
</figtable>
  
</figtable>
   
 
=== PSSM of all hits===
  
=== PSSM of all hits===
 
[[PSSM|PSSM]].
  
[[PSSM|PSSM]].
  +
{|
  +
|<figure id="fig:subst_pssm_all_ali">[[File:subst_ali_all.png|thumb|300px|<caption>Sequence alignment of P04062 derived from all significant hits after 5 rounds PSI-BLAST</caption>]]</figure>
  +
|<figure id="fig:subst_pssm_all">[[File:subst_pssm_all.png|thumb|300px|<caption>PSSM of P04062 derived from all significant hits after 5 rounds PSI-BLAST.</caption>]]</figure>
  +
|}
   
 
<figtable id="tab:subst_pssm_all">
  
<figtable id="tab:subst_pssm_all">
 
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:center" width="500px"
  
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:center" width="500px"
 
|- style="background-color: lightgrey"
  
|- style="background-color: lightgrey"
−
! Nr !! Mutation !! Score<br/>mutation !! Score<br/>min !! Score<br/>max !! Conservation
 +
! Nr !! Mutation !! Score<br/>mutation !! Score<br/>min !! Score<br/>max !! Conservation !! <span style="color:blue">Disease<br/>score</span>
 
|-
  
|-
−
| colspan=6 style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 0 0 1px 0"|
 +
| colspan=7 style="background-color: lightgrey; border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 0 0 1px 0"|
 
|-
  
|-
−
| 1 || H99R || 0 || -4 || 2 || [[File:subst_pssm_all_col99.png|150px]]
 +
| 1 || H99R || 0 || -4 || 2 || [[File:subst_pssm_all_col99.png|150px]] || 0
 
|-
  
|-
−
| 2 || V211I || 4 || -4 || 4 || [[File:subst_pssm_all_col211.png|150px]]
 +
| 2 || V211I || 4 || -4 || 4 || [[File:subst_pssm_all_col211.png|150px]] || -1
 
|-
  
|-
−
| 3 || E150K || 0 || -4 || 5 || [[File:subst_pssm_all_col150.png|150px]]
 +
| 3 || E150K || 0 || -4 || 5 || [[File:subst_pssm_all_col150.png|150px]] || 0
 
|-
  
|-
−
| 4 || L236P || 0 || -3 || 1 || [[File:subst_pssm_all_col236.png|150px]]
 +
| 4 || L236P || 0 || -3 || 1 || [[File:subst_pssm_all_col236.png|150px]] || 0
 
|-
  
|-
−
| 5 || W248R || -2 || -3 || 4 || [[File:subst_pssm_all_col248.png|150px]]
 +
| 5 || W248R || -2 || -3 || 4 || [[File:subst_pssm_all_col248.png|150px]] || 1
 
|-
  
|-
−
| 6 || L509P || -6 || -6 || 4 || [[File:subst_pssm_all_col509.png|150px]]
 +
| 6 || L509P || -6 || -6 || 4 || [[File:subst_pssm_all_col509.png|150px]] || 1
 
|-
  
|-
−
| 7 || W351C || -3 || -6 || 9 || [[File:subst_pssm_all_col351.png|150px]]
 +
| 7 || W351C || -3 || -6 || 9 || [[File:subst_pssm_all_col351.png|150px]] || 1
 
|-
  
|-
−
| 8 || A423D || -3 || -3 || 3 || [[File:subst_pssm_all_col423.png|150px]]
 +
| 8 || A423D || -3 || -3 || 3 || [[File:subst_pssm_all_col423.png|150px]] || 1
 
|-
  
|-
−
| 9 || D482N || 4 || -4 || 4 || [[File:subst_pssm_all_col482.png|150px]]
 +
| 9 || D482N || 4 || -4 || 4 || [[File:subst_pssm_all_col482.png|150px]] || -1
 
|-
  
|-
−
| 10 || R83S || 0 || -3 || 2 || [[File:subst_pssm_all_col83.png|150px]]
 +
| 10 || R83S || 0 || -3 || 2 || [[File:subst_pssm_all_col83.png|150px]] || 0
 
|}
  
|}
−
<caption>Position specific substitution scores derived from all significant hits after 5 rounds PSI-BLAST.</caption>
 +
<caption>Position specific substitution scores derived from all significant hits after 5 rounds PSI-BLAST. The respective profile column is shown on the right.</caption>
 
