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 Hypothyroidism

Debug Stats

### Total Build Time: 66 ms 42.301 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 348 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 577 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=3 ms Completed: 3 ms rowSize= 1.386 KB
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 7.887 KB
CONCEPT_RELATIONSHIPS gt=46 ms Completed: 46 ms rowSize= 14.302 KB
CONCEPT_GENES gt=10 ms Completed: 10 ms rowSize= 16.445 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.159 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Congenital Hypothyroidism C0010308

Definition (1)

A condition in infancy or early childhood due to an in-utero deficiency of THYROID HORMONES that can be caused by genetic or environmental factors, such as thyroid dysgenesis or HYPOTHYROIDISM in infants of mothers treated with THIOURACIL during pregnancy. Endemic cretinism is the result of iodine deficiency. Clinical symptoms include severe MENTAL RETARDATION, impaired skeletal development, short stature, and MYXEDEMA.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (3)

C0005942

C0013336

C0020676

Ancestral Roots

Relationships (56)

Relation Types:

diso_to_anat : 9

diso_to_chem : 8

diso_to_diso : 35

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 21

associated_with : 3

classifies : 2

clinically_similar : 1

expanded_form_of : 1

is_associated_anatomic_site_of : 3

is_normal_tissue_origin_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 5

mapped_to : 16

use : 2

Page Size

Current 25

100

250

ALL

Page 1 of 3

Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	107		genetic aspects C0017399
DISO_to_DISO	98		HYPOTHYROIDISM C0020676
DISO_to_ANAT	80		In Blood C0005768
DISO_to_DISO	67		Complication Aspects C1171258
DISO_to_CHEM	50		Thyroxine C0040165
DISO_to_CHEM	49		Thyrotropin C0040160
DISO_to_ANAT	36		Thyroid Gland C0040132
DISO_to_CHEM	30		Thyroxine C0040165
DISO_to_PHEN	30		genetic aspects C0017399
DISO_to_CHEM	29		Thyrotropin C0040160
DISO_to_DISO	25		Goiter C0018021
DISO_to_ANAT	24		Thyroid Gland C0040132
DISO_to_PHYS	24		Mutation C0026882
DISO_to_CHEM	20		Iodine C0021968
DISO_to_DISO	19		Dysgenesis, Thyroid C1563716
DISO_to_CHEM	18		Iodine C0021968
DISO_to_CHEM	16		Receptors, Thyrotropin C0034844
DISO_to_PHYS	16		Mutation C0026882
DISO_to_ANAT	15		In Blood C0005768
DISO_to_DISO	14		Abnormalities, Multiple C0000772
DISO_to_DISO	14		chemically induced C0007994
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Endocrine System C0014136
DISO_to_ANAT		is_associated_anatomic_site_of	Head and neck structure C0460004
DISO_to_ANAT		is_associated_anatomic_site_of	Neck C0027530
DISO_to_ANAT		is_associated_anatomic_site_of	Thyroid Gland C0040132

Genes (11)

Species:

human : 11

Species	Gene	GeneId	Gene Name	Evidence
Human	IYD	389434	iodotyrosine deiodinase	GENERIF, Score=1000, Pubmed Id: 18765512, UMLKSK CUI: C0010308 This study describes a functional mutation within IYD, demonstrating the molecular basis of the iodine wasting form of congenital hypothyroidism
Human	DUOX2	50506	dual oxidase 2	GENERIF, Score=901, Pubmed Id: 18765513, UMLKSK CUI: C0010308 Loss of DUOX2 activity results in transient congenital hypothyroidism and transient congenital hypothyroidism caused by DUOX2 mutations is inherited as an autosomal recessive trait GENERIF, Score=1000, Pubmed Id: 16322276, UMLKSK CUI: C0010308 Heterozygous mutations in the DUOX2 gene are responsible for iodide organification defect and congenital hypothyroidism
Human	PAX8	7849	paired box 8	GENERIF, Score=875, Pubmed Id: 17468187, UMLKSK CUI: C0010308 identification of a novel PAX8 mutation in a particular variant of non-congenital early-onset hypothyroidism indicates a key function of PAX8 in the postnatal growth and functional maintenance of the thyroid gland
Human	TSHR	7253	thyroid stimulating hormone receptor	GENERIF, Score=1000, Pubmed Id: 18379122, UMLKSK CUI: C0010308 Three heterozygous variants (Pro52Thr, Gly245Ser, Val689Gly) of TSHR gene were firstly detected in Chinese children with congenital hypothyroidism GENERIF, Score=1000, Pubmed Id: 11716047, UMLKSK CUI: C0010308 A familial case of congenital hypothyroidism caused by a homozygous mutation of the thyrotropin receptor gene GAD, Score=946, Pubmed Id: 9589691, UMLKSK CUI: C0010308 Title:Apparent congenital athyreosis contrasting with normal plasma thyroglobulin levels and associated with inactivating mutations in the thyrotropin receptor gene: are athyreosis and ectopic thyroid distinct entities?\|Association:Y\|Conclusion:We conclude that different genetic and nongenetic mechanisms for athyreosis and ectopic thyroid are likely, and that these two distinct entities are themselves heterogeneous. Our results further show that inactivating mutations in TSH-R may account for some cases of apparent congenital athyreosis and should be suspected, especially if plasma thyroglobulin levels are normal.
Human	TPO	7173	thyroid peroxidase	GENERIF, Score=1000, Pubmed Id: 11916616, UMLKSK CUI: C0010308 Two novel missense mutations in the thyroid peroxidase gene, R665W and G771R, result in a localization defect and cause congenital hypothyroidism GENERIF, Score=1000, Pubmed Id: 15745925, UMLKSK CUI: C0010308 results are in accordance with previous observations confirming the genetic heterogeneity of TPO defects in congenital hypothyroidism
Human	TNF	7124	tumor necrosis factor	GENERIF, Score=1000, Pubmed Id: 12799216, UMLKSK CUI: C0010308 evidence of undetectable levels of TNF-alpha and inducible inos enzyme in infants with congenital hypothyroidism
Human	NKX2-1	7080		OMIM, Score=1000, UMLKSK CUI: C0010308 Allelic disorder to choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress ({610978}), which is a more severe disorder GENERIF, Score=1000, Pubmed Id: 18379122, UMLKSK CUI: C0010308 No mutation or polymorphism was detected in the coding region of thyroid transcription factor-1 (TTF-1) gene in Chinese children with congenital hypothyroidism
Human	TG	7038	thyroglobulin	GENERIF, Score=901, Pubmed Id: 11935320, UMLKSK CUI: C0010308 a major locus for familial congenital hypothyroidism GENERIF, Score=1000, Pubmed Id: 17911408, UMLKSK CUI: C0010308 analysis of the recurrence of the p.R277X/p.R1511X compound heterozygous mutation in the TG gene in two unrelated families (one Argentinian and another Brazilian) with congenital hypothyroidism, goiter and impairment of TG synthesis
Human	TAS2R38	5726	taste receptor, type 2, member 38	OMIM, Score=1000, UMLKSK CUI: C0010308 Relationship between PTC nontasting to cretinism
Human	NOS2	4843	nitric oxide synthase 2, inducible	GENERIF, Score=1000, Pubmed Id: 12799216, UMLKSK CUI: C0010308 evidence of undetectable levels of TNF-alpha and NO in infants with congenital hypothyroidism
Human	FOXE1	2304	forkhead box E1 (thyroid transcription factor 2)	GENERIF, Score=1000, Pubmed Id: 12165566, UMLKSK CUI: C0010308 Loss of function mutation of TTF-2 is associated with congenital hypothyroidism, thyroid agenesis and cleft palate

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0010308	Congenital Hypothyroidism	0		self

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