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 - Antiphospholipid Syndrome

Debug Stats

### Total Build Time: 36 ms 51.385 KB
CONCEPT_NAME gt=4 ms Completed: 4 ms rowSize= 348 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 672 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= 555 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 1.508 KB
CONCEPT_RELATIONSHIPS gt=14 ms Completed: 14 ms rowSize= 12.726 KB
CONCEPT_GENES gt=11 ms Completed: 11 ms rowSize= 34.235 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.159 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Antiphospholipid Syndrome C0085278

Definition (1)

The presence of antibodies directed against phospholipids (ANTIBODIES, ANTIPHOSPHOLIPID). The condition is associated with a variety of diseases, notably systemic lupus erythematosus and other connective tissue diseases, thrombopenia, and arterial or venous thromboses. In pregnancy it can cause abortion. Of the phospholipids, the cardiolipins show markedly elevated levels of anticardiolipin antibodies (ANTIBODIES, ANTICARDIOLIPIN). Present also are high levels of lupus anticoagulant (LUPUS COAGULATION INHIBITOR).

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0004364

Ancestral Roots

Root	Root Plus One	Depth	Parent
Immune System Diseases C0021053	Autoimmune Diseases C0004364	3	Autoimmune Diseases C0004364

Relationships (73)

Relation Types:

diso_to_anat : 3

diso_to_chem : 25

diso_to_diso : 43

diso_to_phen : 2

Relationships:

none : 67

isa : 4

mapped_to : 1

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_DISO	729		Complication Aspects C1171258
DISO_to_DISO	676		Complication Aspects C1171258
DISO_to_CHEM	272		Antibodies, Antiphospholipid C0162595
DISO_to_ANAT	222		In Blood C0005768
DISO_to_DISO	180		Lupus Erythematosus, Systemic C0024141
DISO_to_CHEM	172		Antibodies, Antiphospholipid C0162595
DISO_to_DISO	168		Thrombosis C0040053
DISO_to_DISO	159		Lupus Erythematosus, Systemic C0024141
DISO_to_ANAT	138		In Blood C0005768
DISO_to_DISO	130		Thrombosis C0040053
DISO_to_DISO	105		Pregnancy Complications C0032962
DISO_to_CHEM	88		beta 2-Glycoprotein I C0053358
DISO_to_DISO	88		Pregnancy Complications C0032962
DISO_to_CHEM	82		Anticoagulants C0003280
DISO_to_CHEM	77		Anticoagulants C0003280
DISO_to_CHEM	76		Glycoproteins C0017968
DISO_to_CHEM	71		Abs - Autoantibodies C0004358
DISO_to_CHEM	64		Abs - Autoantibodies C0004358
DISO_to_CHEM	60		Antibodies, Anticardiolipin C0162596
DISO_to_CHEM	56		Antibodies, Anticardiolipin C0162596
DISO_to_CHEM	54		Lupus Coagulation Inhibitor C0085240
DISO_to_PHEN	54		genetic aspects C0017399
DISO_to_DISO	46		Venous Thrombosis C0042487
DISO_to_DISO	45		Abortion, Habitual C0000809
DISO_to_DISO	42		Abortion, Habitual C0000809

Genes (20)

Species:

