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 - Congenital ichthyosis

Debug Stats

### Total Build Time: 31 ms 32.338 KB
CONCEPT_NAME gt=12 ms Completed: 12 ms rowSize= 340 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 388 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= 14 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=0 Completed: 0 ms rowSize= 7 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 15 bytes
CONCEPT_RELATIONSHIPS gt=2 ms Completed: 2 ms rowSize= 106 bytes
CONCEPT_GENES gt=15 ms Completed: 15 ms rowSize= 30.298 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.155 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Congenital ichthyosis C0020758

Definition (1)

skin disorders characterized by dryness, roughness, and scaliness, due to hypertrophy of the stratum corneum epidermis that exist at, and usually before, birth regardless of their causation; most ichthyoses are genetically determined.

Genes (30)

Species:

human : 30

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Species	Gene	GeneId	Gene Name	Evidence
Human	SUMF1	285362	sulfatase modifying factor 1	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	NEWENTRY	192343	Record to support submission of GeneRIFs for a gene not in Gene (human; man).	GENERIF, Score=1000, Pubmed Id: 18086569, UMLKSK CUI: C0020758 presented a novel form of ichthyosis in a patient, termed hepoxilin A(3) synthase-linked ichthyosis (HXALI), whose scales expressed high levels of 12R-LOX, but were deficient of HXA(3) synthase [hepoxilin A3 synthase]
Human	ATOD5	117188	Dermatitis, atopic, 5	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	ATOD3	117187	Dermatitis, atopic, 3	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	ATOD6	114477	Dermatitis, atopic, 6	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	SLURP1	57152	secreted LY6/PLAUR domain containing 1	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	PNPLA2	57104	patatin-like phospholipase domain containing 2	GENERIF, Score=1000, Pubmed Id: 17187067, UMLKSK CUI: C0020758 Neutral lipid storage disease subgroup characterized by mild myopathy, absence of ichthyosis and mutations in both alleles of adipose triglyceride lipase
Human	VPS33B	26276	vacuolar protein sorting 33 homolog B (yeast)	GENERIF, Score=1000, Pubmed Id: 18347289, UMLKSK CUI: C0020758 The present observations indicate that VPS33B deficiency results in abnormal secretion of lamellar granules, which underlies ichthyosis in ARC syndrome
Human	ABCA12	26154	ATP-binding cassette, sub-family A (ABC1), member 12	OMIM, Score=1000, UMLKSK CUI: C0020758 Lamellar ichthyosis, type 2 GENERIF, Score=861, Pubmed Id: 12915478, UMLKSK CUI: C0020758 Mutations in the transporter ABCA12 are associated with lamellar ichthyosis type 2
Human	DOLK	22845	dolichol kinase	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	EBP	10682	emopamil binding protein (sterol isomerase)	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	SNAP29	9342	synaptosomal-associated protein, 29kDa	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis GENERIF, Score=1000, Pubmed Id: 15968592, UMLKSK CUI: C0020758 a SNAP29 mutation codes for a SNARE protein involved in intracellular trafficking and causes a novel neurocutaneous syndrome characterized by cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma
Human	TGM5	9333	transglutaminase 5	GENERIF, Score=1000, Pubmed Id: 12230511, UMLKSK CUI: C0020758 transglutaminase 5 contributes, as a secondary effect, to the hyperkeratotic phenotype in ichthyosis (both vulgaris and lamellar) and in psoriasis
Human	TGM1	7051	transglutaminase 1	GENERIF, Score=1000, Pubmed Id: 17024410, UMLKSK CUI: C0020758 a three-dimensional model of the human transglutaminase 1 provides insights into the understanding of lamellar ichthyosis GAD, Score=1000, Pubmed Id: 10694685, UMLKSK CUI: C0020758 Title:Haplotype association and mutation analysis of the transglutaminase 1 gene for prenatal exclusion of lamellar ichthyosis.\|Association:Not Found\|Conclusion:Not Found
Human	ST14	6768	suppression of tumorigenicity 14 (colon carcinoma)	GENERIF, Score=827, Pubmed Id: 17978729, UMLKSK CUI: C0020758 mutation in the ST14 gene is associated with recessive autosomal ichthyosis with hypotrichosis OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis, congenital
Human	MAP2K2	5605	mitogen-activated protein kinase kinase 2	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	PHYH	5264	phytanoyl-CoA 2-hydroxylase	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	PEX7	5191	peroxisomal biogenesis factor 7	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	KRT10	3858	keratin 10	OMIM, Score=1000, UMLKSK CUI: C0020758 Icthyosis of scalp and flexural areas
Human	KRT2	3849	keratin 2	GENERIF, Score=660, Pubmed Id: 17408392, UMLKSK CUI: C0020758 novel H1 domain mutation in a family with icthyosis bullosa Siemens
Human	KRT1	3848	keratin 1	OMIM, Score=1000, UMLKSK CUI: C0020758 Icthyosis of scalp and flexural areas
Human	GJB2	2706	gap junction protein, beta 2, 26kDa	OMIM, Score=1000, UMLKSK CUI: C0020758 HID (Hystrix-like Ichthyosis with Deafness, {602540}) is identical to KID at the molecular level OMIM, Score=1000, UMLKSK CUI: C0020758 Allelic with deafness, autosomal recessive 1, ({220290}), deafness, autosomal dominant 3, ({601544}), Vohwinkel syndrome, ({124500}), keratitis-ichthyosis-deafness syndrome, ({148210}), hystrix-like ichthyosis with deafness, ({602540}), Bart-Pumphrey syndrome, ({149200}) OMIM, Score=1000, UMLKSK CUI: C0020758 Allelic with deafness, autosomal recessive 1, ({220290}), deafness, autosomal dominant 3, ({601544}), keratoderma, palmoplantar, with deafness, ({148350}), keratitis-ichthyosis-deafness syndrome, ({148210}), hystrix-like ichthyosis with deafness, ({602540}), Bart-Pumphrey syndrome, ({149200}) OMIM, Score=1000, UMLKSK CUI: C0020758 KID is an acronym of Keratitis, Ichthyosis, Deafness
Human	GBA	2629	glucosidase, beta, acid	OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	FLG	2312	filaggrin	GENERIF, Score=694, Pubmed Id: 18007582, UMLKSK CUI: C0020758 R501X and c.3321delA in family with ichthyosis vulgasis complicated by atopic dermatitis OMIM, Score=1000, UMLKSK CUI: C0020758 Ichthyosis
Human	ERCC2	2068	excision repair cross-complementing rodent repair deficiency, complementation group 2	OMIM, Score=1000, UMLKSK CUI: C0020758 Linkage with trichothiodystropy including abnormal hair shaft, ichthyosis, hypogenitalism, short stature, and peculiar facies

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0020758	Congenital ichthyosis	0		self

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