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 - Hypoparathyroidism

Debug Stats

### Total Build Time: 72 ms 34.342 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 334 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 256 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=2 ms Completed: 2 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=2 ms Completed: 2 ms rowSize= 556 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 1.513 KB
CONCEPT_RELATIONSHIPS gt=50 ms Completed: 50 ms rowSize= 13.298 KB
CONCEPT_GENES gt=14 ms Completed: 14 ms rowSize= 17.041 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.152 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Hypoparathyroidism C0020626

Definition (1)

A disorder characterized by a decrease in production of parathyroid hormone by the parathyroid glands.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0030517

Ancestral Roots

Root	Root Plus One	Depth	Parent
Endocrine System Diseases C0014130	Parathyroid Diseases C0030517	3	Parathyroid Diseases C0030517

Relationships (44)

Relation Types:

diso_to_anat : 4

diso_to_chem : 11

diso_to_diso : 26

diso_to_phen : 2

diso_to_phys : 1

Relationships:

none : 19

classifies : 1

clinically_similar : 2

is_primary_anatomic_site_of_disease : 1

isa : 6

mapped_to : 9

may_treat : 6

Page Size

Current 25

100

250

ALL

Page 1 of 2

Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	75		Complication Aspects C1171258
DISO_to_DISO	74		Complication Aspects C1171258
DISO_to_PHEN	49		genetic aspects C0017399
DISO_to_PHEN	44		genetic aspects C0017399
DISO_to_DISO	43		Hypocalcemia C0020598
DISO_to_ANAT	39		In Blood C0005768
DISO_to_CHEM	36		Parathyroid Hormone C0030520
DISO_to_DISO	35		Hypocalcemia C0020598
DISO_to_ANAT	26		In Blood C0005768
DISO_to_DISO	24		Calcinosis C0006663
DISO_to_ANAT	23		Parathyroid Glands C0030518
DISO_to_DISO	20		Calcinosis C0006663
DISO_to_DISO	19		COMPL POSTOP C0032787
DISO_to_CHEM	18		Calcium C0006675
DISO_to_CHEM	15		Parathyroid Hormone C0030520
DISO_to_CHEM	14		Calcium C0006675
DISO_to_CHEM	11		GATA 03 TRANSCRIPTION FACTOR C0118891
DISO_to_DISO	11		COMPL POSTOP C0032787
DISO_to_PHYS	11		Mutation C0026882
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Endocrine System C0014136
DISO_to_CHEM		may_treat	Calciferol 1.25mg tablet C0976697
DISO_to_CHEM		may_treat	Calciferol, 500000 iu/ml injectable solution C0976696
DISO_to_CHEM		may_treat	ERGOCALCIFEROL (VIT D2) 50,000UNIT CAP C1176477
DISO_to_CHEM		may_treat	ERGOCALCIFEROL (VITAMIN D) 25000 UNT CAP C0688740
DISO_to_CHEM		may_treat	Ergocalciferol C0014695

Genes (10)

Species:

human : 10

Species	Gene	GeneId	Gene Name	Evidence
Human	DGCR8	54487	DGCR8 microprocessor complex subunit	INFERRED, Score=800, UMLKSK CUI: C0020626
Human	GCM2	9247	glial cells missing homolog 2 (Drosophila)	OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism GENERIF, Score=1000, Pubmed Id: 18583467, UMLKSK CUI: C0020626 The dominant-negative effect observed in vitro for both GCMB mutations provides a plausible explanation for the impaired PTH secretion observed in the two unrelated families with autosomal dominant form of hypoparathyroidism GENERIF, Score=861, Pubmed Id: 18182452, UMLKSK CUI: C0020626 Although GCM2 mutations appear to be an uncommon cause of isolated hypoparathyroidism, the wide variety of GCM2 polymorphisms suggests that variant alleles may have a role in determining parathyroid function
Human	TBX1	6899	T-box 1	INFERRED, Score=800, UMLKSK CUI: C0020626
Human	PTH	5741	parathyroid hormone	OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism
Human	GATA3	2625	GATA binding protein 3	GENERIF, Score=861, Pubmed Id: 17210674, UMLKSK CUI: C0020626 No mutations were identified in patients with isolated hypoparathyroidism, thereby indicating that GATA3 abnormalities are more likely to result in two or more of the phenotypic features of the HDR syndrome GENERIF, Score=1000, Pubmed Id: 14985365, UMLKSK CUI: C0020626 GATA3 mutations may have a role in the hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome GENERIF, Score=861, Pubmed Id: 16912130, UMLKSK CUI: C0020626 Three novel mutations in the GATA3 gene responsible for familial hypoparathyroidism and deafness OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism GENERIF, Score=1000, Pubmed Id: 17114920, UMLKSK CUI: C0020626 A novel heterozygous deletion frameshift mutation of GATA3 in a Japanese kindred with the hypoparathyroidism, deafness and renal dysplasia syndrome GENERIF, Score=1000, Pubmed Id: 16509533, UMLKSK CUI: C0020626 Direct sequencing after PCR amplification of genomic DNA revealed a novel insertional mutation (405insC) in the GATA3 gene of two patients with HDR syndrome (Hypoparathyroidism, sensorineural Deafness and Renal anomaly syndrome)
Human	CTLA4	1493	cytotoxic T-lymphocyte-associated protein 4	GAD, Score=1000, Pubmed Id: 16313305, UMLKSK CUI: C0020626 Title:Polymorphisms at +49A/G and CT60 sites in the 3' UTR of the CTLA-4 gene and APECED-related AIRE gene mutations analysis in sporadic idiopathic hypoparathyroidism\|Association:Not Found\|Conclusion:Not Found
Human	COL4A5	1287	collagen, type IV, alpha 5	OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism
Human	CASR	846	calcium-sensing receptor	GAD, Score=1000, Pubmed Id: 15472173, UMLKSK CUI: C0020626 Title:Parathyroid hormone gene polymorphism and sporadic idiopathic hypoparathyroidism.\|Association:Not Found\|Conclusion:Thus, the data from this report demonstrate that in patients with sporadic idiopathic hypoparathyroidism, neither the clinical manifestations nor the biochemical indexes of the disease are related to the occurrence of mutations or SNPs in the PTH gene. Because neither patient nor control samples exhibited any variations in the sequence of their 3'-UTR regions, it is unlikely that mRNA instability is a factor in the pathogenesis of the disease. Additional studies are required to investigate the role of other genes and autoantigens that may be involved in the genesis of idiopathic hypoparathyroidism. GENERIF, Score=1000, Pubmed Id: 14713274, UMLKSK CUI: C0020626 patients studied had serological evidence of organ-specific autoimmunity against the CaSR protein in hypoparathyroidism GENERIF, Score=1000, Pubmed Id: 15960151, UMLKSK CUI: C0020626 In gain-of-function CaSR mutations, the genetic abnormalities increase CaSR activity leading to the development of such clinical manifestations as hypercalciuric hypocalcemia and hypoparathyroidism OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism
Human	ATP7B	540	ATPase, Cu++ transporting, beta polypeptide	OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism
Human	AIRE	326	autoimmune regulator	GAD, Score=1000, Pubmed Id: 16313305, UMLKSK CUI: C0020626 Title:\|Association:Not Found\|Conclusion:Not Found OMIM, Score=1000, UMLKSK CUI: C0020626 Hypoparathyroidism

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0020626	Hypoparathyroidism	0		self

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