Analysis of agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)
Analysis of agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome) G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)
Method: Md
Chromosome: 15
Genomic position start-stop: 25700000-42600000
length: 16900001
Band: 15q13-q15
 LINKS

EntrezGene: [8124]

MEDLINE:

OMIM: [218000] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 2 papers related to this disease was derived from MEDLINE using the query:
agenesis [tw] AND corpus [tw] AND callosum [tw] AND peripheral [tw] AND neuropathy [tw] AND Andermann [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).

Peripheral Nervous System Diseases [2]
Syndrome [2]
Mental Retardation [2]
Abnormalities [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.

0.001822 regulation of cell migration (process)
0.001822 cytokine binding (function)
0.000911 transformed cell apoptosis (process)
0.000729 C-C chemokine receptor activity (function)
0.000683 tetrahydrobiopterin biosynthesis (process)
0.000622 carboxylesterase activity (function)
0.000622 cobalamin transport (process)
0.000592 cell death (process)
0.000546 peripheral nervous system development (process)
0.000526 nerve ensheathment (process)
We show here only the top 10. You can also see the complete list of 260 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to agenesis of corpus callosum and peripheral neuropathy (Andermann 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_061947]
R-score = 0.000805; GO-score = 0.001822
25700000 bp Chromosome 15 42600000 bp
   
   
1 aa NP_660142 1200 aa

Similarity found to protein:
[3714|NP_660142] | Homo sapiens | jagged 2 isoform b precursor | length=1200 aa
GO annotation:
0.000000 cell fate determination (process)
0.000000 Notch binding (function)
0.000014 calcium ion binding (function)
0.000025 integral to plasma membrane (component)
0.000000 cell cycle (process)
0.000000 Notch signaling pathway (process)
0.000039 cell-cell signaling (process)
0.000000 spermatogenesis (process)
0.000015 sensory perception of sound (process)
0.000063 growth factor activity (function)
0.000000 auditory receptor cell fate commitment (process)
0.000043 membrane (component)
0.000000 cell differentiation (process)
0.000000 T cell differentiation (process)
0.000000 embryonic limb morphogenesis (process)
0.001822 regulation of cell migration (process)
0.000000 regulation of cell proliferation (process)
0.000000 thymic T cell selection (process)
BLASTX hits:
E-value 2e-26 prot=307..502 DNA=39014038..39014586 fr=1200 per=72/201 [EST]
E-value 8e-20 prot=397..501 DNA=39015718..39016047 fr=1200 per=53/110 [EST]
E-value 4e-18 prot=320..424 DNA=39015718..39016041 fr=1200 per=46/109 [EST]
E-value 6e-18 prot=434..536 DNA=39015718..39016038 fr=1200 per=49/107 [EST]
E-value 7e-16 prot=723..829 DNA=39015712..39016044 fr=1200 per=45/111 [EST]
E-value 3e-15 prot=572..671 DNA=39015721..39016029 fr=1200 per=43/104 [EST]
E-value 2e-13 prot=610..709 DNA=39015718..39016029 fr=1200 per=40/104 [EST]
E-value 1e-13 prot=264..306 DNA=39011809..39011937 fr=1200 per=26/43 [EST]
E-value 4e-11 prot=423..640 DNA=39014038..39014586 fr=1200 per=63/223 [EST]
E-value 1e-13 prot=243..262 DNA=39011661..39011720 fr=1200 per=9/20 [EST]
CANDIDATE 2
DNA (Note) PROTEIN: [NP_598378]
R-score = 0.002014; GO-score = 0.000911
25700000 bp Chromosome 15 42600000 bp
   
