Analysis of Amyotrophic lateral sclerosis with frontotemporal dementia
Analysis of Amyotrophic lateral sclerosis with frontotemporal dementia 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 with frontotemporal dementia
Method: Md
Chromosome: 9
Genomic position start-stop: 68600000-99600000
length: 31000001
Band: 9q21-q22
 LINKS

EntrezGene: [60497]

MEDLINE:

OMIM: [105550] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 27 papers related to this disease was derived from MEDLINE using the query:
Amyotrophic [tw] AND lateral [tw] AND sclerosis [tw] AND frontotemporal [tw] AND dementia [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 [18]
Dementia [18]
Motor Neuron Disease [6]
Atrophy [4]
Disease Progression [3]
Pick Disease of the Brain [3]
Supranuclear Palsy, Progressive [3]
Parkinson Disease [3]
Nerve Degeneration [3]
Syndrome [3]
We show here only the 10 most frequent. You can also see the complete list of 27 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.

0.005999 dopamine biosynthesis from tyrosine (process)
0.005999 tyrosine 3-monooxygenase activity (function)
0.005999 catecholamine metabolism (process)
0.003000 aromatic amino acid family metabolism (process)
0.002259 copper, zinc superoxide dismutase activity (function)
0.002259 intracellular copper ion transport (process)
0.001883 intracellular copper ion transporter (function)
0.001412 superoxide metabolism (process)
0.001125 neurofilament (component)
0.001027 copper ion binding (function)
We show here only the top 10. You can also see the complete list of 195 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to Amyotrophic lateral sclerosis with frontotemporal dementia. 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)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.003337; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_062001 505 aa

Similarity found to protein:
[24503|NP_062001] | Rattus norvegicus | internexin, alpha | length=505 aa
GO annotation:

0.000048 structural molecule activity (function)
0.000089 structural constituent of cytoskeleton (function)
0.000000 kinesin complex (component)
0.000021 intermediate filament (component)
0.001125 neurofilament (component)
0.000100 nervous system development (process)
0.000000 tissue regeneration (process)
0.000000 intermediate filament cytoskeleton organization and biogenesis (process)
BLASTX hits:
E-value 2e-15 prot=226..404 DNA=78881538..78881008 fr=505 per=48/179 [EST] [P]
E-value 2e-15 prot=93..217 DNA=78881935..78881561 fr=505 per=31/125 [EST] [P]
E-value 2e-39 prot=92..398 DNA=99147262..99148176 fr=505 per=101/307 [EST] [P]
CANDIDATE 2
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.003395; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_058725 845 aa

Similarity found to protein:
[24588|NP_058725] | Rattus norvegicus | neurofilament 3, medium | length=845 aa
GO annotation:

0.000048 structural molecule activity (function)
0.000089 structural constituent of cytoskeleton (function)
0.000000 kinesin complex (component)
0.000021 intermediate filament (component)
0.001125 neurofilament (component)
0.000000 axon (component)
0.000000 intermediate filament cytoskeleton organization and biogenesis (process)
BLASTX hits:
E-value 2e-19 prot=231..407 DNA=78881538..78881008 fr=845 per=48/177 [EST] [P]
E-value 2e-19 prot=98..222 DNA=78881935..78881561 fr=845 per=36/127 [EST] [P]
E-value 5e-41 prot=97..401 DNA=99147262..99148176 fr=845 per=95/305 [EST] [P]
CANDIDATE 3
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.003452; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_006149 544 aa

Similarity found to protein:
[4747|NP_006149] | Homo sapiens | neurofilament, light polypeptide 68kDa | length=544 aa
GO annotation:

0.000048 structural molecule activity (function)
0.000089 structural constituent of cytoskeleton (function)
0.000015 protein binding (function)
0.000021 intermediate filament (component)
0.001125 neurofilament (component)
0.000000 axon (component)
BLASTX hits:
E-value 2e-12 prot=223..404 DNA=78881538..78880987 fr=544 per=58/184 [EST] [P]
E-value 1e-43 prot=78..392 DNA=99147235..99148176 fr=544 per=110/318 [EST] [P]
CANDIDATE 4
DNA (Note)
R-score = 0.003510; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
   
   
1 aa NP_116116 499 aa

Similarity found to protein:
[9118|NP_116116] | Homo sapiens | internexin neuronal intermediate filament protein, alpha | length=499 aa
GO annotation:
0.000089 structural constituent of cytoskeleton (function)
0.001125 neurofilament (component)
0.000100 nervous system development (process)
0.000000 cell differentiation (process)
BLASTX hits:
E-value 3e-39 prot=92..398 DNA=99147262..99148176 fr=499 per=101/307 [EST]
CANDIDATE 5
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.003567; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_005373 916 aa

