Analysis of Alzheimer disease 5
Analysis of Alzheimer disease 5 G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: Alzheimer disease 5
Method: Md
Chromosome: 12
Genomic position start-stop: 26400000-49800000
length: 23400001
Band: 12p11.23-q13.12
 LINKS

EntrezGene: [8081]

MEDLINE:

OMIM: [602096] XplorMed

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 3137 papers related to this disease was derived from MEDLINE using the query:
Alzheimer [tw] AND disease [tw] AND 5 [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).

Alzheimer Disease [2698]
Dementia [502]
Dementia, Vascular [162]
Parkinson Disease [152]
Down Syndrome [91]
Atrophy [83]
Nerve Degeneration [78]
Dementia, Multi-Infarct [73]
Disease Models, Animal [63]
Disease Progression [55]
We show here only the 10 most frequent. You can also see the complete list of 363 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.

0.010645 copper ion homeostasis (process)
0.010219 amyloid protein (function)
0.007097 cell death (process)
0.006385 beta-aspartyl-peptidase activity (function)
0.005873 serine-type endopeptidase inhibitor activity (function)
0.005385 arylesterase activity (function)
0.005321 chromosome segregation (process)
0.005277 microtubule cytoskeleton organization and biogenesis (process)
0.005041 integral to nuclear inner membrane (component)
We show here only the top 10. You can also see the complete list of 916 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to Alzheimer disease 5. 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 = 0.002301; GO-score = 0.005873
26400000 bp Chromosome 12 49800000 bp
     
   
1 aa NP_000085 2944 aa

Similarity found to protein:
[1294|NP_000085] | Homo sapiens | alpha 1 type VII collagen precursor | length=2944 aa
GO annotation:

0.005873 serine-type endopeptidase inhibitor activity (function)
0.000320 structural molecule activity (function)
0.000357 protein binding (function)
0.000000 collagen type VII (component)
0.001002 basement membrane (component)
0.000530 cytoplasm (component)
0.000000 phosphate transport (process)
0.000277 cell adhesion (process)
0.000334 epidermis development (process)
BLASTX hits:
E-value 3e-15 prot=1857..2780 DNA=39166302..39169187 fr=2944 per=283/1045 [EST] [P]
E-value 8e-20 prot=1277..1794 DNA=49033643..49031940 fr=2944 per=154/590 [EST] [P]
E-value 1e-15 prot=1689..2283 DNA=49033616..49031925 fr=2944 per=155/621 [EST] [P]
E-value 1e-15 prot=1406..1936 DNA=49033568..49032042 fr=2944 per=138/576 [EST] [P]
E-value 1e-14 prot=2143..2740 DNA=49033643..49031910 fr=2944 per=158/625 [EST] [P]
E-value 2e-11 prot=2057..2601 DNA=49033643..49032033 fr=2944 per=144/581 [EST] [P]
CANDIDATE 2
DNA (Note)
R-score = 0.003855; GO-score = 0.005873
26400000 bp Chromosome 12 49800000 bp
   
   
1 aa NP_000005 1474 aa

Similarity found to protein:
[2|NP_000005] | Homo sapiens | alpha 2 macroglobulin precursor | length=1474 aa
GO annotation:
0.005873 serine-type endopeptidase inhibitor activity (function)
0.000282 extracellular space (component)
0.000908 intracellular protein transport (process)
0.000000 protein carrier activity (function)
0.000000 wide-spectrum protease inhibitor activity (function)
0.000000 enzyme binding (function)
0.000000 interleukin-8 binding (function)
0.000000 interleukin-1 binding (function)
0.000000 tumor necrosis factor binding (function)
0.000000 protein homooligomerization (process)
BLASTX hits:
E-value 5e-12 prot=752..824 DNA=31180371..31180153 fr=1474 per=33/73 [EST]
CANDIDATE 3
DNA (Note)
R-score = 0.006789; GO-score = 0.005873
26400000 bp Chromosome 12 49800000 bp
   
   
1 aa NP_031402 1495 aa

Similarity found to protein:
[11287|NP_031402] | Mus musculus | pregnancy zone protein | length=1495 aa
GO annotation:
0.000233 endopeptidase inhibitor activity (function)
0.005873 serine-type endopeptidase inhibitor activity (function)
0.001191 extracellular region (component)
0.000282 extracellular space (component)
0.000000 wide-spectrum protease inhibitor activity (function)
BLASTX hits:
E-value 2e-12 prot=766..837 DNA=31180365..31180150 fr=1495 per=33/72 [EST]
CANDIDATE 4
DNA (Note)
R-score = 0.007479; GO-score = 0.005873
26400000 bp Chromosome 12 49800000 bp
   
