Analysis of Abidi X-linked mental retardation syndrome
Analysis of Abidi X-linked mental retardation syndrome G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: Abidi X-linked mental retardation syndrome
Method: Md
Chromosome: X
Genomic position start-stop: 67850000-77850000
length: 10000001
Band: Xq13.2
 LINKS

EntrezGene: [57792]

MEDLINE:

OMIM: [300262] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 35976 papers related to this disease was derived from MEDLINE using the query:
mental [tw] AND retardation [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).

Mental Retardation [31708]
Syndrome [4105]
Abnormalities, Multiple [3519]
Epilepsy [1649]
Down Syndrome [1170]
Growth Disorders [1060]
Fragile X Syndrome [905]
Cerebral Palsy [900]
Microcephaly [821]
Brain Diseases [768]
We show here only the 10 most frequent. You can also see the complete list of 2042 MeSH-C terms.

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.

0.000563 tetrahydrobiopterin biosynthesis (process)
0.000417 L-phenylalanine metabolism (process)
0.000417 4-alpha-hydroxytetrahydrobiopterin dehydratase activity (function)
0.000401 hyaluronic acid binding (function)
0.000401 glycosaminoglycan catabolism (process)
0.000289 neurotransmitter biosynthesis and storage (process)
0.000267 beta-glucuronidase activity (function)
0.000250 nitric oxide biosynthesis (process)
0.000229 collagen type IX (component)
0.000201 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 Abidi X-linked mental retardation 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) PROTEIN: [NP_065983]
R-score = 0.000863; GO-score = 0.000401
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_031450 2132 aa

Similarity found to protein:
[11595|NP_031450] | Mus musculus | aggrecan 1 | length=2132 aa
GO annotation:
0.000013 cartilage condensation (process)
0.000012 calcium ion binding (function)
0.000000 sugar binding (function)
0.000401 hyaluronic acid binding (function)
0.000019 extracellular matrix (sensu Metazoa) (component)
0.000011 cell adhesion (process)
0.000000 proteoglycan biosynthesis (process)
0.000000 collagen fibril organization (process)
BLASTX hits:
E-value 5e-13 prot=741..1132 DNA=75431091..75432305 fr=2132 per=123/444 [EST]
CANDIDATE 2
DNA (Note)
R-score = 0.010356; GO-score = 0.000099
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_524165 1525 aa

Similarity found to protein:
[40153|NP_524165] | Drosophila melanogaster | Guanyl cyclase at 76C CG8742-PA | length=1525 aa
GO annotation:
0.000099 guanylate cyclase activity (function)
0.000000 protein kinase activity (function)
0.000000 receptor activity (function)
0.000000 ATP binding (function)
0.000025 plasma membrane (component)
0.000000 protein amino acid phosphorylation (process)
0.000013 signal transduction (process)
0.000000 intracellular signaling cascade (process)
0.000000 cyclic nucleotide metabolism (process)
BLASTX hits:
E-value 3e-13 prot=593..822 DNA=74587135..74587794 fr=1525 per=64/235 [EST]
CANDIDATE 3
DNA (Note) PROTEIN: [NP_002556] [NP_005287]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.015419; GO-score = 0.000068
67850000 bp Chromosome X 77850000 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)
0.000016 G-protein coupled receptor activity (function)
0.000013 signal transduction (process)
0.000017 G-protein coupled receptor protein signaling pathway (process)
0.000068 blood coagulation (process)
0.000000 peptidase activity (function)
0.000000 thrombin receptor activity (function)
0.000016 integral to membrane (component)
BLASTX hits:
E-value 4e-23 prot=91..379 DNA=69262388..69261489 fr=396 per=95/306 [EST] [P]
E-value 5e-25 prot=94..361 DNA=77816642..77817472 fr=396 per=81/281 [EST] [P]
CANDIDATE 4
DNA (Note) PROTEIN: [NP_001012995]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.016167; GO-score = 0.000068
67850000 bp Chromosome X 77850000 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)
0.000068 blood coagulation (process)
0.000000 poly(A) binding (function)
0.000000 response to pest, pathogen or parasite (process)
BLASTX hits:
E-value 3e-84 prot=8..206 DNA=72006498..72007094 fr=644 per=151/199 [EST] [P]
E-value 3e-84 prot=8..206 DNA=72082253..72081657 fr=644 per=151/199 [EST] [P]
E-value 2e-19 prot=98..275 DNA=72006504..72007022 fr=644 per=62/180 [EST] [P]
E-value 2e-19 prot=98..275 DNA=72082247..72081729 fr=644 per=62/180 [EST] [P]
E-value 5e-17 prot=189..376 DNA=72082250..72081732 fr=644 per=60/190 [EST] [P]
E-value 5e-17 prot=189..376 DNA=72006501..72007019 fr=644 per=60/190 [EST] [P]
E-value 4e-35 prot=523..643 DNA=73586322..73585963 fr=644 per=92/124 [EST] [P]
CANDIDATE 5
DNA (Note) PROTEIN: [NP_002628]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.021403; GO-score = 0.000054
67850000 bp Chromosome X 77850000 bp
   
