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 - Amyloid Neuropathies, Familial

Debug Stats

### Total Build Time: 234 ms 38.823 KB
CONCEPT_NAME gt=4 ms Completed: 4 ms rowSize= 358 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 467 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=0 Completed: 0 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=5 ms Completed: 5 ms rowSize= 1.424 KB
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=6 ms Completed: 6 ms rowSize= 9.342 KB
CONCEPT_RELATIONSHIPS gt=4 ms Completed: 4 ms rowSize= 13.009 KB
CONCEPT_GENES gt=212 ms Completed: 212 ms rowSize= 12.860 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.164 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Amyloid Neuropathies, Familial C0206245

Definition (1)

Inherited disorders of the peripheral nervous system associated with the deposition of AMYLOID in nerve tissue. The different clinical types based on symptoms correspond to the presence of a variety of mutations in several different proteins including transthyretin (PREALBUMIN); APOLIPOPROTEIN A-I; and GELSOLIN.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (3)

C0751870

C0740340

C0206247

Ancestral Roots

Root	Root Plus One	Depth	Parent
Nervous System Diseases C0027765	Neurodegenerative Diseases C0524851	4	Heredodegenerative Disorders, Nervous System C0751870
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	4	Heredodegenerative Disorders, Nervous System C0751870
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	5	Amyloidosis, Familial C0740340
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	5	Amyloidosis, Familial C0740340
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	6	Amyloidosis, Familial C0740340
Nervous System Diseases C0027765	Neuromuscular Diseases C0027868	5	Amyloid Neuropathies C0206247
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	6	Amyloid Neuropathies C0206247

Relationships (28)

Relation Types:

diso_to_anat : 5

diso_to_chem : 4

diso_to_diso : 12

diso_to_phen : 2

diso_to_phys : 5

Relationships:

none : 18

is_associated_anatomic_site_of : 1

is_primary_anatomic_site_of_disease : 1

isa : 7

permuted_term_of : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	110		genetic aspects C0017399
DISO_to_CHEM	93		Prealbumin C0032923
DISO_to_PHEN	92		genetic aspects C0017399
DISO_to_CHEM	65		Prealbumin C0032923
DISO_to_DISO	29		Complication Aspects C1171258
DISO_to_DISO	28		Complication Aspects C1171258
DISO_to_CHEM	27		Amyloid C0002716
DISO_to_CHEM	16		Amyloid C0002716
DISO_to_ANAT	12		Vitreous Body C0042905
DISO_to_ANAT	10		In Blood C0005768
DISO_to_DISO	10		Disorder of eye C0015397
DISO_to_PHYS	10		Mutation C0026882
DISO_to_DISO	9		Amyloidosis C0002726
DISO_to_PHYS	8		Mutation C0026882
DISO_to_PHYS	8		Mutation, Point C0162735
DISO_to_PHYS	7		Mutation, Point C0162735
DISO_to_ANAT	6		In Blood C0005768
DISO_to_PHYS	6		Missense Mutation C0599155
DISO_to_ANAT		is_associated_anatomic_site_of	Nervous System C0027763
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Peripheral Nerves C0031119
DISO_to_DISO		isa	AMYLOIDOSIS, NEUROPATHIC C0268384
DISO_to_DISO		permuted_term_of	Amyloid Neuropathies, Familial C0206245
DISO_to_DISO		isa	Amyloid Polyneuropathy, British Type (disorder) C0342608
DISO_to_DISO		isa	Amyloid Polyneuropathy, Swiss Type C0268386
DISO_to_DISO		isa	Familial Amyloid Polyneuropathy, Jewish Type C0268385

Genes (3)