</figtable>
  
</figtable>
  +
  +
  +
=== PSSM of close homologous sequences ===
  +
[[PSSM of close homologous sequences|PSSM]].
  +
{|
  +
|<figure id="fig:subst_pssm_best_ali">[[File:subst_pssm_best_ali.png|thumb|300px|<caption>Sequence alignment of P04062 derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST</caption>]]</figure>
  +
|<figure id="fig:subst_pssm_best">[[File:subst_pssm_best.png|thumb|300px|<caption>PSSM of P04062 derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST.</caption>]]</figure>
  +
|}
  +
  +
<figtable id="tab:subst_pssm_best">
  +
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:center" width="500px"
  +
|- style="background-color: lightgrey"
  +
! Nr !! Mutation !! Score<br/>mutation !! Score<br/>min !! Score<br/>max !! Conservation !! <span style="color:blue">Disease<br/>score</span>
  +
|-
  +
| colspan=7 style="background-color: lightgrey; border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 0 0 1px 0"|
  +
|-
  +
| 1 || H99R || 0 || -3 || 8 || [[File:subst_pssm_best_col99.png|150px]] || 0
  +
|-
  +
| 2 || V211I || 3 || -3 || 4 || [[File:subst_pssm_best_col211.png|150px]] || -1
  +
|-
  +
| 3 || E150K || 1 || -4 || 5 || [[File:subst_pssm_best_col150.png|150px]] || 0
  +
|-
  +
| 4 || L236P || -3 || -4 || 4 || [[File:subst_pssm_best_col236.png|150px]] || 1
  +
|-
  +
| 5 || W248R || -3 || -4 || 11 || [[File:subst_pssm_best_col248.png|150px]] || 1
  +
|-
  +
| 6 || L509P || -3 || -4 || 4 || [[File:subst_pssm_best_col509.png|150px]] || 1
  +
|-
  +
| 7 || W351C || -2 || -4 || 11 || [[File:subst_pssm_best_col351.png|150px]] || 1
  +
|-
  +
| 8 || A423D || -2 || -3 || 4 || [[File:subst_pssm_best_col423.png|150px]] || 1
  +
|-
  +
| 9 || D482N || 1 || -4 || 6 || [[File:subst_pssm_best_col482.png|150px]] || -1
  +
|-
  +
| 10 || R83S || -1 || -3 || 6 || [[File:subst_pssm_best_col83.png|150px]] || 0
  +
|}
  +
<caption>Position specific substitution scores derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST. The respective profile column is shown on the right.</caption>
  +
</figtable>
  +
   
 
== Scoring Mutants ==
  
== Scoring Mutants ==

Revision as of 09:01, 17 June 2012

The aim of this task was to carry out a thorough analysis of ten mutations and to classify them as disease-causing and non-disease causing. The mutations have been selected by another group from our [Researching SNPs Gaucher Disease|set of collected mutations] such that their impact had been unknown for us prior to this task. Technical details are reported in our protocol.

Mutations

<figtable id="tab:mutations">

Nr Position From To
1 99 H R
2 211 V I
3 150 E K
4 236 L P
5 248 W R
6 509 L P
7 351 W C
8 423 A D
9 482 D N
10 83 R S

Randomly selected mutations from HGMD and dbSNP which were used for the sequence-based mutation analysis. </figtable>

Physicochemical properties

<figtable id="tab:props">

Nr Wildtype Mutant Severe change
AA Charge Polarity Size Aromatic AA Charge Polarity Size Aromatic
1 H negative polar large no R negative polar large no no
2 V neutral unpolar medium no I neutral unpolar medium no no
3 E positive polar large no K negative polar large no yes
4 L neutral unpolar medium no P neutral unpolar medium no no
5 W neutral unpolar large yes R negative polar large no yes
6 L neutral unpolar medium no P neutral unpolar medium no no
7 W neutral unpolar large yes C neutral polar small no yes
8 A neutral unpolar small no D positive polar medium no yes
9 D positive polar medium no N neutral polar medium no no
10 R negative polar large no S neutral polar small no no