           
1 aa NP_000283 1235 aa

Similarity found to protein:
[5256|NP_000283] | Homo sapiens | phosphorylase kinase, alpha 2 (liver) | length=1235 aa
GO annotation:

0.000000 phosphorylase kinase activity (function)
0.000000 calmodulin binding (function)
0.000000 phosphorylase kinase complex (component)
0.000022 carbohydrate metabolism (process)
0.000000 glycogen metabolism (process)
0.000054 generation of precursor metabolites and energy (process)
0.000000 protein modification (process)
BLASTX hits:
E-value 5e-22 prot=14..93 DNA=71715840..71715598 fr=1235 per=56/81 [EST] [P]
E-value 8e-20 prot=1107..1190 DNA=71585488..71585237 fr=1235 per=54/84 [EST] [P]
E-value 8e-20 prot=95..152 DNA=71698751..71698578 fr=1235 per=49/58 [EST] [P]
E-value 3e-14 prot=307..356 DNA=71659114..71658965 fr=1235 per=36/50 [EST] [P]
E-value 9e-13 prot=518..571 DNA=71638189..71638028 fr=1235 per=36/54 [EST] [P]
E-value 9e-11 prot=892..936 DNA=71608275..71608141 fr=1235 per=37/45 [EST] [P]
CANDIDATE 6
DNA (Note)
R-score = 0.021748; GO-score = 0.000054
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_006204 387 aa

Similarity found to protein:
[5260|NP_006204] | Homo sapiens | phosphorylase kinase, gamma 1 (muscle) | length=387 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000000 protein serine/threonine kinase activity (function)
0.000000 phosphorylase kinase activity (function)
0.000000 protein-tyrosine kinase activity (function)
0.000000 calmodulin binding (function)
0.000000 ATP binding (function)
0.000000 phosphorylase kinase complex (component)
0.000022 carbohydrate metabolism (process)
0.000000 glycogen biosynthesis (process)
0.000054 generation of precursor metabolites and energy (process)
0.000000 protein amino acid phosphorylation (process)
0.000000 muscle development (process)
0.000000 transferase activity (function)
BLASTX hits:
E-value 5e-11 prot=26..230 DNA=72528692..72528093 fr=387 per=64/210 [EST]
CANDIDATE 7
DNA (Note)
R-score = 0.021805; GO-score = 0.000054
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_000199 1382 aa

Similarity found to protein:
[3643|NP_000199] | Homo sapiens | insulin receptor | length=1382 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000000 protein serine/threonine kinase activity (function)
0.000000 receptor signaling protein tyrosine kinase activity (function)
0.000000 receptor activity (function)
0.000000 epidermal growth factor receptor activity (function)
0.000000 transmembrane receptor protein tyrosine kinase signaling protein activity (function)
0.000000 protein binding (function)
0.000000 ATP binding (function)
0.000025 plasma membrane (component)
0.000020 integral to plasma membrane (component)
0.000022 carbohydrate metabolism (process)
0.000054 generation of precursor metabolites and energy (process)
0.000000 protein amino acid phosphorylation (process)
0.000013 signal transduction (process)
0.000000 transmembrane receptor protein tyrosine kinase signaling pathway (process)
0.000017 development (process)
0.000000 transferase activity (function)
BLASTX hits:
E-value 1e-12 prot=1135..1291 DNA=74587303..74587794 fr=1382 per=53/168 [EST]
CANDIDATE 8
DNA (Note)
R-score = 0.024682; GO-score = 0.000054
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_058767 1383 aa

