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 - Ophthalmoplegia, Chronic Progressive External

Debug Stats

### Total Build Time: 43 ms 43.117 KB
CONCEPT_NAME gt=10 ms Completed: 10 ms rowSize= 462 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 592 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=8 ms Completed: 8 ms rowSize= 1.403 KB
CONCEPT_CHILDREN gt=3 ms Completed: 3 ms rowSize= 559 bytes
CONCEPT_ANCESTRAL_ROOTS gt=1 ms Completed: 1 ms rowSize= 14.326 KB
CONCEPT_RELATIONSHIPS gt=8 ms Completed: 8 ms rowSize= 6.124 KB
CONCEPT_GENES gt=11 ms Completed: 11 ms rowSize= 18.299 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.179 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (2)

Ophthalmoplegia, Chronic Progressive External C0162674

Chronic progressive external ophthalmoplegia

Definition (1)

A mitochondrial myopathy characterized by slowly progressive paralysis of the levator palpebrae, orbicularis oculi, and extraocular muscles. Ragged-red fibers and atrophy are found on muscle biopsy. Familial and sporadic forms may occur. Disease onset is usually in the first or second decade of life, and the illness slowly progresses until usually all ocular motility is lost. (From Adams et al., Principles of Neurology, 6th ed, p1422)

Semantic Types (1)

Disease or Syndrome (T047)

Parents (3)

C0162670

C0028850

C0029089

Children (1)

C0022541

Ancestral Roots

Root	Root Plus One	Depth	Parent
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	5	Mitochondrial Myopathies C0162670
Nervous System Diseases C0027765	Neuromuscular Diseases C0027868	5	Mitochondrial Myopathies C0162670
Musculoskeletal Diseases C0026857	Muscular Diseases C0026848	4	Mitochondrial Myopathies C0162670
Eye Diseases C0015397	Ocular Motility Disorders C0028850	3	Ocular Motility Disorders C0028850
Nervous System Diseases C0027765	Central Nervous System Diseases C0007682	4	Ocular Motility Disorders C0028850
Nervous System Diseases C0027765	Cranial Nerve Diseases C0010266	4	Ocular Motility Disorders C0028850
Eye Diseases C0015397	Ocular Motility Disorders C0028850	4	Ophthalmoplegia C0029089
Nervous System Diseases C0027765	Central Nervous System Diseases C0007682	5	Ophthalmoplegia C0029089
Nervous System Diseases C0027765	Cranial Nerve Diseases C0010266	5	Ophthalmoplegia C0029089
Pathological Conditions, Signs and Symptoms C0039058	Signs and Symptoms C0037088	6	Ophthalmoplegia C0029089
Nervous System Diseases C0027765	Neurologic Manifestations C0027854	5	Ophthalmoplegia C0029089

Relationships (13)

Relation Types:

diso_to_chem : 4

diso_to_diso : 5

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 10

classifies : 1

mapped_to : 2

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	70		genetic aspects C0017399
DISO_to_PHEN	62		genetic aspects C0017399
DISO_to_CHEM	32		DNA, Mitochondrial C0012929
DISO_to_CHEM	31		DNA, Mitochondrial C0012929
DISO_to_PHYS	28		Mutation C0026882
DISO_to_CHEM	21		DNA-Directed DNA Polymerase C0012892
DISO_to_DISO	20		Complication Aspects C1171258
DISO_to_CHEM	18		DNA Helicases C0920283
DISO_to_DISO	17		Complication Aspects C1171258
DISO_to_PHYS	14		Mutation C0026882
DISO_to_DISO		mapped_to	Chronic progressive external ophthalmoplegia C0162674
DISO_to_DISO		classifies	Other disease of eye C0497217
DISO_to_DISO		mapped_to	PEOA5 C2751319

Genes (10)

Species:

human : 10

Species	Gene	GeneId	Gene Name	Evidence
Human	C10orf2	56652	chromosome 10 open reading frame 2	GENERIF, Score=884, Pubmed Id: 17722119, UMLKSK CUI: C0162674 Identifying other Twinkle mutations in mitochondrial DNA depletion and/or autosomal dominant progressive external ophthalmoplegia and studying their impact on proteins should help in understanding why some mutations are recessive and others are dominant GENERIF, Score=1000, Pubmed Id: 18971204, UMLKSK CUI: C0162674 MtDNA replication pausing is the consequence of Twinkle mutations that predisposes to progressive external ophthalmoplegia
Human	APTX	54840	aprataxin	OMIM, Score=1000, UMLKSK CUI: C0162674 Progressive external ophthalmoplegia
Human	TFAM	7019	transcription factor A, mitochondrial	GENERIF, Score=884, Pubmed Id: 12921794, UMLKSK CUI: C0162674 This study describe a family with autosomal dominant progressive external ophthalmoplegia caused by a novel heterozygous A to C transversion at nucleotide 956 of the Twinkle gene
Human	SDHA	6389	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	INFERRED, Score=800, UMLKSK CUI: C0162674
Human	ATXN7	6314	ataxin 7	INFERRED, Score=800, UMLKSK CUI: C0162674
Human	POLRMT	5442	polymerase (RNA) mitochondrial (DNA directed)	GENERIF, Score=884, Pubmed Id: 15258572, UMLKSK CUI: C0162674 human mitochondrial DNA polymerase has a role in autosomal dominant progressive external ophthalmoplegia
Human	POLG	5428	polymerase (DNA directed), gamma	GENERIF, Score=1000, Pubmed Id: 11897778, UMLKSK CUI: C0162674 Active site mutation in DNA polymerase gamma associated with progressive external ophthalmoplegia causes error-prone DNA synthesis GENERIF, Score=1000, Pubmed Id: 14745080, UMLKSK CUI: C0162674 2 new heterozygous missense transitions (C2794T, G3151C)were found in the POLG gene in a family with an autosomal recessive syndrome: progressive external ophthalmoplegia, polyneuropathy, ataxia, sensorineural hearing loss, and affective disorders GENERIF, Score=923, Pubmed Id: 12210792, UMLKSK CUI: C0162674 Mutations of mitochondrial DNA polymerase gammaA are a frequent cause of autosomal dominant or recessive progressive external ophthalmoplegia GENERIF, Score=1000, Pubmed Id: 14694057, UMLKSK CUI: C0162674 The authors report on a patient homozygous for a recessive missense mutation in POLG who presented with a multisystem disorder without progressive external ophthalmoplegia; the clinical picture overlapped with the MERRF syndrome GENERIF, Score=756, Pubmed Id: 12565911, UMLKSK CUI: C0162674 recessive POLG mutations in compound heterozygote patients with progressive external ophthalmoplegia presenting with sensory ataxic neuropathy GENERIF, Score=756, Pubmed Id: 16682683, UMLKSK CUI: C0162674 Causative POLG1 mutations were identified in approximately 10% of progressive external ophthalmoplegia cases, with two unrelated individuals harboring a novel premature stop codon mutation (1356T>G) GENERIF, Score=884, Pubmed Id: 17420318, UMLKSK CUI: C0162674 Both autosomal dominant progressive external ophthalmoplegia and parkinsonism caused by mutations that directly affect the polymerase domain of polymerase gamma GENERIF, Score=1000, Pubmed Id: 17725985, UMLKSK CUI: C0162674 Mutation in DNA polymerase gamma is associated with progressive external ophthalmoplegia and parkinsonism GENERIF, Score=1000, Pubmed Id: 15981013, UMLKSK CUI: C0162674 We found Alzheimer pathology associated with POLG1 mutation, multiple mtDNA deletions, and APOE4/4 and progressive external ophthalmoplegia GAD, Score=1000, Pubmed Id: 12975295, UMLKSK CUI: C0162674 Title:Clinical and genetic heterogeneity in progressive external ophthalmoplegia due to mutations in polymerase gamma.\|Association:Not Found\|Conclusion:Our results demonstrate that POLG mutations account for a substantial proportion of patients (13%) with PEO and multiple mitochondrial DNA deletions and cause both clinically and genetically heterogeneous disorders.
Human	TRNI	4565	tRNA	GENERIF, Score=1000, Pubmed Id: 17965958, UMLKSK CUI: C0162674 Chronic progressive external ophthalmoplegia caused by an m.4267A > G mutation in the mitochondrial tRNAIle
Human	RNR2	4550	l-rRNA	GENERIF, Score=1000, Pubmed Id: 16639504, UMLKSK CUI: C0162674 Humanin expression may reflect a physiological response against degenerative changes in the muscles of patients with chronic progressive external ophthalmoplegia
Human	SLC25A4	291	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4	GENERIF, Score=1000, Pubmed Id: 15792871, UMLKSK CUI: C0162674 report a novel heterozygous C to A transversion at nucleotide 269 in the ANT1 gene in a German family with Progressive External Ophthalmoplegia , predicted to convert a highly conserved alanine at codon 90 to aspartic acid GENERIF, Score=884, Pubmed Id: 12140186, UMLKSK CUI: C0162674 A114P missense mutation in the human Ant1 protein was found to be associated with autosomal dominant progressive external ophthalmoplegia

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0162674	Ophthalmoplegia, Chronic Progressive External	0		self

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