Physicochemical properiets of the wildtype and mutatant amino acid which were used to classify the mutation as severe or non-severe. </figtable>

Structural analysis

<figtable id="tab:structure">

Nr Mutation Accessibility 2nd structure Domain region Mutation
1 H99R exposed C no Structure nr1.png
2 V211I exposed C no Structure nr2.png
3 E150K exposed C no Structure nr3.png
4 L236P exposed C no Structure nr4.png
5 W248R buried H yes Structure nr5.png
6 L509P exposed S yes Structure nr6.png
7 W351C exposed S yes Structure nr7.png
8 A423D buried C yes Structure nr8.png
9 D482N exposed C yes Structure nr9.png
10 R83S exposed C yes Structure nr10.png

Location of mutations in 2nt0_A. Blue: wildtype; Red: mutant. </figtable>

<figure id="fig:structure_all">

2nt0_A along with the selected wildtype residues from <xr id="tab:mutations"/> in blue.

</figure>


Substitution scores

BLOSUM62 scores

The scores were taken from the BLOSUM62 matrix.

<figtable id="tab:subst_blosum">

Nr Mutation Score
mutation		 Score
min		 Score
max
1 H99R 0 -3 8
2 V211I 3 -3 4
3 E150K 1 -4 5
4 L236P -3 -4 4
5 W248R -3 -4 11
6 L509P -3 -4 4
7 W351C -2 -4 11
8 A423D -2 -3 4
9 D482N 1 -4 6
10 R83S -1 -3 5

BLOSUM62 scores of the selected mutations. </figtable>

PSSM of all hits

PSSM.

</figure> </figure>
<figure id="fig:subst_pssm_all_ali">
Sequence alignment of P04062 derived from all significant hits after 5 rounds PSI-BLAST
<figure id="fig:subst_pssm_all">
PSSM of P04062 derived from all significant hits after 5 rounds PSI-BLAST.

<figtable id="tab:subst_pssm_all">

Nr Mutation Score
mutation		 Score
min		 Score
max		 Conservation Disease
score
1 H99R 0 -4 2 Subst pssm all col99.png 0
2 V211I 4 -4 4 Subst pssm all col211.png -1
3 E150K 0 -4 5 Subst pssm all col150.png 0
4 L236P 0 -3 1 Subst pssm all col236.png 0
5 W248R -2 -3 4 Subst pssm all col248.png 1
6 L509P -6 -6 4 Subst pssm all col509.png 1
7 W351C -3 -6 9 Subst pssm all col351.png 1
8 A423D -3 -3 3 Subst pssm all col423.png 1
9 D482N 4 -4 4 Subst pssm all col482.png -1
10 R83S 0 -3 2 Subst pssm all col83.png 0

Position specific substitution scores derived from all significant hits after 5 rounds PSI-BLAST. The respective profile column is shown on the right. </figtable>


PSSM of close homologous sequences

PSSM.

</figure> </figure>
<figure id="fig:subst_pssm_best_ali">
Sequence alignment of P04062 derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST
<figure id="fig:subst_pssm_best">
PSSM of P04062 derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST.

<figtable id="tab:subst_pssm_best">

Nr Mutation Score
mutation		 Score
min		 Score
max		 Conservation Disease
score
1 H99R 0 -3 8 Subst pssm best col99.png 0
2 V211I 3 -3 4 Subst pssm best col211.png -1
3 E150K 1 -4 5 Subst pssm best col150.png 0
4 L236P -3 -4 4 Subst pssm best col236.png 1
5 W248R -3 -4 11 Subst pssm best col248.png 1
6 L509P -3 -4 4 Subst pssm best col509.png 1
7 W351C -2 -4 11 Subst pssm best col351.png 1
8 A423D -2 -3 4 Subst pssm best col423.png 1
9 D482N 1 -4 6 Subst pssm best col482.png -1
10 R83S -1 -3 6 Subst pssm best col83.png 0

