Analysis of Allan-Herndon-Dudley syndrome
Analysis of Allan-Herndon-Dudley syndrome G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: Allan-Herndon-Dudley syndrome
Chromosome: X
Genomic position start-stop: 75800000-98200000
length: 22400001
Band: Xq21
 LINKS

EntrezGene: [193]

MEDLINE:

OMIM: [309600] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 1 papers related to this disease was derived from MEDLINE using the query:
Allan-Herndon-Dudley [tw] AND syndrome [tw]

MESH-C TERMS
The MeSH-C terms associated to the derived papers were collected.

Here you can see the terms ordered by the number of papers where they were found (number in brackets).

Syndrome [1]
Paraplegia [1]
Mental Retardation [1]

Each name is linked to the corresponding term description by the NLM. The number in brackets is linked to the list of papers that contained the term. The points to the related MeSH-D terms.

 GO terms
We computed the GO terms associated to the MeSH-C terms selected for this disease.

Here you can see those with higher score of association.

0.000683 tetrahydrobiopterin biosynthesis (process)
0.000506 L-phenylalanine metabolism (process)
0.000506 4-alpha-hydroxytetrahydrobiopterin dehydratase activity (function)
0.000487 hyaluronic acid binding (function)
0.000487 glycosaminoglycan catabolism (process)
0.000350 neurotransmitter biosynthesis and storage (process)
0.000324 beta-glucuronidase activity (function)
0.000303 nitric oxide biosynthesis (process)
0.000278 collagen type IX (component)
0.000243 cell recognition (process)
We show here only the top 10. You can also see the complete list of 107 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to Allan-Herndon-Dudley syndrome. The points to the related MeSH-D terms.
Follow the green arrows to navigate MeSH-C / MeSH-D / GO-terms relationship derived from our analysis of the whole MEDLINE database, and used to relate the phenotype of this disease to terms of gene functionality.

OVERVIEW OF CANDIDATES IN THE REGION

The graph represents the BLASTX hits found in the region and the genes predicted or known in the region.

Legend:
BLASTX hits RefSeq genes Ensembl genes
                                                                                                                             
> 1e-10 > 1e-20 > 1e-50 > 1e-80 > 1e-100 > 0
                                                             
                                                 

Graph with GO scoring vs genomic position [PostScript graphic]

BEST SCORING 10 CANDIDATES
Here we show only the best scoring ten candidates but there are more. You can see the best scoring 100 candidates.

What is in a candidate?

CANDIDATE 1
DNA (Note)
R-score = 0.003510; GO-score = 0.000303
75800000 bp Chromosome X 98200000 bp
   
  
1 aa NP_034569 215 aa

Similarity found to protein:
[15289|NP_034569] | Mus musculus | high mobility group box 1 | length=215 aa
GO annotation:
0.000000 chromatin (component)
0.000027 DNA binding (function)
0.000000 protein binding (function)
0.000017 extracellular space (component)
0.000000 nucleus (component)
0.000000 chromosome (component)
0.000000 DNA packaging (process)
0.000000 regulation of transcription, DNA-dependent (process)
0.000303 nitric oxide biosynthesis (process)
0.000000 transport (process)
0.000000 heparin binding (function)
0.000000 nitric-oxide synthase regulator activity (function)
BLASTX hits:
E-value 5e-33 prot=20..178 DNA=97483334..97483900 fr=215 per=91/194 [EST]
E-value 5e-33 prot=1..19 DNA=97483279..97483335 fr=215 per=14/19 [EST]
CANDIDATE 2
DNA (Note)
R-score = 0.003797; GO-score = 0.000303
75800000 bp Chromosome X 98200000 bp
   
  
1 aa NP_037095 215 aa

Similarity found to protein:
[25459|NP_037095] | Rattus norvegicus | high mobility group box 1 | length=215 aa
GO annotation:
0.000000 chromatin (component)
0.000000 cellular morphogenesis (process)
0.000027 DNA binding (function)
0.000000 protein binding (function)
0.000017 extracellular space (component)
0.000000 nucleus (component)
0.000000 chromosome (component)
0.000000 DNA packaging (process)
0.000000 regulation of transcription, DNA-dependent (process)
0.000303 nitric oxide biosynthesis (process)
0.000000 transport (process)
0.000000 nervous system development (process)
0.000000 heparin binding (function)
0.000000 nitric-oxide synthase regulator activity (function)
BLASTX hits:
E-value 5e-33 prot=20..178 DNA=97483334..97483900 fr=215 per=91/194 [EST]
E-value 5e-33 prot=1..19 DNA=97483279..97483335 fr=215 per=14/19 [EST]
CANDIDATE 3
DNA (Note)
R-score = 0.011910; GO-score = 0.000114
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_003299 308 aa