   
1 aa NP_036620 1472 aa

Similarity found to protein:
[24153|NP_036620] | Rattus norvegicus | alpha-2-macroglobulin | length=1472 aa
GO annotation:
0.000233 endopeptidase inhibitor activity (function)
0.005873 serine-type endopeptidase inhibitor activity (function)
0.000460 receptor binding (function)
0.001191 extracellular region (component)
0.000282 extracellular space (component)
0.000908 intracellular protein transport (process)
0.000420 acute-phase response (process)
0.000198 inflammatory response (process)
0.000000 protein carrier activity (function)
0.001368 response to wounding (process)
0.000000 wide-spectrum protease inhibitor activity (function)
0.000000 enzyme binding (function)
0.000000 interleukin-8 binding (function)
0.000000 interleukin-1 binding (function)
0.000000 protease inhibitor activity (function)
0.000000 tumor necrosis factor binding (function)
0.000000 negative regulation of calcium-mediated signaling (process)
0.000000 protein homooligomerization (process)
BLASTX hits:
E-value 4e-11 prot=750..822 DNA=31180371..31180153 fr=1472 per=30/73 [EST]
CANDIDATE 5
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.011104; GO-score = 0.005321
26400000 bp Chromosome 12 49800000 bp
   
  
1 aa NP_649324 769 aa

Similarity found to protein:
[40384|NP_649324] | Drosophila melanogaster | SAK gene product CG7186-PA | length=769 aa
GO annotation:

0.000199 protein kinase activity (function)
0.000165 protein serine/threonine kinase activity (function)
0.000025 receptor signaling protein serine/threonine kinase activity (function)
0.000037 protein-tyrosine kinase activity (function)
0.000093 ATP binding (function)
0.000195 protein amino acid phosphorylation (process)
0.005321 chromosome segregation (process)
0.000469 mitosis (process)
0.000032 intracellular signaling cascade (process)
0.000000 embryonic development (process)
BLASTX hits:
E-value 6e-11 prot=114..207 DNA=45362445..45362164 fr=769 per=33/95 [EST] [P]
E-value 6e-11 prot=1..103 DNA=45362779..45362471 fr=769 per=32/104 [EST] [P]
CANDIDATE 6
DNA (Note) PROTEIN: [NP_006000] [NP_006073] [NP_116093]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.012255; GO-score = 0.005277
26400000 bp Chromosome 12 49800000 bp
       
  
1 aa NP_059075 449 aa

Similarity found to protein:
[53857|NP_059075] | Mus musculus | tubulin, alpha 8 | length=449 aa
GO annotation:

0.000000 nucleotide binding (function)
0.005277 microtubule cytoskeleton organization and biogenesis (process)
0.000054 GTPase activity (function)
0.000320 structural molecule activity (function)
0.000570 structural constituent of cytoskeleton (function)
0.000182 GTP binding (function)
0.000152 microtubule (component)
0.000231 microtubule-based movement (process)
0.000000 protein complex (component)
0.000000 protein polymerization (process)
BLASTX hits:
E-value 3e-26 prot=140..434 DNA=34209887..34209036 fr=449 per=90/306 [EST] [P]
E-value 3e-14 prot=93..188 DNA=34210029..34209742 fr=449 per=41/96 [EST] [P]
E-value 6e-44 prot=235..443 DNA=36883213..36883815 fr=449 per=68/209 [EST] [P]
E-value 6e-44 prot=169..235 DNA=36883010..36883210 fr=449 per=32/67 [EST] [P]
E-value 1e-162 prot=127..432 DNA=47808986..47808069 fr=449 per=290/306 [EST] [P]
E-value 1e-162 prot=127..432 DNA=47952307..47953224 fr=449 per=289/306 [EST] [P]
E-value 1e-161 prot=127..430 DNA=47866038..47865127 fr=449 per=288/304 [EST] [P]
E-value 1e-25 prot=2..82 DNA=47866884..47866642 fr=449 per=58/81 [EST] [P]
E-value 3e-49 prot=2..82 DNA=47949516..47949758 fr=449 per=58/81 [EST] [P]
E-value 3e-49 prot=2..82 DNA=47809773..47809531 fr=449 per=58/81 [EST] [P]
E-value 6e-22 prot=159..219 DNA=47755616..47755798 fr=449 per=52/61 [EST] [P]
E-value 2e-18 prot=76..125 DNA=47866510..47866361 fr=449 per=47/50 [EST] [P]
E-value 3e-49 prot=76..125 DNA=47949878..47950027 fr=449 per=47/50 [EST] [P]
E-value 3e-49 prot=76..125 DNA=47809442..47809293 fr=449 per=47/50 [EST] [P]
CANDIDATE 7
DNA (Note) PROTEIN: [NP_056983]

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.016800; GO-score = 0.004548
26400000 bp Chromosome 12 49800000 bp
   
   
1 aa NP_002547 807 aa

Similarity found to protein:
[5007|NP_002547] | Homo sapiens | oxysterol binding protein | length=807 aa
GO annotation:

0.000530 cytoplasm (component)
0.000058 Golgi stack (component)
0.004548 lipid transport (process)
0.000000 oxysterol binding (function)
0.000000 steroid metabolism (process)
BLASTX hits:
E-value 9e-11 prot=95..283 DNA=43854752..43854246 fr=807 per=58/192 [EST] [P]
CANDIDATE 8
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.022553; GO-score = 0.003097
26400000 bp Chromosome 12 49800000 bp
     
   
1 aa NP_057367 172 aa

Similarity found to protein:
[6880|NP_057367] | Homo sapiens | adrenal gland protein AD-004 | length=172 aa
GO annotation:

0.000000 nucleotide binding (function)
0.000159 DNA binding (function)
0.000028 transcription coactivator activity (function)
0.000000 adenylate kinase activity (function)
0.000000 shikimate kinase activity (function)
0.000093 ATP binding (function)
0.000350 nucleus (component)
0.000000 transcription factor TFIID complex (component)
0.000049 transcription (process)
0.000000 transcription initiation (process)
0.000113 regulation of transcription, DNA-dependent (process)
0.000039 transcription from RNA polymerase II promoter (process)
0.003097 protein C-terminus binding (function)
0.000000 amino acid biosynthesis (process)
0.000000 general RNA polymerase II transcription factor activity (function)
0.000000 transferase activity (function)
0.000000 nucleotide kinase activity (function)
BLASTX hits:
E-value 4e-65 prot=68..158 DNA=34293886..34294158 fr=172 per=77/91 [EST] [P]
E-value 4e-65 prot=2..68 DNA=34293689..34293889 fr=172 per=57/67 [EST] [P]
E-value 3e-60 prot=9..159 DNA=36759048..36758599 fr=172 per=123/154 [EST] [P]
CANDIDATE 9
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.025890; GO-score = 0.002902
26400000 bp Chromosome 12 49800000 bp
   
  
1 aa NP_004929 1431 aa

Similarity found to protein:
[1612|NP_004929] | Homo sapiens | death-associated protein kinase 1 | length=1431 aa
GO annotation:

0.000000 nucleotide binding (function)
0.000165 protein serine/threonine kinase activity (function)
0.000000 calmodulin-dependent protein kinase I activity (function)
0.000058 calcium- and calmodulin-dependent protein kinase activity (function)
0.000037 protein-tyrosine kinase activity (function)
0.000098 calmodulin binding (function)
0.000093 ATP binding (function)
0.000195 protein amino acid phosphorylation (process)
0.002456 apoptosis (process)
0.000472 signal transduction (process)
0.000079 protein kinase cascade (process)
0.002902 induction of apoptosis by extracellular signals (process)
0.000108 actin cytoskeleton (component)
0.000000 transferase activity (function)
BLASTX hits:
E-value 1e-11 prot=114..221 DNA=45362448..45362134 fr=1431 per=36/109 [EST] [P]
E-value 1e-11 prot=13..107 DNA=45362737..45362465 fr=1431 per=33/95 [EST] [P]
CANDIDATE 10
DNA (Note) PROTEIN: [NP_056085] [NP_066193]
R-score = 0.026811; GO-score = 0.002688
26400000 bp Chromosome 12 49800000 bp
   
       
1 aa NP_511156 2248 aa

Similarity found to protein:
[32406|NP_511156] | Drosophila melanogaster | rutabaga CG9533-PA | length=2248 aa
GO annotation:
0.000030 adenylate cyclase activity (function)
0.000013 guanylate cyclase activity (function)
0.000997 integral to plasma membrane (component)
0.000027 cAMP biosynthesis (process)
0.000477 G-protein coupled receptor protein signaling pathway (process)
0.000000 molting cycle (sensu Insecta) (process)
0.000188 learning and/or memory (process)
0.000108 learning (process)
0.002688 memory (process)
0.000000 mating behavior (process)
0.000000 courtship behavior (process)
0.000000 grooming behavior (process)
0.000000 calcium- and calmodulin-responsive adenylate cyclase activity (function)
0.000000 olfactory learning (process)
0.000163 cAMP-mediated signaling (process)
0.000000 behavioral response to ethanol (process)
BLASTX hits:
E-value 2e-23 prot=907..1003 DNA=47452042..47451755 fr=2248 per=58/97 [EST]
E-value 4e-24 prot=357..403 DNA=47456633..47456493 fr=2248 per=39/47 [EST]
E-value 1e-13 prot=241..311 DNA=47457772..47457464 fr=2248 per=52/103 [EST]
E-value 7e-13 prot=313..355 DNA=47457282..47457154 fr=2248 per=35/43 [EST]
E-value 3e-12 prot=1075..1117 DNA=47449113..47448985 fr=2248 per=37/43 [EST]
E-value 4e-24 prot=409..455 DNA=47456400..47456260 fr=2248 per=23/47 [EST]