human : 20

Species	Gene	GeneId	Gene Name	Evidence
Human	NEWENTRY	192343	Record to support submission of GeneRIFs for a gene not in Gene (human; man).	GENERIF, Score=1000, Pubmed Id: 18029906, UMLKSK CUI: C0085278 Compared lupus anticoagulant levels in patients with/without antiphospholipid syndrome
Human	PROZ	8858	protein Z, vitamin K-dependent plasma glycoprotein	GENERIF, Score=1000, Pubmed Id: 15314579, UMLKSK CUI: C0085278 protein Z deficiency could be also a risk factor for acute coronary syndromes, early fetal losses, and increased the arterial risk in antiphospholipid syndrome--REVIEW
Human	TNF	7124	tumor necrosis factor	GAD, Score=1000, Pubmed Id: 11246532, UMLKSK CUI: C0085278 Title:Plasma tumor necrosis factor alpha levels and the -238*A promoter polymorphism in patients with antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Raised plasma TNFalpha levels were found in patients with APS. As a prothrombotic and proinflammatory cytokine, TNFalpha may be involved in the development of clinical features of APS. The lack of correlation between the TNFA-238 polymorphism and plasma levels associated with disease suggests that the TNF genetic marker may only indirectly relate to protein levels by virtue of allelic association with a functional marker which may reside in the HLA class II region.
Human	TFPI	7035	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	GENERIF, Score=1000, Pubmed Id: 15339683, UMLKSK CUI: C0085278 Immunoglobulin G fractions from subjects with antiphospholipid syndrome have inhibitory activity against tissue factor pathway inhibitor (TFPI)
Human	PLAT	5327	plasminogen activator, tissue	GENERIF, Score=1000, Pubmed Id: 14630788, UMLKSK CUI: C0085278 anti-tPA antibodies specifically interacting with the catalytic domain of tPA can be found in patients with antiphospholipid syndrome, representing a possible cause of hypofibrinolysis GENERIF, Score=734, Pubmed Id: 16320350, UMLKSK CUI: C0085278 Some of the plasmin-reactive anticardiolipin antibodies in antiphospholipid syndrome patients may bind to tPA
Human	SERPINB2	5055	serpin peptidase inhibitor, clade B (ovalbumin), member 2	GENERIF, Score=1000, Pubmed Id: 17657675, UMLKSK CUI: C0085278 Data indicate that this family did not follow the Mendelian inheritance pattern; the Ser(413)/Ser genotype in 60% of the affected members might increase the risk for autoimmune syndromes such as anti-phospholipid syndrome or systemic lupus erythematosus
Human	SERPINE1	5054	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	GAD, Score=1000, Pubmed Id: 11454529, UMLKSK CUI: C0085278 Title:The combination of thrombophilic genotypes is associated with definite antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Present data indicate that testing for heritable thrombophilia would be important to identify aPL subjects with an increased risk of developing APS.
Human	MTHFR	4524	methylenetetrahydrofolate reductase (NAD(P)H)	GAD, Score=1000, Pubmed Id: 11454529, UMLKSK CUI: C0085278 Title:The combination of thrombophilic genotypes is associated with definite antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Present data indicate that testing for heritable thrombophilia would be important to identify aPL subjects with an increased risk of developing APS. GENERIF, Score=923, Pubmed Id: 16133896, UMLKSK CUI: C0085278 Female with Takayasu arteritis, primary antiphospholipid antibody syndrome and methylene tetrahydrofolate reductase C 677 T and A 1298 C polymorphism, who was treated with carotid stenting and anticoagulants
Human	IGFBP1	3484	insulin-like growth factor binding protein 1	GENERIF, Score=734, Pubmed Id: 12861174, UMLKSK CUI: C0085278 serum concentrations of insulin-like growth factor binding protein-1 are abnormal in antiphospholipid syndrome pregnancies
Human	IGF1	3479	insulin-like growth factor 1 (somatomedin C)	GENERIF, Score=734, Pubmed Id: 12861174, UMLKSK CUI: C0085278 serum concentrations of insulin-like growth factor binding protein-1 are abnormal in antiphospholipid syndrome pregnancies
Human	HLA-DRB1	3123		GAD, Score=1000, Pubmed Id: 11246532, UMLKSK CUI: C0085278 Title:Plasma tumor necrosis factor alpha levels and the -238*A promoter polymorphism in patients with antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Raised plasma TNFalpha levels were found in patients with APS. As a prothrombotic and proinflammatory cytokine, TNFalpha may be involved in the development of clinical features of APS. The lack of correlation between the TNFA-238 polymorphism and plasma levels associated with disease suggests that the TNF genetic marker may only indirectly relate to protein levels by virtue of allelic association with a functional marker which may reside in the HLA class II region. GAD, Score=1000, Pubmed Id: 11157139, UMLKSK CUI: C0085278 Title:HLA class II gene polymorphisms in antiphospholipid syndrome: haplotype analysis in 83 Caucasoidpatients.\|Association:Not Found\|Conclusion:These alleles and haplotypes might affect anti-ss2GPI production and APS development in different and heterogeneous fashion.
Human	HLA-DQB1	3119		GAD, Score=1000, Pubmed Id: 11246532, UMLKSK CUI: C0085278 Title:Plasma tumor necrosis factor alpha levels and the -238*A promoter polymorphism in patients with antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Raised plasma TNFalpha levels were found in patients with APS. As a prothrombotic and proinflammatory cytokine, TNFalpha may be involved in the development of clinical features of APS. The lack of correlation between the TNFA-238 polymorphism and plasma levels associated with disease suggests that the TNF genetic marker may only indirectly relate to protein levels by virtue of allelic association with a functional marker which may reside in the HLA class II region.