Position specific substitution scores derived from the 60 closest homologous sequences after 5 rounds PSI-BLAST. The respective profile column is shown on the right. </figtable>


Scoring Mutants

SIFT

The predicted results from SIFT Blink is shown here: 

Substitution at pos 83 from R to S is predicted to be TOLERATED with a score of 0.17.
   Median sequence conservation: 2.12
   Sequences represented at this position:77

Substitution at pos 99 from H to R is predicted to be TOLERATED with a score of 0.64.
   Median sequence conservation: 2.14
   Sequences represented at this position:80

Substitution at pos 150 from E to K is predicted to be TOLERATED with a score of 0.76.
   Median sequence conservation: 2.10
   Sequences represented at this position:86

Substitution at pos 211 from V to I is predicted to be TOLERATED with a score of 0.56.
   Median sequence conservation: 2.09
   Sequences represented at this position:86

Substitution at pos 236 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.02.
   Median sequence conservation: 2.09
   Sequences represented at this position:86

Substitution at pos 248 from W to R is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 2.09
   Sequences represented at this position:86

Substitution at pos 351 from W to C is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 2.10
   Sequences represented at this position:87

Substitution at pos 423 from A to D is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01.
   Median sequence conservation: 2.10
   Sequences represented at this position:85

Substitution at pos 482 from D to N is predicted to be TOLERATED with a score of 0.69.
   Median sequence conservation: 2.18
   Sequences represented at this position:66

Substitution at pos 509 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 2.10
   Sequences represented at this position:79


The predicted results from SIFT is shown here: 

Substitution at pos 83 from R to S is predicted to AFFECT PROTEIN FUNCTION with a score of 0.05.
   Median sequence conservation: 3.10
   Sequences represented at this position:15

Substitution at pos 99 from H to R is predicted to be TOLERATED with a score of 0.74.
   Median sequence conservation: 3.11
   Sequences represented at this position:14

Substitution at pos 150 from E to K is predicted to be TOLERATED with a score of 0.44.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 211 from V to I is predicted to be TOLERATED with a score of 1.00.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 236 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 248 from W to R is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 351 from W to C is predicted to AFFECT PROTEIN FUNCTION with a score of 0.00.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 423 from A to D is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 482 from D to N is predicted to be TOLERATED with a score of 0.77.
   Median sequence conservation: 3.10
   Sequences represented at this position:16

Substitution at pos 509 from L to P is predicted to AFFECT PROTEIN FUNCTION with a score of 0.01.
   Median sequence conservation: 3.11
   Sequences represented at this position:14

Polyphen2

H99R
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)

V211I
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
This mutation is predicted to be benign with a score of 0.001 (sensitivity: 0.99; specificity: 0.09)

E150K
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
This mutation is predicted to be benign with a score of 0.001 (sensitivity: 0.99; specificity: 0.09)

L236P
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)

W248R
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
This mutation is predicted to be probably damaging with a score of 0.999 (sensitivity: 0.09; specificity: 0.99)

L509P
This mutation is predicted to be probably damaging with a score of 0.992 (sensitivity: 0.70; specificity: 0.97)
This mutation is predicted to be probably damaging with a score of 0.988 (sensitivity: 0.53; specificity: 0.95)

W351C
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)

A423D
This mutation is predicted to be probably damaging with a score of 1.000 (sensitivity: 0.00; specificity: 1.00)
This mutation is predicted to be probably damaging with a score of 0.996 (sensitivity: 0.36; specificity: 0.97)

D482N
This mutation is predicted to be benign with a score of 0.000 (sensitivity: 1.00; specificity: 0.00)
his mutation is predicted to be benign with a score of 0.002 (sensitivity: 0.99; specificity: 0.18)

R83S
This mutation is predicted to be benign with a score of 0.007 (sensitivity: 0.96; specificity: 0.75)
This mutation is predicted to be benign with a score of 0.019 (sensitivity: 0.95; specificity: 0.55)

SNAP

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Sequence-based_mutation_analysis_Gaucher_Disease&oldid=23397"