GATACA

Credits

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Data

Data - ToppGene Sources

The vast majority of all data in Gataca is from ToppGene so its credits cover data sources that are used within Gataca. The primary reason for utilizing the same sources between these applications is to help ensure consistancy between them. ToppGene, and Gataca, uses data from over 20 sources.

For ToppGene Credits, please visit:

ToppGene Links (Credits)

Data - GUDMAP

GUDMAP

The GUDMAP data within Gataca is only availble within the GUDMAP interface:

Gataca's GUDMAP

Data - UMLSKS

UMLSKS website

Software

Software - Solr

Solr website

Software - PrototypeJS

Prototype JS website

Prototype JavaScript framework, version 1.7
(c) 2005-2010 Sam Stephenson
 
Prototype is freely distributable under the terms of an MIT-style license.
For details, see the Prototype web site: http://www.prototypejs.org/

Software - script.aculo.us

Script.aculo.us website

NOTE: Only the effects.js and dragdrop.js modules from Script.aculo.us are being used.

// script.aculo.us scriptaculous.js v1.9.0, Thu Dec 23 16:54:48 -0500 2010

// Copyright (c) 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
//
// Permission is hereby granted, free of charge, to any person obtaining
// a copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to
// permit persons to whom the Software is furnished to do so, subject to
// the following conditions:
//
// The above copyright notice and this permission notice shall be
// included in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
// LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
// OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//
// For details, see the script.aculo.us web site: http://script.aculo.us/

Software - canvasXpress

canvasXpress website

CanvasXpress is a javascript library based on the <canvas> tag implemented in HTML5.

This package is currently being used for the Venn Diagram within SetBuilder. Plans are to utilize it in other areas in the generation of other graphs.

Software - Oracle Enterprise Edition

Oracle website

The data within Gataca is being stored in an Oracle 11g database.

Software - Modernizr

modernizr

modernizr provides simple interfacing to check to see what features are available within the client's browser. This is predomantly used to test for HTML 5 features such as canvas or local storage support.

Software - JQTouch

JQTouch website

JQTouch is being used for the mobile edition of Gataca.

Software - jQuery

JQuery website

jQuery is used within JQTouch only.

Software - tablesort

tablesort website

Copyright (c) 2006 Andrew Tetlaw 
http://tetlaw.id.au/view/blog/table-sorting-with-prototype/

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

Software - Firebug Light

Firebug Light website

firebugx.js - There is no disclaimer in the original file, but it is an open source project. The main website is http://www.getfirebug.com It is an open source project hosted by Google code.

Link-It Detail - Disease - Cerebral Amyloid Angiopathy

Debug Stats

### Total Build Time: 40 ms 36.680 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 352 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 706 bytes
Skipping details on: CONCEPT_SYNONYM gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
Skipping details on: CONCEPT_TEXT gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_SEMANTIC_TYPE gt=1 ms Completed: 1 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 991 bytes
CONCEPT_CHILDREN gt=2 ms Completed: 2 ms rowSize= 575 bytes
CONCEPT_ANCESTRAL_ROOTS gt=9 ms Completed: 9 ms rowSize= 4.084 KB
CONCEPT_RELATIONSHIPS gt=13 ms Completed: 13 ms rowSize= 13.121 KB
CONCEPT_GENES gt=9 ms Completed: 9 ms rowSize= 15.540 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.161 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Cerebral Amyloid Angiopathy C0085220

Definition (1)

A heterogeneous group of sporadic or familial disorders characterized by AMYLOID deposits in the walls of small and medium sized blood vessels of CEREBRAL CORTEX and MENINGES. Clinical features include multiple, small lobar CEREBRAL HEMORRHAGE; cerebral ischemia (BRAIN ISCHEMIA); and CEREBRAL INFARCTION. Cerebral amyloid angiopathy is unrelated to generalized AMYLOIDOSIS. Amyloidogenic peptides in this condition are nearly always the same ones found in ALZHEIMER DISEASE. (from Kumar: Robbins and Cotran: Pathologic Basis of Disease, 7th ed., 2005)

