Analysis of Asthma chr17
Analysis of Asthma chr17 G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: Asthma chr17
Method: Md
Chromosome: 17
Genomic position start-stop: 70213402-80213402
length: 10000001
Band: q25.1-q25.3
 LINKS

EntrezGene: no link

MEDLINE:

OMIM: no link

REASONS FOR ASSOCIATION

MEDLINE QUERY
A set of 4317 papers related to asthma was derived from MEDLINE using the query:
Asthma [MH] AND Case Report [MH]

MESH-C TERMS
The MeSH-C terms associated to the derived papers were collected and manually filtered.

Here you can see the terms ordered by the fraction of papers where they were found.

Asthma [0.957365269461078]
Status Asthmaticus [0.0548502994011976]
Drug Hypersensitivity [0.0431137724550898]
Bronchial Spasm [0.0304191616766467]
Eosinophilia [0.0297005988023952]
Bronchitis [0.0239520958083832]
Airway Obstruction [0.0239520958083832]
Rhinitis [0.0208383233532934]
Food Hypersensitivity [0.0205988023952096]
Anaphylaxis [0.0203592814371257]
We show here only the 10 most frequent. You can also see the complete list of 50 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.

0.000797 peptidyl-dipeptidase activity (function)
0.000404 interleukin-5 receptor activity (function)
0.000356 fluid secretion (process)
0.000291 peroxidase activity (function)
0.000283 protein kinase inhibitor activity (function)
0.000261 pancreatic elastase activity (function)
0.000233 leukotriene-C4 synthase activity (function)
0.000230 renin activity (function)
0.000230 cathepsin D activity (function)
0.000228 angiotensin type II receptor activity (function)
We show here only the top 10. You can also see the complete list of 2490 GO terms.

Each name is linked to the corresponding term description by GO. The number indicates the strength of association to Asthma chr17. 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_003946] (Itself)
R-score = 0.004430; GO-score = 0.000283
70213402 bp Chromosome 17 80213402 bp
   
 
1 aa NP_003946 225 aa

Similarity found to protein:
[9021|NP_003946] | Homo sapiens | suppressor of cytokine signaling 3 | length=225 aa
GO annotation:
0.000002 regulation of cell growth (process)
0.000283 protein kinase inhibitor activity (function)
0.000017 anti-apoptosis (process)
0.000008 intracellular signaling cascade (process)
0.000020 JAK-STAT cascade (process)
0.000000 negative regulation of signal transduction (process)
BLASTX hits:
E-value 1e-105 prot=1..225 DNA=73866772..73866098 fr=225 per=224/225 [EST]
CANDIDATE 2
DNA (Note) PROTEIN: [NP_003848]
R-score = 0.010471; GO-score = 0.000164
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_037203 398 aa

Similarity found to protein:
[25601|NP_037203] | Rattus norvegicus | opioid receptor, mu 1 | length=398 aa
GO annotation:
0.000000 rhodopsin-like receptor activity (function)
0.000008 receptor activity (function)
0.000013 G-protein coupled receptor activity (function)
0.000019 neuropeptide Y receptor activity (function)
0.000005 opioid receptor activity (function)
0.000024 mu-opioid receptor activity (function)
0.000006 membrane fraction (component)
0.000005 endoplasmic reticulum (component)
0.000002 Golgi apparatus (component)
0.000015 integral to plasma membrane (component)
0.000018 immune response (process)
0.000032 G-protein coupled receptor protein signaling pathway (process)
0.000015 G-protein signaling, coupled to cyclic nucleotide second messenger (process)
0.000012 dopamine receptor, adenylate cyclase activating pathway (process)
0.000007 G-protein signaling, adenylate cyclase inhibiting pathway (process)
0.000019 sensory perception (process)
0.000164 behavior (process)
0.000005 negative regulation of cell proliferation (process)
0.000005 integral to membrane (component)
0.000000 purinergic nucleotide receptor activity, G-protein coupled (function)
BLASTX hits:
E-value 3e-18 prot=166..351 DNA=71584314..71584865 fr=398 per=58/189 [EST]
CANDIDATE 3
DNA (Note) PROTEIN: [NP_000204] [NP_001005619] [NP_001005731]
R-score = 0.012830; GO-score = 0.000162
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_058060 787 aa