Similarity found to protein:
[7258|NP_003299] | Homo sapiens | testis specific protein, Y-linked | length=308 aa
GO annotation:
0.000000 molecular function unknown (function)
0.000000 nucleus (component)
0.000000 nucleosome assembly (process)
0.000000 spermatogenesis (process)
0.000000 gonadal mesoderm development (process)
0.000114 sex differentiation (process)
0.000019 cell proliferation (process)
0.000000 cellular component unknown (component)
0.000000 cell differentiation (process)
BLASTX hits:
E-value 2e-22 prot=108..288 DNA=83816419..83816985 fr=308 per=60/190 [EST]
CANDIDATE 4
DNA (Note) PROTEIN: [NP_005287] [NP_055314] [NP_115942] [NP_938147]
R-score = 0.015419; GO-score = 0.000083
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_032001 396 aa

Similarity found to protein:
[14065|NP_032001] | Mus musculus | coagulation factor II (thrombin) receptor-like 3 | length=396 aa
GO annotation:
0.000000 rhodopsin-like receptor activity (function)
0.000000 signal transducer activity (function)
0.000000 receptor activity (function)
0.000020 G-protein coupled receptor activity (function)
0.000016 signal transduction (process)
0.000021 G-protein coupled receptor protein signaling pathway (process)
0.000083 blood coagulation (process)
0.000000 peptidase activity (function)
0.000000 thrombin receptor activity (function)
0.000020 integral to membrane (component)
BLASTX hits:
E-value 5e-25 prot=94..361 DNA=77816642..77817472 fr=396 per=81/281 [EST]
E-value 1e-14 prot=96..363 DNA=78232726..78233559 fr=396 per=76/281 [EST]
E-value 2e-13 prot=91..385 DNA=78022269..78023168 fr=396 per=83/309 [EST]
CANDIDATE 5
DNA (Note) PROTEIN: [NP_543022]
R-score = 0.016167; GO-score = 0.000083
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_003810 644 aa

Similarity found to protein:
[8761|NP_003810] | Homo sapiens | poly A binding protein, cytoplasmic 4 | length=644 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000000 nucleic acid binding (function)
0.000000 RNA binding (function)
0.000000 protein binding (function)
0.000000 cytoplasm (component)
0.000000 RNA processing (process)
0.000000 RNA catabolism (process)
0.000000 protein biosynthesis (process)
0.000083 blood coagulation (process)
0.000000 poly(A) binding (function)
0.000000 response to pest, pathogen or parasite (process)
BLASTX hits:
E-value 1e-125 prot=15..369 DNA=90496786..90497853 fr=644 per=239/356 [EST]
E-value 5e-32 prot=103..371 DNA=90496786..90497553 fr=644 per=93/272 [EST]
E-value 7e-13 prot=201..378 DNA=90496804..90497292 fr=644 per=56/179 [EST]
CANDIDATE 6
DNA (Note)
R-score = 0.050803; GO-score = 0.000038
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_036697 465 aa

Similarity found to protein:
[24385|NP_036697] | Rattus norvegicus | glucokinase | length=465 aa
GO annotation:
0.000000 cell glucose homeostasis (process)
0.000000 glucokinase activity (function)
0.000000 hexokinase activity (function)
0.000000 protein binding (function)
0.000000 ATP binding (function)
0.000000 glucose binding (function)
0.000000 soluble fraction (component)
0.000038 mitochondrion (component)
0.000000 glycolysis (process)
0.000000 response to glucose stimulus (process)
0.000000 kinase activity (function)
0.000000 transferase activity (function)
0.000000 second-messenger-mediated signaling (process)
BLASTX hits:
E-value 1e-135 prot=16..460 DNA=79636189..79634861 fr=465 per=232/445 [EST]
E-value 1e-127 prot=226..458 DNA=79634220..79633540 fr=465 per=123/233 [EST]
E-value 1e-127 prot=17..225 DNA=79634842..79634222 fr=465 per=115/210 [EST]
CANDIDATE 7
DNA (Note)
R-score = 0.052011; GO-score = 0.000038
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_002602 407 aa