Species:

human : 3

Species	Gene	GeneId	Gene Name	Evidence
Human	TTR	7276	transthyretin	GENERIF, Score=756, Pubmed Id: 12095258, UMLKSK CUI: C0206245 The correlation between destabilization of the transthyretin core strands and the tendency for amyloid formation(familial amyloid polyneuropathy variants) supports the view that these strands are involved in amyloidogenicity GENERIF, Score=1000, Pubmed Id: 16751191, UMLKSK CUI: C0206245 show involvement of ER stress response in familial amyloid polyneuropathy by showing activation of classical unfolded protein response pathways in tissues not specialized in TTR synthesis but presenting extracellular TTR aggregate and fibril deposition GENERIF, Score=694, Pubmed Id: 18460047, UMLKSK CUI: C0206245 The origin of the the TTR Val30Met familial amyloid polyneuropathy mutation arose independently in Portugal and in Sweden, and spread out from Portugal to Brazil GENERIF, Score=1000, Pubmed Id: 18925456, UMLKSK CUI: C0206245 TTR Val30Met mutation is associated with familial amyloid polyneuropathy GENERIF, Score=1000, Pubmed Id: 16076613, UMLKSK CUI: C0206245 Mutataion in the TTR-amyloid fibril protein is associated with familial amyloid polyneuropathy GENERIF, Score=717, Pubmed Id: 12039669, UMLKSK CUI: C0206245 Transthyretin Val 107 in a Japanese patient with familial amyloid polyneuropathy. point mutation responsible for substitution of valine for isoleucine at position 107 GENERIF, Score=679, Pubmed Id: 12433265, UMLKSK CUI: C0206245 Differences in clinical and geographic features between early- and late-onset familial amyloid polyneuropathy TTR Met30 have been confirmed in Japanese patients with onset before and after 50 years of age GENERIF, Score=1000, Pubmed Id: 14673473, UMLKSK CUI: C0206245 genotype-phenotype correlations in familial amyloid polyneuropathy (V30M) in Portugal and Sweden GENERIF, Score=1000, Pubmed Id: 17577688, UMLKSK CUI: C0206245 present two families, from Spain and Portugal, with familial amyloid polyneuropathy (FAP) associated with the mutation TTRSer50Arg GAD, Score=1000, Pubmed Id: 15649951, UMLKSK CUI: C0206245 Title:Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy:complexity in a single gene disease\|Association:Y\|Conclusion:Thus, while the TTR V30M mutation is required for disease in Portuguese patients, different genetic factors may govern the age of onset as well as the occurrence of anticipation. GENERIF, Score=923, Pubmed Id: 17698792, UMLKSK CUI: C0206245 DNA testing for transthyretin is the most reliable test for transthyretin familial amyloid polyneuropathy in patients with a progressive length-dependent small fiber polyneuropathy of unknown origin, especially when associated with autonomic dysfunction GENERIF, Score=923, Pubmed Id: 18688962, UMLKSK CUI: C0206245 DNA testing for transthyretin is the most reliable test for transthyretin familial amyloid polyneuropathy in patient of Russian family GAD, Score=787, Pubmed Id: 10611951, UMLKSK CUI: C0206245 Title:Familial amyloidotic polyneuropathy type 1 in Brazil is associated with the transthyretin Val30Met variant.\|Association:Y\|Conclusion:TTR Val30Met mutation was the sole TTR variant found in Brazilian FAP1 patients in this cohort, and it was present even in those subjects without a clear history of Portuguese ancestry.
Human	APP	351	amyloid beta (A4) precursor protein	GENERIF, Score=756, Pubmed Id: 17701472, UMLKSK CUI: C0206245 Data demonstrate severe amyloid deposition in mammary glands of familial amyloid polyneuropathy patients
Human	APCS	325	amyloid P component, serum	GAD, Score=1000, Pubmed Id: 15649951, UMLKSK CUI: C0206245 Title:Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy:complexity in a single gene disease\|Association:Not Found\|Conclusion:Thus, while the TTR V30M mutation is required for disease in Portuguese patients, different genetic factors may govern the age of onset as well as the occurrence of anticipation.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0206245	Amyloid Neuropathies, Familial	0		self

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