Similarity found to protein:
[16416|NP_058060] | Mus musculus | integrin beta 3 | length=787 aa
GO annotation:
0.000008 receptor activity (function)
0.000005 protein binding (function)
0.000000 cell-substrate junction assembly (process)
0.000013 cell adhesion (process)
0.000011 cell-matrix adhesion (process)
0.000007 integrin-mediated signaling pathway (process)
0.000003 metabolism (process)
0.000009 integrin complex (component)
0.000000 external side of plasma membrane (component)
0.000005 integral to membrane (component)
0.000000 oxidoreductase activity (function)
0.000162 regulation of cell migration (process)
BLASTX hits:
E-value 9e-11 prot=261..356 DNA=71237924..71238208 fr=787 per=43/98 [EST]
CANDIDATE 4
DNA (Note) PROTEIN: [NP_001249]
R-score = 0.013578; GO-score = 0.000162
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_031694 292 aa

Similarity found to protein:
[12568|NP_031694] | Mus musculus | cyclin-dependent kinase 5 | length=292 aa
GO annotation:
0.000005 nucleotide binding (function)
0.000004 protein kinase activity (function)
0.000004 protein serine/threonine kinase activity (function)
0.000001 cyclin-dependent protein kinase activity (function)
0.000005 protein binding (function)
0.000004 ATP binding (function)
0.000006 cytosol (component)
0.000004 protein amino acid phosphorylation (process)
0.000006 cell cycle (process)
0.000011 cell-matrix adhesion (process)
0.000002 axonogenesis (process)
0.000002 kinase activity (function)
0.000024 cell migration (process)
0.000003 transferase activity (function)
0.000001 lamellipodium (component)
0.000000 filopodium (component)
0.000162 regulation of cell migration (process)
0.000000 cell division (process)
BLASTX hits:
E-value 2e-32 prot=64..163 DNA=71509694..71510101 fr=292 per=63/136 [EST]
E-value 2e-32 prot=158..205 DNA=71510176..71510319 fr=292 per=24/48 [EST]
CANDIDATE 5
DNA (Note)
R-score = 0.015362; GO-score = 0.000124
70213402 bp Chromosome 17 80213402 bp
   
  
1 aa NP_112734 1424 aa

Similarity found to protein:
[1285|NP_112734] | Homo sapiens | alpha 3 type IV collagen isoform 5, precursor | length=1424 aa
GO annotation:
0.000124 serine carboxypeptidase activity (function)
0.000010 integrin binding (function)
0.000041 extracellular matrix structural constituent (function)
0.000005 protein binding (function)
0.000014 collagen (component)
0.000010 collagen type IV (component)
0.000005 cytoplasm (component)
0.000023 proteolysis (process)
0.000000 phosphate transport (process)
0.000015 induction of apoptosis (process)
0.000006 caspase activation (process)
0.000013 cell adhesion (process)
0.000023 cell surface receptor linked signal transduction (process)
0.000005 sensory perception of sound (process)
0.000043 circulation (process)
0.000017 metalloendopeptidase inhibitor activity (function)
0.000008 cell proliferation (process)
0.000005 negative regulation of cell proliferation (process)
0.000000 negative regulation of angiogenesis (process)
BLASTX hits:
E-value 2e-38 prot=578..1275 DNA=78526076..78528247 fr=1424 per=216/784 [EST]
E-value 7e-37 prot=586..1370 DNA=78526028..78528202 fr=1424 per=224/846 [EST]
E-value 2e-33 prot=736..1420 DNA=78526077..78528332 fr=1424 per=211/794 [EST]
E-value 2e-25 prot=126..833 DNA=78526027..78528114 fr=1424 per=211/787 [EST]
E-value 4e-24 prot=253..1033 DNA=78526032..78528317 fr=1424 per=214/855 [EST]
E-value 1e-22 prot=170..958 DNA=78526056..78528317 fr=1424 per=224/861 [EST]
E-value 9e-21 prot=43..690 DNA=78526057..78528117 fr=1424 per=194/737 [EST]
E-value 2e-17 prot=1124..1420 DNA=78526056..78526970 fr=1424 per=99/324 [EST]
E-value 4e-16 prot=43..642 DNA=78526426..78528129 fr=1424 per=166/651 [EST]
CANDIDATE 6
DNA (Note) PROTEIN: [NP_036550]
R-score = 0.021920; GO-score = 0.000094
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_062515 498 aa