Similarity found to protein:
[4741|NP_005373] | Homo sapiens | neurofilament 3 (150kDa medium) | length=916 aa
GO annotation:

0.000089 structural constituent of cytoskeleton (function)
0.001125 neurofilament (component)
0.000000 axon (component)
BLASTX hits:
E-value 8e-20 prot=233..409 DNA=78881538..78881008 fr=916 per=48/177 [EST] [P]
E-value 8e-20 prot=100..224 DNA=78881935..78881561 fr=916 per=36/127 [EST] [P]
E-value 1e-41 prot=99..403 DNA=99147262..99148176 fr=916 per=95/305 [EST] [P]
CANDIDATE 6
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.003625; GO-score = 0.001125
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_032717 849 aa

Similarity found to protein:
[18040|NP_032717] | Mus musculus | neurofilament 3, medium | length=849 aa
GO annotation:

0.000048 structural molecule activity (function)
0.000021 intermediate filament (component)
0.001125 neurofilament (component)
0.000000 intermediate filament cytoskeleton organization and biogenesis (process)
BLASTX hits:
E-value 1e-19 prot=232..408 DNA=78881538..78881008 fr=849 per=48/177 [EST] [P]
E-value 1e-19 prot=99..223 DNA=78881935..78881561 fr=849 per=36/127 [EST] [P]
E-value 3e-41 prot=98..402 DNA=99147262..99148176 fr=849 per=95/305 [EST] [P]
CANDIDATE 7
DNA (Note) PROTEIN: [NP_001001662] [NP_001007102] [NP_055745] [NP_113674] [NP_919301]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.005581; GO-score = 0.001027
68600000 bp Chromosome 9 99600000 bp
       
   
1 aa NP_038942 287 aa

Similarity found to protein:
[30927|NP_038942] | Mus musculus | snail homolog 3 | length=287 aa
GO annotation:

0.000000 nucleic acid binding (function)
0.000000 transcription factor activity (function)
0.000000 electron transporter activity (function)
0.001027 copper ion binding (function)
0.000000 nucleus (component)
0.000000 transcription factor complex (component)
0.000000 electron transport (process)
0.000000 regulation of transcription, DNA-dependent (process)
0.000000 zinc ion binding (function)
0.000000 heme binding (function)
0.000000 metal ion binding (function)
BLASTX hits:
E-value 1e-20 prot=147..280 DNA=92688635..92688237 fr=287 per=58/137 [EST] [P]
E-value 3e-20 prot=147..281 DNA=92688971..92688570 fr=287 per=52/137 [EST] [P]
E-value 2e-18 prot=147..279 DNA=92689307..92688912 fr=287 per=54/136 [EST] [P]
E-value 4e-18 prot=147..279 DNA=92688887..92688492 fr=287 per=50/136 [EST] [P]
E-value 1e-17 prot=147..280 DNA=92689391..92688993 fr=287 per=50/137 [EST] [P]
E-value 2e-16 prot=147..278 DNA=92688803..92688411 fr=287 per=53/135 [EST] [P]
E-value 5e-16 prot=147..280 DNA=92689559..92689161 fr=287 per=47/136 [EST] [P]
E-value 2e-15 prot=147..270 DNA=92688551..92688183 fr=287 per=48/127 [EST] [P]
E-value 1e-14 prot=147..279 DNA=92689223..92688828 fr=287 per=50/136 [EST] [P]
E-value 7e-13 prot=147..279 DNA=92689643..92689248 fr=287 per=45/135 [EST] [P]
E-value 1e-19 prot=147..279 DNA=94142516..94142911 fr=287 per=54/135 [EST] [P]
E-value 3e-16 prot=130..279 DNA=94142306..94142743 fr=287 per=50/152 [EST] [P]
E-value 1e-13 prot=149..281 DNA=94142102..94142497 fr=287 per=41/136 [EST] [P]
E-value 3e-13 prot=147..275 DNA=94142600..94142983 fr=287 per=48/132 [EST] [P]
E-value 9e-13 prot=149..278 DNA=94142774..94143160 fr=287 per=48/133 [EST] [P]
E-value 1e-23 prot=147..281 DNA=96660177..96659776 fr=287 per=58/138 [EST] [P]
E-value 1e-22 prot=131..279 DNA=96660384..96659950 fr=287 per=60/152 [EST] [P]
E-value 5e-21 prot=131..278 DNA=96660636..96660205 fr=287 per=62/151 [EST] [P]
E-value 3e-20 prot=129..280 DNA=96601419..96600976 fr=287 per=56/154 [EST] [P]
E-value 9e-19 prot=147..279 DNA=96601458..96601063 fr=287 per=52/136 [EST] [P]
E-value 7e-18 prot=146..262 DNA=96601041..96600694 fr=287 per=48/120 [EST] [P]
E-value 1e-17 prot=147..279 DNA=96601206..96600811 fr=287 per=50/136 [EST] [P]
E-value 1e-16 prot=146..279 DNA=96601125..96600727 fr=287 per=49/137 [EST] [P]
E-value 2e-16 prot=147..279 DNA=96660093..96659698 fr=287 per=51/136 [EST] [P]
E-value 3e-16 prot=176..278 DNA=96601464..96601150 fr=287 per=44/105 [EST] [P]
E-value 7e-16 prot=147..279 DNA=96601290..96600895 fr=287 per=48/136 [EST] [P]
E-value 6e-15 prot=116..279 DNA=96660933..96660454 fr=287 per=54/166 [EST] [P]
E-value 7e-11 prot=203..279 DNA=96601461..96601231 fr=287 per=33/77 [EST] [P]
CANDIDATE 8
DNA (Note) PROTEIN: [NP_004551]
R-score = 0.009148; GO-score = 0.000791
68600000 bp Chromosome 9 99600000 bp
   
