Analysis of amyotrophic lateral sclerosis 3 (autosomal dominant)
Analysis of amyotrophic lateral sclerosis 3 (autosomal dominant) G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: amyotrophic lateral sclerosis 3 (autosomal dominant)
Chromosome: 18
Genomic position start-stop: 41800000-59800000
length: 18000001
Band: 18q21
 LINKS

EntrezGene: [253]

MEDLINE:

OMIM: [606640] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 16 papers related to this disease was derived from MEDLINE using the query:
amyotrophic [tw] AND lateral [tw] AND sclerosis [tw] AND 3 [tw] AND (autosomal [tw] AND dominant) [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).

Amyotrophic Lateral Sclerosis [13]
Motor Neuron Disease [3]
Parkinson Disease [2]
Multiple System Atrophy [1]
Alzheimer Disease [1]
Nerve Degeneration [1]
Dementia [1]
Disease Progression [1]
Muscle Spasticity [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.

0.013563 dopamine biosynthesis from tyrosine (process)
0.013563 catecholamine metabolism (process)
0.013563 tyrosine 3-monooxygenase activity (function)
0.006782 aromatic amino acid family metabolism (process)
0.005534 copper, zinc superoxide dismutase activity (function)
0.005534 intracellular copper ion transport (process)
0.004612 intracellular copper ion transporter (function)
0.003459 superoxide metabolism (process)
0.002754 neurofilament (component)
0.002515 copper ion binding (function)
We show here only the top 10. You can also see the complete list of 456 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to amyotrophic lateral sclerosis 3 (autosomal dominant). 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_000624] [NP_000648]
R-score = 0.009608; GO-score = 0.001596
41800000 bp Chromosome 18 59800000 bp
   
   
1 aa NP_113723 232 aa

Similarity found to protein:
[24888|NP_113723] | Rattus norvegicus | Bcl2-like 1 | length=232 aa
GO annotation:
0.000000 integral to membrane of membrane fraction (component)
0.000091 protein binding (function)
0.000000 mitochondrion (component)
0.000000 mitochondrial envelope (component)
0.000000 mitochondrial outer membrane (component)
0.000198 apoptosis (process)
0.000118 anti-apoptosis (process)
0.001596 response to oxidative stress (process)
0.000000 negative regulation of survival gene product activity (process)
0.000000 apoptotic mitochondrial changes (process)
0.000000 response to radiation (process)
0.000021 membrane (component)
0.000049 integral to membrane (component)
0.000000 regulation of apoptosis (process)
0.000000 caspase inhibitor activity (function)
0.000000 negative regulation of apoptosis (process)
BLASTX hits:
E-value 2e-37 prot=5..189 DNA=59136850..59136293 fr=232 per=89/190 [EST]
CANDIDATE 2
DNA (Note) PROTEIN: [NP_003190]
R-score = 0.010989; GO-score = 0.001596
41800000 bp Chromosome 18 59800000 bp
   
   
1 aa NP_477189 710 aa

Similarity found to protein:
[34413|NP_477189] | Drosophila melanogaster | da-P1 CG5102-PA | length=710 aa
GO annotation:
0.000040 DNA binding (function)
0.000061 transcription factor activity (function)
0.000038 specific RNA polymerase II transcription factor activity (function)
0.000000 cysteine-type endopeptidase activity (function)
0.000000 peroxidase activity (function)
0.000089 nucleus (component)
0.000029 regulation of transcription, DNA-dependent (process)
0.000021 regulation of transcription from RNA polymerase II promoter (process)
0.000140 proteolysis (process)
0.001596 response to oxidative stress (process)
0.000304 nervous system development (process)
0.000421 peripheral nervous system development (process)
0.000000 sex determination (process)
0.000000 sex determination, primary response to X:A ratio (process)
0.000000 oogenesis (sensu Insecta) (process)
0.000000 second mitotic wave (sensu Endopterygota) (process)
0.000000 transcriptional activator activity (function)
0.000000 ovarian follicle cell development (sensu Insecta) (process)
0.000000 R8 cell fate specification (process)
0.000000 positive regulation of transcription (process)
BLASTX hits:
E-value 9e-21 prot=536..612 DNA=51047308..51047078 fr=710 per=55/77 [EST]
CANDIDATE 3
DNA (Note) PROTEIN: [NP_000131] [NP_001012533]
R-score = 0.016340; GO-score = 0.001233
41800000 bp Chromosome 18 59800000 bp
   