Similarity found to protein:
[5164|NP_002602] | Homo sapiens | pyruvate dehydrogenase kinase, isoenzyme 2 | length=407 aa
GO annotation:
0.000000 [pyruvate dehydrogenase (lipoamide)] kinase activity (function)
0.000000 ATP binding (function)
0.000038 mitochondrion (component)
0.000000 glucose metabolism (process)
0.000000 protein amino acid phosphorylation (process)
BLASTX hits:
E-value 5e-45 prot=14..147 DNA=80661780..80662181 fr=407 per=57/137 [EST]
E-value 5e-45 prot=148..348 DNA=80662178..80662777 fr=407 per=73/209 [EST]
E-value 9e-13 prot=186..276 DNA=80662294..80662566 fr=407 per=37/91 [EST]
E-value 5e-45 prot=349..386 DNA=80662777..80662890 fr=407 per=22/38 [EST]
E-value 5e-45 prot=387..399 DNA=80662887..80662925 fr=407 per=9/13 [EST]
CANDIDATE 8
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.054600; GO-score = 0.000038
75800000 bp Chromosome X 98200000 bp
     
  
1 aa NP_035825 295 aa

Similarity found to protein:
[22334|NP_035825] | Mus musculus | voltage-dependent anion channel 2 | length=295 aa
GO annotation:

0.000038 mitochondrion (component)
0.000000 mitochondrial outer membrane (component)
0.000030 mitochondrial inner membrane (component)
0.000000 transport (process)
0.000000 ion transport (process)
0.000000 anion transport (process)
0.000000 voltage-gated ion-selective channel activity (function)
0.000000 porin activity (function)
0.000000 voltage-gated anion channel porin activity (function)
0.000000 membrane (component)
0.000020 integral to membrane (component)
0.000000 outer membrane (component)
BLASTX hits:
E-value 1e-116 prot=61..295 DNA=79991287..79991991 fr=295 per=172/235 [EST] [P]
E-value 1e-116 prot=13..62 DNA=79991145..79991294 fr=295 per=32/50 [EST] [P]
E-value 1e-92 prot=120..295 DNA=91044327..91043800 fr=295 per=119/176 [EST] [P]
E-value 1e-92 prot=13..122 DNA=91044650..91044321 fr=295 per=56/110 [EST] [P]
CANDIDATE 9
DNA (Note)
R-score = 0.056441; GO-score = 0.000038
75800000 bp Chromosome X 98200000 bp
   
       
1 aa NP_002603 411 aa

Similarity found to protein:
[5166|NP_002603] | Homo sapiens | pyruvate dehydrogenase kinase, isoenzyme 4 | length=411 aa
GO annotation:
0.000000 [pyruvate dehydrogenase (lipoamide)] kinase activity (function)
0.000000 ATP binding (function)
0.000038 mitochondrion (component)
0.000000 glucose metabolism (process)
0.000000 protein amino acid phosphorylation (process)
BLASTX hits:
E-value 1e-61 prot=8..151 DNA=80661753..80662181 fr=411 per=57/145 [EST]
E-value 1e-61 prot=190..270 DNA=80662297..80662539 fr=411 per=36/81 [EST]
E-value 1e-61 prot=290..352 DNA=80662595..80662777 fr=411 per=39/63 [EST]
E-value 1e-61 prot=349..386 DNA=80662765..80662878 fr=411 per=22/38 [EST]
E-value 1e-61 prot=152..182 DNA=80662178..80662270 fr=411 per=16/31 [EST]
E-value 1e-61 prot=391..403 DNA=80662887..80662925 fr=411 per=10/13 [EST]
E-value 1e-61 prot=275..290 DNA=80662551..80662598 fr=411 per=10/16 [EST]
CANDIDATE 10
DNA (Note) PROTEIN: [NP_001857]
R-score = 0.058455; GO-score = 0.000038
75800000 bp Chromosome X 98200000 bp
   
   
1 aa NP_079655 80 aa

Similarity found to protein:
[66142|NP_079655] | Mus musculus | cytochrome c oxidase subunit VIIb | length=80 aa
GO annotation:
0.000000 cytochrome-c oxidase activity (function)
0.000000 nucleus (component)
0.000038 mitochondrion (component)
0.000000 mitochondrial electron transport chain (component)
0.000000 electron transport (process)
0.000000 membrane (component)
0.000020 integral to membrane (component)
0.000000 oxidoreductase activity (function)
0.000000 organelle inner membrane (component)
BLASTX hits:
E-value 5e-12 prot=14..58 DNA=76964285..76964419 fr=80 per=34/45 [EST]