Similarity found to protein:
[56223|NP_062515] | Mus musculus | fascin 3 | length=498 aa
GO annotation:
0.000013 actin binding (function)
0.000005 cytoplasm (component)
0.000094 spermatid development (process)
0.000000 protein binding, bridging (function)
0.000000 actin filament binding (function)
BLASTX hits:
E-value 7e-13 prot=16..278 DNA=77110187..77110972 fr=498 per=72/265 [EST]
CANDIDATE 7
DNA (Note) PROTEIN: [NP_002350] [NP_116100]
R-score = 0.032392; GO-score = 0.000081
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_611500 132 aa

Similarity found to protein:
[37336|NP_611500] | Drosophila melanogaster | CG9954 gene product CG9954-PA | length=132 aa
GO annotation:
0.000004 transcription factor activity (function)
0.000003 nucleus (component)
0.000007 transcription (process)
0.000005 regulation of transcription from RNA polymerase II promoter (process)
0.000002 mesoderm development (process)
0.000081 hemopoiesis (process)
0.000000 salivary gland cell autophagic cell death (process)
0.000000 protein homodimerization activity (function)
0.000000 protein heterodimerization activity (function)
0.000000 autophagic cell death (process)
BLASTX hits:
E-value 4e-14 prot=13..118 DNA=77474253..77473909 fr=132 per=55/117 [EST]
CANDIDATE 8
DNA (Note) PROTEIN: [NP_004101] [NP_077728]
R-score = 0.035038; GO-score = 0.000078
70213402 bp Chromosome 17 80213402 bp
   
    
1 aa NP_032023 494 aa

Similarity found to protein:
[14149|NP_032023] | Mus musculus | ferredoxin reductase | length=494 aa
GO annotation:
0.000001 ferredoxin-NADP+ reductase activity (function)
0.000018 mitochondrion (component)
0.000007 mitochondrial inner membrane (component)
0.000003 electron transport (process)
0.000013 lipid metabolism (process)
0.000007 transport (process)
0.000008 steroid metabolism (process)
0.000078 cholesterol metabolism (process)
0.000001 disulfide oxidoreductase activity (function)
0.000000 oxidoreductase activity (function)
BLASTX hits:
E-value 2e-41 prot=395..455 DNA=70370965..70370783 fr=494 per=53/61 [EST]
E-value 2e-43 prot=337..402 DNA=70371788..70371588 fr=494 per=51/67 [EST]
E-value 2e-43 prot=240..337 DNA=70372291..70371866 fr=494 per=72/142 [EST]
E-value 2e-41 prot=452..494 DNA=70370666..70370538 fr=494 per=40/43 [EST]
E-value 5e-11 prot=135..173 DNA=70373962..70373846 fr=494 per=34/39 [EST]
CANDIDATE 9
DNA (Note) PROTEIN: [NP_005315]
R-score = 0.042403; GO-score = 0.000065
70213402 bp Chromosome 17 80213402 bp
   
   
1 aa NP_001800 140 aa

Similarity found to protein:
[1058|NP_001800] | Homo sapiens | centromere protein A | length=140 aa
GO annotation:
0.000000 chromosome, pericentric region (component)
0.000000 nucleosome (component)
0.000003 DNA binding (function)
0.000065 chromatin binding (function)
0.000003 nucleus (component)
0.000000 chromosome (component)
0.000001 nucleosome assembly (process)
0.000003 chromosome organization and biogenesis (sensu Eukaryota) (process)
BLASTX hits:
E-value 3e-15 prot=95..134 DNA=71286403..71286284 fr=140 per=28/40 [EST]
E-value 3e-15 prot=30..95 DNA=71286693..71286487 fr=140 per=36/71 [EST]
CANDIDATE 10
DNA (Note) PROTEIN: [NP_005180]
R-score = 0.043208; GO-score = 0.000065
70213402 bp Chromosome 17 80213402 bp
   
  
1 aa NP_031649 519 aa

Similarity found to protein:
[12416|NP_031649] | Mus musculus | chromobox homolog 2 | length=519 aa
GO annotation:
0.000000 chromatin (component)
0.000003 DNA binding (function)
0.000065 chromatin binding (function)
0.000005 protein binding (function)
0.000003 nucleus (component)
0.000000 chromatin assembly or disassembly (process)
0.000007 transcription (process)
0.000005 regulation of transcription, DNA-dependent (process)
0.000000 chromatin modification (process)
BLASTX hits:
E-value 1e-145 prot=96..519 DNA=75372124..75373434 fr=519 per=332/439 [EST]