Similarity found to protein:
[24954|NP_058767] | Rattus norvegicus | insulin receptor | length=1383 aa
GO annotation:
0.000000 protein kinase activity (function)
0.000000 protein-tyrosine kinase activity (function)
0.000000 transmembrane receptor protein tyrosine kinase activity (function)
0.000000 receptor signaling protein tyrosine kinase activity (function)
0.000000 receptor activity (function)
0.000000 epidermal growth factor receptor activity (function)
0.000000 transmembrane receptor protein tyrosine kinase signaling protein activity (function)
0.000000 protein binding (function)
0.000000 ATP binding (function)
0.000025 plasma membrane (component)
0.000020 integral to plasma membrane (component)
0.000022 carbohydrate metabolism (process)
0.000054 generation of precursor metabolites and energy (process)
0.000000 protein amino acid phosphorylation (process)
0.000013 signal transduction (process)
0.000000 transmembrane receptor protein tyrosine kinase signaling pathway (process)
0.000017 development (process)
0.000000 insulin receptor signaling pathway (process)
0.000000 organ morphogenesis (process)
0.000000 membrane (component)
0.000016 integral to membrane (component)
0.000000 transferase activity (function)
0.000000 male sex determination (process)
BLASTX hits:
E-value 1e-12 prot=1136..1292 DNA=74587303..74587794 fr=1383 per=50/167 [EST]
CANDIDATE 9
DNA (Note) PROTEIN: [NP_116192]
R-score = 0.026523; GO-score = 0.000052
67850000 bp Chromosome X 77850000 bp
   
    
1 aa NP_003037 657 aa

Similarity found to protein:
[6542|NP_003037] | Homo sapiens | solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 | length=657 aa
GO annotation:
0.000019 membrane fraction (component)
0.000020 integral to plasma membrane (component)
0.000052 amino acid metabolism (process)
0.000000 transport (process)
0.000000 amino acid transport (process)
0.000000 basic amino acid transporter activity (function)
0.000000 amino acid permease activity (function)
0.000000 membrane (component)
0.000016 integral to membrane (component)
BLASTX hits:
E-value 1e-38 prot=2..126 DNA=69932869..69932498 fr=657 per=92/126 [EST]
E-value 5e-48 prot=277..439 DNA=69930896..69930132 fr=657 per=101/255 [EST]
E-value 5e-48 prot=245..281 DNA=69931116..69931006 fr=657 per=29/37 [EST]
CANDIDATE 10
DNA (Note) PROTEIN: [NP_001005609] [NP_001390]
R-score = 0.045797; GO-score = 0.000041
67850000 bp Chromosome X 77850000 bp
   
   
1 aa NP_034229 391 aa

Similarity found to protein:
[13607|NP_034229] | Mus musculus | ectodysplasin-A | length=391 aa
GO annotation:
0.000000 tumor necrosis factor receptor binding (function)
0.000000 cytoplasm (component)
0.000041 endoplasmic reticulum membrane (component)
0.000020 integral to plasma membrane (component)
0.000000 phosphate transport (process)
0.000011 immune response (process)
0.000000 cell-matrix adhesion (process)
0.000017 development (process)
0.000000 salivary gland development (process)
0.000000 membrane (component)
0.000016 integral to membrane (component)
0.000000 cell differentiation (process)
0.000000 positive regulation of NF-kappaB import into nucleus (process)
0.000000 apical part of cell (component)
BLASTX hits:
E-value 3e-37 prot=308..386 DNA=69038227..69038463 fr=391 per=78/79 [EST]
E-value 6e-17 prot=265..309 DNA=69036269..69036403 fr=391 per=45/45 [EST]