Human	HLA-DQA1	3117		GAD, Score=1000, Pubmed Id: 11157139, UMLKSK CUI: C0085278 Title:HLA class II gene polymorphisms in antiphospholipid syndrome: haplotype analysis in 83 Caucasoidpatients.\|Association:Not Found\|Conclusion:These alleles and haplotypes might affect anti-ss2GPI production and APS development in different and heterogeneous fashion.
Human	HLA-DMB	3109		GAD, Score=1000, Pubmed Id: 15547089, UMLKSK CUI: C0085278 Title:Association of HLA-DM polymorphism with the production of antiphospholipid antibodies.\|Association:Not Found\|Conclusion:The results suggest that HLA-DMA*0102 or its linked gene(s) form one of the genetic risks for the production of aPL.
Human	HLA-DMA	3108		GAD, Score=1000, Pubmed Id: 15547089, UMLKSK CUI: C0085278 Title:Association of HLA-DM polymorphism with the production of antiphospholipid antibodies.\|Association:Y\|Conclusion:The results suggest that HLA-DMA*0102 or its linked gene(s) form one of the genetic risks for the production of aPL.
Human	FCGR2A	2212	Fc fragment of IgG, low affinity IIa, receptor (CD32)	GENERIF, Score=1000, Pubmed Id: 12847687, UMLKSK CUI: C0085278 The FcgammaRIIA-R/H131 polymorphism is an important determinant of predisposition to antiphospholipid syndrome, with different influences on SLE and APS susceptibility per se GAD, Score=1000, Pubmed Id: 12847687, UMLKSK CUI: C0085278 Title:Role of the Fcgamma receptor IIA polymorphism in the antiphospholipid syndrome: an internationalmeta-analysis.\|Association:Y\|Conclusion:The FcgammaRIIA-R/H131 polymorphism is an important determinant of predisposition to APS, with different influences on SLE and APS susceptibility per se.
Human	F5	2153	coagulation factor V (proaccelerin, labile factor)	GAD, Score=1000, Pubmed Id: 11454529, UMLKSK CUI: C0085278 Title:The combination of thrombophilic genotypes is associated with definite antiphospholipid syndrome.\|Association:Not Found\|Conclusion:Present data indicate that testing for heritable thrombophilia would be important to identify aPL subjects with an increased risk of developing APS.
Human	F2	2147	coagulation factor II (thrombin)	GAD, Score=1000, Pubmed Id: 11454529, UMLKSK CUI: C0085278 Title:The combination of thrombophilic genotypes is associated with definite antiphospholipid syndrome.\|Association:Y\|Conclusion:Present data indicate that testing for heritable thrombophilia would be important to identify aPL subjects with an increased risk of developing APS.
Human	APOH	350	apolipoprotein H (beta-2-glycoprotein I)	GENERIF, Score=1000, Pubmed Id: 11953211, UMLKSK CUI: C0085278 serum specimens from APS (antiphospholipid syndrome) patients showed characteristic immunofluorescent pattern GAD, Score=1000, Pubmed Id: 15641049, UMLKSK CUI: C0085278 Title:Significance of valine/leucine(247) polymorphism of beta(2)-glycoprotein I in antiphospholipid syndrome: Increased reactivity ofanti-beta(2)-glycoprotein I autoantibodies to the valine(247) beta(2)-glycoprotein I variant\|Association:Not Found\|Conclusion:The Val(247) beta(2)GPI allele was associated with both a high frequency of anti-beta(2)GPI antibodies and stronger reactivity with anti-beta(2)GPI antibodies compared with the Leu(247) beta(2)GPI allele, suggesting that the Val(247) beta(2)GPI allele may be one of the genetic risk factors for development of APS. GENERIF, Score=1000, Pubmed Id: 12471146, UMLKSK CUI: C0085278 Binding of beta-2-glycoprotein I autoantibodies purified from sera of patients with antiphospholipid syndrome is significantly affected by a number of single point mutations in domain I of B2GI, particularly by mutations in the region of residues 40-43 GENERIF, Score=1000, Pubmed Id: 15507264, UMLKSK CUI: C0085278 Beta2-glycoprotein I has roles in antiphospholipid syndrome and T-cell reactivity [review] GENERIF, Score=1000, Pubmed Id: 19002041, UMLKSK CUI: C0085278 direct correlation between a major clinical symptom of antiphospholipid syndrome (thrombosis), a diagnostic assay (beta2-GPI-dependent LAC) and a potential mechanism responsible for thrombosis in the antiphospholipid syndrome (increased APC resistance) GENERIF, Score=734, Pubmed Id: 15507263, UMLKSK CUI: C0085278 Beta 2 glycoprotein I has roles in blood coagulation and antiphospholipid syndrome [review] GENERIF, Score=734, Pubmed Id: 17469158, UMLKSK CUI: C0085278 These data demonstrate that some anticardiolipin antibody in antiphospholipid syndrome patients recognize one or more conformational epitopes shared by beta2GPI and the catalytic domains of disease-relevant serine proteases GENERIF, Score=1000, Pubmed Id: 14601646, UMLKSK CUI: C0085278 A high degree of simultaneous reactivity against several beta2GPI-peptides was found in patients with the antiphospholipid syndrome GENERIF, Score=1000, Pubmed Id: 14768953, UMLKSK CUI: C0085278 autoantibodies against beta2-glycoprotein I/oxidized low density lipoprotein complexes are etiologically important in the development of atherosclerosis in antiphospholipid syndrome GENERIF, Score=673, Pubmed Id: 18328538, UMLKSK CUI: C0085278 IgG anti-oxLDL/beta2GPI are not specifically associated to arterial thromboembolism in Category I antiphospholipid syndrome patients
Human	ANXA2	302	annexin A2	GENERIF, Score=1000, Pubmed Id: 16493010, UMLKSK CUI: C0085278 anti-A2 antibodies contribute to the prothrombotic diathesis in antiphospholipid syndrome

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0085278	Antiphospholipid Syndrome	0		self

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