   
1 aa NP_037213 1055 aa

Similarity found to protein:
[25614|NP_037213] | Rattus norvegicus | protein tyrosine kinase 2 | length=1055 aa
GO annotation:
0.000791 microtubule cytoskeleton organization and biogenesis (process)
0.000000 blood vessel development (process)
0.000000 neuron migration (process)
0.000000 protein kinase activity (function)
0.000000 protein serine/threonine kinase activity (function)
0.000000 protein-tyrosine kinase activity (function)
0.000000 binding (function)
0.000015 protein binding (function)
0.000000 ATP binding (function)
0.000000 cytoskeleton (component)
0.000000 focal adhesion (component)
0.000000 protein amino acid phosphorylation (process)
0.000027 cell motility (process)
0.000000 integrin-mediated signaling pathway (process)
0.000000 kinase activity (function)
0.000000 transferase activity (function)
0.000000 extracellular matrix organization and biogenesis (process)
0.000000 establishment of nucleus localization (process)
BLASTX hits:
E-value 6e-46 prot=416..676 DNA=91566933..91566094 fr=1055 per=103/280 [EST]
CANDIDATE 9
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.011507; GO-score = 0.000652
68600000 bp Chromosome 9 99600000 bp
     
   
1 aa NP_006112 644 aa

Similarity found to protein:
[3848|NP_006112] | Homo sapiens | keratin 1 | length=644 aa
GO annotation:

0.000000 complement activation, lectin pathway (process)
0.000038 receptor activity (function)
0.000048 structural molecule activity (function)
0.000089 structural constituent of cytoskeleton (function)
0.000015 protein binding (function)
0.000000 sugar binding (function)
0.000000 cytoskeleton (component)
0.000021 intermediate filament (component)
0.000652 response to oxidative stress (process)
0.000101 epidermis development (process)
0.000000 membrane (component)
0.000000 fibrinolysis (process)
0.000000 regulation of angiogenesis (process)
BLASTX hits:
E-value 7e-15 prot=314..511 DNA=78881538..78880945 fr=644 per=44/198 [EST] [P]
E-value 7e-15 prot=180..305 DNA=78881932..78881561 fr=644 per=35/127 [EST] [P]
E-value 1e-100 prot=155..483 DNA=99147193..99148173 fr=644 per=190/329 [EST] [P]
CANDIDATE 10
DNA (Note) PROTEIN: [NP_000371]
R-score = 0.011737; GO-score = 0.000652
68600000 bp Chromosome 9 99600000 bp
   
    
1 aa NP_035858 272 aa

Similarity found to protein:
[22590|NP_035858] | Mus musculus | xeroderma pigmentosum, complementation group A | length=272 aa
GO annotation:
0.000000 DNA binding (function)
0.000000 damaged DNA binding (function)
0.000000 nucleus (component)
0.000000 DNA repair (process)
0.000000 nucleotide-excision repair (process)
0.000000 response to DNA damage stimulus (process)
0.000652 response to oxidative stress (process)
0.000000 metal ion binding (function)
BLASTX hits:
E-value 7e-23 prot=129..185 DNA=97529101..97528931 fr=272 per=53/57 [EST]
E-value 2e-19 prot=224..272 DNA=97517426..97517280 fr=272 per=45/49 [EST]
E-value 4e-13 prot=94..129 DNA=97531478..97531371 fr=272 per=34/36 [EST]