      
1 aa NP_032024 422 aa

Similarity found to protein:
[14151|NP_032024] | Mus musculus | ferrochelatase | length=422 aa
GO annotation:
0.000000 ferrochelatase activity (function)
0.001233 iron ion binding (function)
0.000000 mitochondrion (component)
0.000000 mitochondrial inner membrane (component)
0.000000 porphyrin biosynthesis (process)
0.000000 heme biosynthesis (process)
0.000000 detection of UV (process)
0.000000 lyase activity (function)
0.000000 metal ion binding (function)
0.000000 iron-sulfur cluster binding (function)
0.000000 2 iron, 2 sulfur cluster binding (function)
BLASTX hits:
E-value 1e-21 prot=304..361 DNA=53372655..53372482 fr=422 per=52/58 [EST]
E-value 7e-19 prot=154..203 DNA=53384813..53384664 fr=422 per=46/50 [EST]
E-value 7e-18 prot=104..153 DNA=53389773..53389624 fr=422 per=47/50 [EST]
E-value 4e-14 prot=378..422 DNA=53369080..53368946 fr=422 per=39/45 [EST]
E-value 2e-11 prot=192..234 DNA=53381233..53381105 fr=422 per=34/43 [EST]
CANDIDATE 4
DNA (Note)
R-score = 0.032507; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
  
1 aa NP_031418 377 aa

Similarity found to protein:
[11475|NP_031418] | Mus musculus | actin, alpha 2, smooth muscle, aorta | length=377 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000032 motor activity (function)
0.000031 structural molecule activity (function)
0.000217 structural constituent of cytoskeleton (function)
0.000091 protein binding (function)
0.000000 ATP binding (function)
0.000040 cytoskeleton (component)
0.000000 actin filament (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000020 muscle development (process)
BLASTX hits:
E-value 1e-158 prot=166..377 DNA=58260714..58261340 fr=377 per=168/212 [EST]
E-value 1e-158 prot=60..174 DNA=58260395..58260739 fr=377 per=91/115 [EST]
E-value 1e-158 prot=4..59 DNA=58260226..58260393 fr=377 per=42/56 [EST]
CANDIDATE 5
DNA (Note)
R-score = 0.032852; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
  
1 aa NP_033740 393 aa

Similarity found to protein:
[11468|NP_033740] | Mus musculus | actin, gamma 2, smooth muscle, enteric | length=393 aa
GO annotation:
0.000000 nucleotide binding (function)
0.000032 motor activity (function)
0.000031 structural molecule activity (function)
0.000217 structural constituent of cytoskeleton (function)
0.000091 protein binding (function)
0.000000 ATP binding (function)
0.000040 cytoskeleton (component)
0.000000 actin filament (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000020 muscle development (process)
0.000034 structural constituent of muscle (function)
0.000022 actin cytoskeleton (component)
BLASTX hits:
E-value 1e-134 prot=165..334 DNA=58260714..58261214 fr=393 per=126/170 [EST]
E-value 1e-134 prot=59..173 DNA=58260395..58260739 fr=393 per=91/115 [EST]
E-value 1e-134 prot=3..58 DNA=58260226..58260393 fr=393 per=42/56 [EST]
E-value 1e-134 prot=334..354 DNA=58261222..58261284 fr=393 per=12/21 [EST]
CANDIDATE 6
DNA (Note)
R-score = 0.033485; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
     
1 aa NP_523968 418 aa

Similarity found to protein:
[38898|NP_523968] | Drosophila melanogaster | Actin-related protein 66B CG7558-PA | length=418 aa
GO annotation:
0.000000 actin binding (function)
0.000217 structural constituent of cytoskeleton (function)
0.000000 actin filament (component)
0.000000 Arp2/3 protein complex (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000000 cytoplasmic transport, nurse cell to oocyte (process)
0.000000 axonal fasciculation (process)
0.000000 regulation of actin polymerization and/or depolymerization (process)
0.000000 ovarian ring canal stabilization (process)
0.000022 actin cytoskeleton (component)
0.000000 actin filament reorganization during cell cycle (process)
0.000000 pseudocleavage (sensu Insecta) (process)
BLASTX hits:
E-value 5e-20 prot=73..183 DNA=58260419..58260727 fr=418 per=49/111 [EST]
E-value 3e-15 prot=173..410 DNA=58260696..58261331 fr=418 per=62/238 [EST]
E-value 5e-20 prot=7..65 DNA=58260241..58260393 fr=418 per=17/59 [EST]
CANDIDATE 7
DNA (Note)
R-score = 0.034118; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
                 
