Analysis of Asthma chr5
Analysis of Asthma chr5 G2D Home
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REASONS FOR ASSOCIATION OVERVIEW OF CANDIDATES BEST 10 CANDIDATES BEST 100 CANDIDATES

CHROMOSOMAL REGION
Disease mapped: Asthma chr5
Method: Md
Chromosome: 5
Genomic position start-stop: 11752823-26460245
length: 14707423
Band: p15.2-p14.1
 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 chr5. 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_009049]
R-score = 0.003395; GO-score = 0.000291
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_597681 27118 aa

Similarity found to protein:
[7273|NP_597681] | Homo sapiens | titin isoform novex-3 | length=27118 aa
GO annotation:
0.000002 biological process unknown (process)
0.000000 condensed nuclear chromosome (component)
0.000291 peroxidase activity (function)
0.000004 protein serine/threonine kinase activity (function)
0.000004 protein-tyrosine kinase activity (function)
0.000008 receptor activity (function)
0.000000 hematopoietin/interferon-class (D200-domain) cytokine receptor activity (function)
0.000005 protein binding (function)
0.000006 calmodulin binding (function)
0.000004 ATP binding (function)
0.000007 cytoskeleton (component)
0.000005 carbohydrate metabolism (process)
0.000004 protein amino acid phosphorylation (process)
0.000019 muscle contraction (process)
0.000020 striated muscle contraction (process)
0.000001 regulation of striated muscle contraction (process)
0.000018 immune response (process)
0.000045 response to oxidative stress (process)
0.000003 mitosis (process)
0.000022 muscle development (process)
0.000013 structural constituent of muscle (function)
0.000006 membrane (component)
0.000000 myosin binding (function)
0.000000 myofibril (component)
0.000000 sarcomere (component)
0.000003 Z disc (component)
0.000000 myofibril assembly (process)
0.000000 identical protein binding (function)
0.000000 protein amino acid autophosphorylation (process)
0.000000 alpha-actinin binding (function)
BLASTX hits:
E-value 5e-14 prot=25066..25188 DNA=14560280..14560651 fr=27118 per=47/124 [EST]
CANDIDATE 2
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.022783; GO-score = 0.000094
11752823 bp Chromosome 5 26460245 bp
     
  
1 aa NP_524925 648 aa

Similarity found to protein:
[48572|NP_524925] | Drosophila melanogaster | Heat shock protein 60 related CG2830-PA | length=648 aa
GO annotation:

0.000004 ATP binding (function)
0.000018 mitochondrion (component)
0.000006 mitochondrial matrix (component)
0.000005 protein folding (process)
0.000000 'de novo' protein folding (process)
0.000000 protein targeting to mitochondrion (process)
0.000094 spermatid development (process)
0.000004 response to heat (process)
0.000000 protein refolding (process)
0.000000 ATPase activity, coupled (function)
0.000000 unfolded protein binding (function)
BLASTX hits:
E-value 3e-41 prot=20..120 DNA=19269308..19269610 fr=648 per=56/101 [EST] [P]
E-value 3e-41 prot=180..227 DNA=19269783..19269926 fr=648 per=24/48 [EST] [P]
E-value 3e-41 prot=124..179 DNA=19269616..19269783 fr=648 per=29/56 [EST] [P]
E-value 1e-157 prot=48..543 DNA=21918617..21920101 fr=648 per=281/496 [EST] [P]
E-value 1e-157 prot=1..38 DNA=21918472..21918585 fr=648 per=15/38 [EST] [P]
CANDIDATE 3
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.023014; GO-score = 0.000094
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_036802 556 aa

Similarity found to protein:
[24818|NP_036802] | Rattus norvegicus | t-complex protein 1 | length=556 aa
GO annotation:

0.000000 pericentriolar material (component)
0.000000 heterochromatin (component)
0.000004 ATP binding (function)
0.000000 nuclear heterochromatin (component)
0.000001 microtubule organizing center (component)
0.000006 cytosol (component)
0.000005 protein folding (process)
0.000000 tubulin folding (process)
0.000094 spermatid development (process)
0.000000 unfolded protein binding (function)
BLASTX hits:
E-value 2e-33 prot=57..390 DNA=14693251..14692262 fr=556 per=83/342 [EST] [P]
E-value 2e-33 prot=391..532 DNA=14692260..14691859 fr=556 per=44/142 [EST] [P]
E-value 2e-33 prot=15..55 DNA=14693379..14693257 fr=556 per=12/41 [EST] [P]
CANDIDATE 4
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.042403; GO-score = 0.000065
11752823 bp Chromosome 5 26460245 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 5e-19 prot=8..140 DNA=17544827..17544468 fr=140 per=66/136 [EST] [P]
E-value 9e-19 prot=20..133 DNA=17688340..17688002 fr=140 per=59/116 [EST] [P]
E-value 1e-11 prot=11..120 DNA=17703399..17703085 fr=140 per=49/111 [EST] [P]
E-value 1e-11 prot=119..134 DNA=17703085..17703038 fr=140 per=9/16 [EST] [P]
CANDIDATE 5
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.044819; GO-score = 0.000065
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_524354 430 aa

Similarity found to protein:
[41836|NP_524354] | Drosophila melanogaster | Chromatin assembly factor 1 subunit CG4236-PA | length=430 aa
GO annotation:

0.000010 negative regulation of transcription from RNA polymerase II promoter (process)
0.000065 chromatin binding (function)
0.000003 nucleus (component)
0.000003 transcription factor complex (component)
0.000000 chromatin assembly complex (component)
0.000000 polytene chromosome (component)
0.000004 DNA repair (process)
0.000001 nucleosome assembly (process)
0.000000 DNA replication-dependent nucleosome assembly (process)
0.000049 chromatin silencing (process)
0.000007 transcription (process)
0.000000 chorion gene amplification (process)
0.000000 histone methylation (process)
0.000000 histone acetylation (process)
0.000000 nucleosome spacing (process)
0.000001 chromatin remodeling complex (component)
0.000000 NURF complex (component)
0.000000 ACF complex (component)
0.000000 Myb complex (component)
0.000000 histone acetyltransferase binding (function)
0.000000 ESC/E(Z) complex (component)
0.000000 histone binding (function)
0.000000 nucleosome mobilization (process)
0.000000 histone deacetylase binding (function)
0.000000 histone lysine N-methyltransferase activity (H3-K9 specific) (function)
0.000000 histone lysine N-methyltransferase activity (H3-K27 specific) (function)
BLASTX hits:
E-value 0.0 prot=11..419 DNA=14850791..14849565 fr=430 per=355/409 [EST] [P]
CANDIDATE 6
DNA (Note) PROTEIN: [NP_064612]
R-score = 0.047638; GO-score = 0.000065
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_523867 502 aa

Similarity found to protein:
[38012|NP_523867] | Drosophila melanogaster | Kruppel CG3340-PA | length=502 aa
GO annotation:
0.000010 negative regulation of transcription from RNA polymerase II promoter (process)
0.000003 DNA binding (function)
0.000065 chromatin binding (function)
0.000005 specific RNA polymerase II transcription factor activity (function)
0.000003 nucleus (component)
0.000000 zygotic determination of anterior/posterior axis, embryo (process)
0.000000 neuroblast fate determination (process)
0.000000 ganglion mother cell fate determination (process)
0.000017 axon guidance (process)
0.000000 ventral cord development (process)
0.000001 Malpighian tubule morphogenesis (process)
0.000015 eye development (sensu Endopterygota) (process)
0.000022 muscle development (process)
0.000003 zinc ion binding (function)
0.000008 cell proliferation (process)
0.000002 transcriptional repressor activity (function)
0.000000 specific transcriptional repressor activity (function)
0.000000 trunk segmentation (process)
0.000000 regulation of development, heterochronic (process)
BLASTX hits:
E-value 5e-33 prot=219..353 DNA=23563020..23563424 fr=502 per=63/135 [EST]
E-value 9e-32 prot=219..353 DNA=23563104..23563508 fr=502 per=63/135 [EST]
E-value 2e-31 prot=219..353 DNA=23562936..23563340 fr=502 per=62/135 [EST]
E-value 1e-29 prot=219..353 DNA=23562852..23563256 fr=502 per=61/135 [EST]
E-value 2e-29 prot=219..353 DNA=23562768..23563172 fr=502 per=61/135 [EST]
E-value 7e-29 prot=219..353 DNA=23562684..23563088 fr=502 per=61/135 [EST]
E-value 3e-28 prot=219..353 DNA=23563188..23563592 fr=502 per=60/135 [EST]
E-value 8e-28 prot=219..336 DNA=23563272..23563625 fr=502 per=58/118 [EST]
E-value 2e-26 prot=219..353 DNA=23562600..23563004 fr=502 per=59/135 [EST]
E-value 6e-26 prot=86..353 DNA=23562084..23562920 fr=502 per=90/285 [EST]
CANDIDATE 7
DNA (Note)
R-score = 0.056901; GO-score = 0.000061
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_038866 930 aa