   
1 aa NP_004031 196 aa

Similarity found to protein:
[388|NP_004031] | Homo sapiens | ras homolog gene family, member B | length=196 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000000 angiogenesis (process)
0.000019 protein binding (function)
0.000000 GTP binding (function)
0.000000 nucleus (component)
0.000030 plasma membrane (component)
0.000911 transformed cell apoptosis (process)
0.000000 cell cycle (process)
0.000014 cell adhesion (process)
0.000000 small GTPase mediated signal transduction (process)
0.000000 endosome to lysosome transport (process)
0.000000 endosome membrane (component)
0.000000 protein transport (process)
0.000000 cell differentiation (process)
0.000000 positive regulation of angiogenesis (process)
0.000000 negative regulation of progression through cell cycle (process)
BLASTX hits:
E-value 2e-22 prot=63..182 DNA=38952995..38952633 fr=196 per=56/121 [EST]
CANDIDATE 3
DNA (Note) PROTEIN: [NP_054825] [NP_689668]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.007940; GO-score = 0.000546
25700000 bp Chromosome 15 42600000 bp
     
   
1 aa NP_524818 541 aa

Similarity found to protein:
[45328|NP_524818] | Drosophila melanogaster | Lyra CG32120-PA | length=541 aa
GO annotation:

0.000025 transcription factor activity (function)
0.000013 RNA polymerase II transcription factor activity (function)
0.000000 nucleus (component)
0.000022 regulation of transcription from RNA polymerase II promoter (process)
0.000546 peripheral nervous system development (process)
0.000000 sensory organ development (process)
0.000011 zinc ion binding (function)
0.000054 cell proliferation (process)
0.000000 photoreceptor cell morphogenesis (sensu Endopterygota) (process)
0.000000 eye photoreceptor development (sensu Endopterygota) (process)
0.000000 negative regulation of epidermal growth factor receptor signaling pathway (process)
0.000000 regulation of transcription (process)
0.000000 R8 cell fate specification (process)
0.000000 R8 cell differentiation (process)
BLASTX hits:
E-value 2e-11 prot=356..497 DNA=33062622..33062197 fr=541 per=42/142 [EST] [P]
E-value 5e-11 prot=380..517 DNA=33062670..33062221 fr=541 per=44/152 [EST] [P]
E-value 1e-23 prot=389..522 DNA=41440995..41440594 fr=541 per=54/134 [EST] [P]
E-value 1e-22 prot=413..526 DNA=41441091..41440750 fr=541 per=53/114 [EST] [P]
E-value 3e-22 prot=375..524 DNA=41441118..41440672 fr=541 per=58/150 [EST] [P]
E-value 7e-16 prot=411..524 DNA=41441178..41440840 fr=541 per=47/114 [EST] [P]
E-value 5e-14 prot=413..495 DNA=41440839..41440591 fr=541 per=40/83 [EST] [P]
CANDIDATE 4
DNA (Note) PROTEIN: [NP_002390] [NP_064534] [NP_733774] [NP_733775] [NP_733776] [NP_733777] [NP_758526] [NP_758527]
R-score = 0.011162; GO-score = 0.000546
25700000 bp Chromosome 15 42600000 bp
   
   
1 aa NP_476578 457 aa

Similarity found to protein:
[41273|NP_476578] | Drosophila melanogaster | hth-P3 CG17117-PC | length=457 aa
GO annotation:
0.000000 eye photoreceptor fate commitment (sensu Endopterygota) (process)
0.000025 transcription factor activity (function)
0.000000 nucleus (component)
0.000022 regulation of transcription from RNA polymerase II promoter (process)
0.000103 brain development (process)
0.000546 peripheral nervous system development (process)
0.000000 salivary gland determination (process)
0.000000 eye development (sensu Endopterygota) (process)
0.000000 leg disc proximal/distal pattern formation (process)
0.000000 proximal/distal pattern formation (process)
0.000000 specification of organ identity (process)
BLASTX hits:
E-value 3e-17 prot=86..134 DNA=35175923..35175777 fr=457 per=42/49 [EST]
CANDIDATE 5
DNA (Note) PROTEIN: [NP_060023] [NP_115572]
R-score = 0.012830; GO-score = 0.000521
25700000 bp Chromosome 15 42600000 bp
   