1 aa NP_058779 1846 aa

Similarity found to protein:
[25132|NP_058779] | Rattus norvegicus | myosin 5B | length=1846 aa
GO annotation:
0.000032 motor activity (function)
0.000000 actin binding (function)
0.000025 calmodulin binding (function)
0.000000 ATP binding (function)
0.000040 cytoskeleton (component)
0.000000 kinesin complex (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000000 myosin (component)
BLASTX hits:
E-value 2e-44 prot=1592..1711 DNA=45618247..45617885 fr=1846 per=98/121 [EST]
E-value 2e-41 prot=353..441 DNA=45754984..45754718 fr=1846 per=83/89 [EST]
E-value 3e-30 prot=860..939 DNA=45683202..45682963 fr=1846 per=70/80 [EST]
E-value 5e-29 prot=1158..1278 DNA=45644866..45644513 fr=1846 per=77/122 [EST]
E-value 6e-28 prot=734..803 DNA=45687008..45686799 fr=1846 per=62/70 [EST]
E-value 5e-24 prot=939..1017 DNA=45675546..45675310 fr=1846 per=59/79 [EST]
E-value 1e-22 prot=49..104 DNA=45820677..45820510 fr=1846 per=52/56 [EST]
E-value 1e-19 prot=469..516 DNA=45742775..45742632 fr=1846 per=48/48 [EST]
E-value 3e-19 prot=102..154 DNA=45817370..45817212 fr=1846 per=49/53 [EST]
E-value 4e-19 prot=151..204 DNA=45781785..45781624 fr=1846 per=52/54 [EST]
E-value 5e-19 prot=1565..1615 DNA=45619666..45619514 fr=1846 per=49/51 [EST]
E-value 1e-18 prot=1797..1846 DNA=45606992..45606843 fr=1846 per=47/50 [EST]
E-value 7e-18 prot=203..252 DNA=45772806..45772657 fr=1846 per=46/50 [EST]
E-value 9e-18 prot=1356..1405 DNA=45633967..45633818 fr=1846 per=48/50 [EST]
E-value 8e-17 prot=1710..1770 DNA=45617259..45617077 fr=1846 per=58/61 [EST]
E-value 4e-16 prot=1492..1535 DNA=45623741..45623610 fr=1846 per=43/44 [EST]
E-value 5e-16 prot=515..563 DNA=45734807..45734661 fr=1846 per=41/49 [EST]
E-value 2e-14 prot=1130..1180 DNA=45656202..45656047 fr=1846 per=46/52 [EST]
E-value 4e-14 prot=1090..1131 DNA=45658257..45658132 fr=1846 per=41/42 [EST]
E-value 1e-11 prot=1445..1488 DNA=45627635..45627504 fr=1846 per=37/44 [EST]
E-value 2e-11 prot=4..47 DNA=45835765..45835634 fr=1846 per=35/44 [EST]
E-value 3e-11 prot=1274..1312 DNA=45643714..45643598 fr=1846 per=35/39 [EST]
E-value 9e-11 prot=638..736 DNA=45692691..45692431 fr=1846 per=47/103 [EST]
CANDIDATE 8
DNA (Note)
R-score = 0.034175; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
    
1 aa NP_033741 440 aa

Similarity found to protein:
[11470|NP_033741] | Mus musculus | actin-like 7a | length=440 aa
GO annotation:
0.000000 male germ cell nucleus (component)
0.000031 structural molecule activity (function)
0.000217 structural constituent of cytoskeleton (function)
0.000091 protein binding (function)
0.000040 cytoskeleton (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000000 flagellum (sensu Eukaryota) (component)
BLASTX hits:
E-value 5e-25 prot=227..440 DNA=58260696..58261340 fr=440 per=77/219 [EST]
E-value 1e-24 prot=134..237 DNA=58260416..58260727 fr=440 per=45/104 [EST]
E-value 1e-24 prot=74..124 DNA=58260235..58260387 fr=440 per=17/51 [EST]
CANDIDATE 9
DNA (Note)
R-score = 0.034290; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
  
1 aa NP_524331 376 aa

Similarity found to protein:
[41566|NP_524331] | Drosophila melanogaster | Actin-related protein 87C CG6174-PA | length=376 aa
GO annotation:
0.000032 motor activity (function)
0.000000 actin binding (function)
0.000217 structural constituent of cytoskeleton (function)
0.000000 dynactin complex (component)
0.000000 actin filament (component)
0.000918 cytoskeleton organization and biogenesis (process)
0.000022 actin cytoskeleton (component)
BLASTX hits:
E-value 6e-82 prot=169..376 DNA=58260714..58261340 fr=376 per=91/212 [EST]
E-value 6e-82 prot=61..177 DNA=58260392..58260739 fr=376 per=62/117 [EST]
E-value 6e-82 prot=12..64 DNA=58260244..58260402 fr=376 per=24/53 [EST]
CANDIDATE 10
DNA (Note)
R-score = 0.034808; GO-score = 0.000918
41800000 bp Chromosome 18 59800000 bp
   
    
1 aa NP_079547 418 aa

Similarity found to protein:
[11471|NP_079547] | Mus musculus | actin-like 7b | length=418 aa
GO annotation:
0.000031 structural molecule activity (function)
0.000217 structural constituent of cytoskeleton (function)
0.000091 protein binding (function)
0.000134 cytoplasm (component)
0.000040 cytoskeleton (component)
0.000918 cytoskeleton organization and biogenesis (process)
BLASTX hits:
E-value 5e-27 prot=205..418 DNA=58260696..58261337 fr=418 per=83/218 [EST]
E-value 6e-22 prot=112..215 DNA=58260416..58260727 fr=418 per=44/104 [EST]
E-value 6e-22 prot=53..102 DNA=58260241..58260387 fr=418 per=19/50 [EST]