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0002726

C0007774

Children (1)

C0268393

Ancestral Roots

Root	Root Plus One	Depth	Parent
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	5	Amyloidosis C0002726
Cardiovascular Diseases C0007222	Vascular Diseases C0042373	6	Cerebral Arterial Diseases C0007774
Nervous System Diseases C0027765	Central Nervous System Diseases C0007682	7	Cerebral Arterial Diseases C0007774

Relationships (33)

Relation Types:

diso_to_anat : 9

diso_to_chem : 6

diso_to_diso : 15

diso_to_phen : 2

diso_to_phys : 1

Relationships:

none : 24

is_associated_anatomic_site_of : 4

is_primary_anatomic_site_of_disease : 1

isa : 2

mapped_to : 1

permuted_term_of : 1

Page Size

Current 25

100

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Page 1 of 2

Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	96		Complication Aspects C1171258
DISO_to_DISO	59		Complication Aspects C1171258
DISO_to_DISO	54		Alzheimer Disease C0002395
DISO_to_ANAT	53		Brain C0006104
DISO_to_DISO	53		Alzheimer Disease C0002395
DISO_to_CHEM	50		Amyloid beta-Peptides C0078939
DISO_to_DISO	47		Cerebral Hemorrhage C2937358
DISO_to_PHEN	47		genetic aspects C0017399
DISO_to_PHEN	45		genetic aspects C0017399
DISO_to_ANAT	36		Brain C0006104
DISO_to_CHEM	35		Amyloid beta-Peptides C0078939
DISO_to_DISO	30		Cerebral Hemorrhage C2937358
DISO_to_ANAT	14		Cerebral Arteries C0007770
DISO_to_CHEM	14		Amyloid beta-Protein Precursor C0085151
DISO_to_DISO	12		Plaque, Amyloid C2936349
DISO_to_ANAT	11		Cerebral Cortex C0007776
DISO_to_CHEM	11		Apolipoprotein E C0003595
DISO_to_CHEM	11		Fragments, Peptide C0030935
DISO_to_DISO	11		Dementia C0497327
DISO_to_DISO	11		HEMORRHAGE SUBARACHNOID C0038525
DISO_to_CHEM	9		Amyloid beta-Protein Precursor C0085151
DISO_to_DISO	9		ANGIITIS CNS C0751878
DISO_to_DISO	9		BLEEDING INTRACRANIAL C0151699
DISO_to_PHYS	9		Aging C0001811
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Brain C0006104

Genes (9)

Species:

human : 9

Species	Gene	GeneId	Gene Name	Evidence
Human	HSPB8	26353	heat shock 22kDa protein 8	GENERIF, Score=1000, Pubmed Id: 16485107, UMLKSK CUI: C0085220 HspB8 might play important role in regulating Abeta aggregation and, therefore, development of classic senile plaques in Alzheimer's disease and cerebral amyloid angiopathy in hereditary cerebral hemorrhage with amyloidosis of Dutch type
Human	PSEN1	5663	presenilin 1	GAD, Score=1000, Pubmed Id: 9368568, UMLKSK CUI: C0085220 Title:Association of presenilin-1 polymorphism with cerebral amyloid angiopathy in the elderly.\|Association:Y\|Conclusion:Our results suggest that PS-1 intronic polymorphism may be associated with the severity of CAA in the elderly.
Human	MME	4311	membrane metallo-endopeptidase	GENERIF, Score=1000, Pubmed Id: 12387451, UMLKSK CUI: C0085220 Expression declines in Alzheimer disease vasculature; possibly involved in cerebral amyloid angiopathy GENERIF, Score=1000, Pubmed Id: 12754344, UMLKSK CUI: C0085220 nep gene polymorphism is associated with cerebral amyloid angiopathy
Human	MBP	4155	myelin basic protein	GENERIF, Score=679, Pubmed Id: 17259179, UMLKSK CUI: C0085220 MBP inhibits the fibril assembly of cerebral amyloid angiopathy mutant amyloid beta-protein (Abeta)
Human	LRP1	4035	low density lipoprotein receptor-related protein 1	GAD, Score=1000, Pubmed Id: 15634227, UMLKSK CUI: C0085220 Title:Genetic-morphologic association study: associationbetween the low density lipoprotein-receptor related protein (LRP) and cerebral amyloid angiopathy.\|Association:Y\|Conclusion:Our results lead us to postulate that the LRP5'87 bp and the LRP exon 3 C alleles of the LRP gene (or another locus that might be in linkage disequilibrium with these LRP polymorphic sites) could modify cerebrovascular LRP function or expression in noncapillary cerebral vessels, leading to an increased cerebrovascular amyloid deposition.
Human	CST3	1471	cystatin C	GENERIF, Score=923, Pubmed Id: 16612983, UMLKSK CUI: C0085220 Accumulating data suggest involvement of cystatin C in the pathogenic processes leading to amyloid deposition in cerebral vasculature and most significantly to cerebral hemorrhage in patients with cerebral amyloid angiopathy {REVIEW}
Human	APP	351	amyloid beta (A4) precursor protein	GENERIF, Score=1000, Pubmed Id: 18413480, UMLKSK CUI: C0085220 Positron emission tomography with 11C-PiB and magnetic resonance imaging were performed for 2 patients, 49-year-old and 60-year-old siblings with APP locus duplication, with hereditary Alzheimer disease and cerebral amyloid angiopathy GENERIF, Score=1000, Pubmed Id: 16555084, UMLKSK CUI: C0085220 This suggests that distinct mechanisms are responsible for the differential deposition of Abeta in cerebral amyloid angiopathy associated with Alzheimer's disease and that associated with ischemic/cerebrovascular disease GENERIF, Score=1000, Pubmed Id: 12944403, UMLKSK CUI: C0085220 beta-sheet content of Abeta mutants correlates with their aggregation and role in cerebral amyloid angiopathy
Human	APOE	348	apolipoprotein E	GENERIF, Score=717, Pubmed Id: 11676291, UMLKSK CUI: C0085220 gene polymorphism as a risk factor for cerebral amyloid angiopathy-related hemorrhage GENERIF, Score=1000, Pubmed Id: 11676289, UMLKSK CUI: C0085220 APOE polymorphisms in cerebral amyloid angiopathy GAD, Score=1000, Pubmed Id: 15634227, UMLKSK CUI: C0085220 Title:Genetic-morphologic association study: associationbetween the low density lipoprotein-receptor related protein (LRP) and cerebral amyloid angiopathy.\|Association:Not Found\|Conclusion:Our results lead us to postulate that the LRP5'87 bp and the LRP exon 3 C alleles of the LRP gene (or another locus that might be in linkage disequilibrium with these LRP polymorphic sites) could modify cerebrovascular LRP function or expression in noncapillary cerebral vessels, leading to an increased cerebrovascular amyloid deposition. GENERIF, Score=1000, Pubmed Id: 12960780, UMLKSK CUI: C0085220 possession of epsilon4 does not by itself confer an increased risk of cerebral amyloid angiopathy but may be associated with reduced longevity even in the absence of alzheimer's disease or cerebral haemorrhage
Human	SERPINA3	12	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	GAD, Score=1000, Pubmed Id: 11132933, UMLKSK CUI: C0085220 Title:Increased frequency of the alpha-1-antichymotrypsin T allele in cerebral amyloid angiopathy.\|Association:Not Found\|Conclusion:There was a significantly increased T allele and TT genotype frequency in the CAA group, but not in the AD group, suggesting a role for the ACT genotype in the development of vascular lesions.The presence of the apolipoprotein E4 allele (ApoE4) did not correlate with the ACT-A allele, as previously reported, and appeared to be independent of the risk for developing AD.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0085220	Cerebral Amyloid Angiopathy	0		self

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