   
1 aa NP_524833 3198 aa

Similarity found to protein:
[45655|NP_524833] | Drosophila melanogaster | domino CG9696-PE | length=3198 aa
GO annotation:
0.000000 larval or pupal development (sensu Insecta) (process)
0.000000 nucleic acid binding (function)
0.000027 DNA binding (function)
0.000000 DNA helicase activity (function)
0.000000 DNA ligase (ATP) activity (function)
0.000000 DNA topoisomerase (ATP-hydrolyzing) activity (function)
0.000000 helicase activity (function)
0.000000 ATP binding (function)
0.000000 nucleus (component)
0.000015 DNA replication (process)
0.000000 DNA topological change (process)
0.000000 DNA repair (process)
0.000033 DNA recombination (process)
0.000000 establishment and/or maintenance of chromatin architecture (process)
0.000022 regulation of transcription from RNA polymerase II promoter (process)
0.000000 border follicle cell migration (sensu Insecta) (process)
0.000000 DNA-dependent ATPase activity (function)
0.000054 cell proliferation (process)
0.000000 oogenesis (sensu Insecta) (process)
0.000000 general RNA polymerase II transcription factor activity (function)
0.000000 gene silencing (process)
0.000000 chromatin remodeling complex (component)
0.000521 hemopoiesis (process)
0.000000 negative regulation of hemocyte proliferation (sensu Arthropoda) (process)
BLASTX hits:
E-value 9e-11 prot=1748..1802 DNA=39067465..39067301 fr=3198 per=33/55 [EST]
CANDIDATE 6
DNA (Note) PROTEIN: [NP_619649]
R-score = 0.026811; GO-score = 0.000305
25700000 bp Chromosome 15 42600000 bp
   
   
1 aa NP_057241 1387 aa

Similarity found to protein:
[7216|NP_057241] | Homo sapiens | trophinin isoform 4 | length=1387 aa
GO annotation:
0.000019 protein binding (function)
0.000030 plasma membrane (component)
0.000025 integral to plasma membrane (component)
0.000014 cell adhesion (process)
0.000305 homophilic cell adhesion (process)
0.000000 embryo implantation (process)
BLASTX hits:
E-value 5e-49 prot=400..606 DNA=27348950..27348324 fr=1387 per=100/210 [EST]
CANDIDATE 7
DNA (Note) PROTEIN: [NP_005249] (Itself)
R-score = 0.029170; GO-score = 0.000303
25700000 bp Chromosome 15 42600000 bp
   
  
1 aa NP_005249 84 aa

Similarity found to protein:
[2644|NP_005249] | Homo sapiens | GTP cyclohydrolase I feedback regulatory protein | length=84 aa
GO annotation:
0.000303 nitric oxide biosynthesis (process)
0.000000 neurotransmitter metabolism (process)
BLASTX hits:
E-value 8e-15 prot=45..84 DNA=38846718..38846837 fr=84 per=40/40 [EST]
CANDIDATE 8
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.030148; GO-score = 0.000268
25700000 bp Chromosome 15 42600000 bp
     
       
1 aa NP_651678 1374 aa

Similarity found to protein:
[43450|NP_651678] | Drosophila melanogaster | CG11897-PB | length=1374 aa
GO annotation:

0.000000 nucleotide binding (function)
0.000000 ATP binding (function)
0.000000 extracellular transport (process)
0.000040 defense response (process)
0.000000 xenobiotic-transporting ATPase activity (function)
0.000000 nitrogen fixation (process)
0.000268 response to toxin (process)
0.000000 multidrug transporter activity (function)
0.000020 integral to membrane (component)
0.000000 nitrogenase activity (function)
BLASTX hits:
E-value 4e-21 prot=1222..1331 DNA=26323423..26323752 fr=1374 per=41/110 [EST] [P]
E-value 3e-11 prot=1231..1331 DNA=26551138..26550836 fr=1374 per=39/101 [EST] [P]
E-value 2e-14 prot=561..660 DNA=26323417..26323713 fr=1374 per=33/100 [EST] [P]
E-value 2e-13 prot=561..660 DNA=26551171..26550875 fr=1374 per=32/100 [EST] [P]
E-value 4e-21 prot=1095..1192 DNA=26323025..26323324 fr=1374 per=31/100 [EST] [P]
E-value 2e-14 prot=469..538 DNA=26323091..26323339 fr=1374 per=26/83 [EST] [P]
E-value 2e-13 prot=469..538 DNA=26551497..26551249 fr=1374 per=26/83 [EST] [P]
CANDIDATE 9
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.030493; GO-score = 0.000268
25700000 bp Chromosome 15 42600000 bp
     
   
1 aa NP_647634 606 aa

Similarity found to protein:
[38193|NP_647634] | Drosophila melanogaster | CG7955-PC | length=606 aa
GO annotation:

0.000000 nucleotide binding (function)
0.000024 transporter activity (function)
0.000000 ATP binding (function)
0.000030 mitochondrial inner membrane (component)
0.000000 extracellular transport (process)
0.000040 defense response (process)
0.000268 response to toxin (process)
0.000000 heme transporter activity (function)
0.000000 heme transport (process)
0.000020 integral to membrane (component)
0.000000 iron-sulfur cluster assembly (process)
0.000000 ATPase activity, coupled to transmembrane movement of substances (function)
0.000000 ATP-binding cassette (ABC) transporter complex (component)
BLASTX hits:
E-value 6e-44 prot=453..584 DNA=26551225..26550827 fr=606 per=64/133 [EST] [P]
E-value 4e-43 prot=453..584 DNA=26323363..26323761 fr=606 per=63/133 [EST] [P]
E-value 6e-44 prot=347..445 DNA=26551557..26551255 fr=606 per=44/101 [EST] [P]
E-value 4e-43 prot=347..445 DNA=26323031..26323333 fr=606 per=44/101 [EST] [P]
CANDIDATE 10
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.031011; GO-score = 0.000268
25700000 bp Chromosome 15 42600000 bp
     
     
1 aa NP_609215 1327 aa

Similarity found to protein:
[34148|NP_609215] | Drosophila melanogaster | CG7627-PA | length=1327 aa
GO annotation:

0.000000 nucleotide binding (function)
0.000024 transporter activity (function)
0.000000 ATP binding (function)
0.000000 extracellular transport (process)
0.000040 defense response (process)
0.000000 xenobiotic-transporting ATPase activity (function)
0.000268 response to toxin (process)
0.000020 integral to membrane (component)
0.000000 ATPase activity, coupled to transmembrane movement of substances (function)
0.000000 ATP-binding cassette (ABC) transporter complex (component)
BLASTX hits:
E-value 4e-19 prot=1168..1287 DNA=26323360..26323719 fr=1327 per=40/120 [EST] [P]
E-value 3e-16 prot=509..627 DNA=26323369..26323713 fr=1327 per=40/119 [EST] [P]
E-value 3e-18 prot=1168..1287 DNA=26551228..26550869 fr=1327 per=39/120 [EST] [P]
E-value 5e-16 prot=509..627 DNA=26551219..26550875 fr=1327 per=40/119 [EST] [P]
E-value 4e-19 prot=1060..1159 DNA=26323025..26323324 fr=1327 per=30/101 [EST] [P]
E-value 3e-18 prot=1060..1159 DNA=26551563..26551264 fr=1327 per=30/101 [EST] [P]
E-value 5e-16 prot=439..503 DNA=26551488..26551255 fr=1327 per=23/78 [EST] [P]
E-value 3e-16 prot=439..503 DNA=26323100..26323333 fr=1327 per=23/78 [EST] [P]