Similarity found to protein:
[22068|NP_038866] | Mus musculus | transient receptor potential cation channel, subfamily C, member 6 | length=930 aa
GO annotation:
0.000008 receptor activity (function)
0.000003 ion channel activity (function)
0.000003 cation channel activity (function)
0.000035 calcium channel activity (function)
0.000015 calcium ion binding (function)
0.000015 integral to plasma membrane (component)
0.000007 transport (process)
0.000004 ion transport (process)
0.000006 cation transport (process)
0.000009 calcium ion transport (process)
0.000061 elevation of cytosolic calcium ion concentration (process)
0.000004 store-operated calcium channel activity (function)
0.000006 membrane (component)
0.000005 integral to membrane (component)
BLASTX hits:
E-value 1e-27 prot=639..786 DNA=24785637..24785209 fr=930 per=84/159 [EST]
E-value 6e-17 prot=671..721 DNA=24785549..24785397 fr=930 per=45/51 [EST]
CANDIDATE 8
DNA (Note)
R-score = 0.057131; GO-score = 0.000061
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_035774 1172 aa

Similarity found to protein:
[22064|NP_035774] | Mus musculus | transient receptor potential cation channel, subfamily C, member 2 | length=1172 aa
GO annotation:
0.000002 single strand break repair (process)
0.000004 Golgi membrane (component)
0.000001 damaged DNA binding (function)
0.000008 receptor activity (function)
0.000003 ion channel activity (function)
0.000003 cation channel activity (function)
0.000035 calcium channel activity (function)
0.000015 calcium ion binding (function)
0.000005 protein binding (function)
0.000003 nucleus (component)
0.000007 nuclear envelope (component)
0.000010 endoplasmic reticulum membrane (component)
0.000007 transport (process)
0.000004 ion transport (process)
0.000006 cation transport (process)
0.000009 calcium ion transport (process)
0.000061 elevation of cytosolic calcium ion concentration (process)
0.000004 store-operated calcium channel activity (function)
0.000006 membrane (component)
0.000005 integral to membrane (component)
BLASTX hits:
E-value 1e-16 prot=917..973 DNA=24785400..24785230 fr=1172 per=35/57 [EST]
E-value 1e-16 prot=861..915 DNA=24785564..24785397 fr=1172 per=20/57 [EST]
CANDIDATE 9
DNA (Note)
R-score = 0.104367; GO-score = 0.000043
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_004428 588 aa

Similarity found to protein:
[2035|NP_004428] | Homo sapiens | erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked) | length=588 aa
GO annotation:
0.000013 actin binding (function)
0.000007 structural constituent of cytoskeleton (function)
0.000015 binding (function)
0.000003 nucleus (component)
0.000005 cytoplasm (component)
0.000007 cytoskeleton (component)
0.000020 plasma membrane (component)
0.000043 circulation (process)
0.000002 spectrin (component)
0.000000 cortical actin cytoskeleton organization and biogenesis (process)
BLASTX hits:
E-value 2e-19 prot=86..286 DNA=25945648..25946274 fr=588 per=60/213 [EST]
E-value 2e-19 prot=10..56 DNA=25945406..25945546 fr=588 per=14/47 [EST]
E-value 2e-19 prot=58..83 DNA=25945566..25945634 fr=588 per=11/26 [EST]
CANDIDATE 10
DNA (Note)

This candidate may be overlapping with a pseudogene (Note)
R-score = 0.125482; GO-score = 0.000040
11752823 bp Chromosome 5 26460245 bp
   
   
1 aa NP_610288 456 aa

Similarity found to protein:
[35681|NP_610288] | Drosophila melanogaster | CG12736-PA | length=456 aa
GO annotation:

0.000000 translation elongation factor activity (function)
0.000010 GTPase activity (function)
0.000006 GTP binding (function)
0.000018 mitochondrion (component)
0.000003 protein biosynthesis (process)
0.000040 translational elongation (process)
0.000003 regulation of translation (process)
BLASTX hits:
E-value 2e-23 prot=53..336 DNA=14705729..14704767 fr=456 per=91/324 [EST] [P]