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 - Bernard-Soulier Syndrome

Debug Stats

### Total Build Time: 32 ms 38.537 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 346 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 294 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=4 ms Completed: 4 ms rowSize= 1.422 KB
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 5.438 KB
CONCEPT_RELATIONSHIPS gt=15 ms Completed: 15 ms rowSize= 13.243 KB
CONCEPT_GENES gt=6 ms Completed: 6 ms rowSize= 16.432 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.158 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Bernard-Soulier Syndrome C0005129

Definition (1)

A familial coagulation disorder characterized by a prolonged bleeding time, unusually large platelets, and impaired prothrombin consumption.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (3)

C0019087

C0005818

C0852077

Ancestral Roots

Relationships (26)

Relation Types:

diso_to_chem : 3

diso_to_diso : 21

diso_to_phen : 2

Relationships:

none : 6

alias_of : 1

expanded_form_of : 1

manifestation_of : 14

related_to : 3

used_for : 1

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Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	33		genetic aspects C0017399
DISO_to_PHEN	22		genetic aspects C0017399
DISO_to_CHEM	19		GPIB IX C0017966
DISO_to_DISO	19		Complication Aspects C1171258
DISO_to_CHEM	14		GPIB IX C0017966
DISO_to_CHEM	14		Platelet Glycoprotein GPIb-IX Complex C0017966
DISO_to_DISO		manifestation_of	Abnormal or prolonged bleeding time C0151529
DISO_to_DISO		manifestation_of	Absent platelet agglutination in presence of ristocetin C1856451
DISO_to_DISO		related_to	BERNARD-SOULIER SYNDROME, TYPE A1 C3278148
DISO_to_DISO		related_to	BERNARD-SOULIER SYNDROME, TYPE B C1856447
DISO_to_DISO		related_to	BERNARD-SOULIER SYNDROME, TYPE C C1856448
DISO_to_DISO		expanded_form_of	Bernard-Soulier Syndrome C0005129
DISO_to_DISO		manifestation_of	Caused by mutation in the platelet glycoprotein IX gene (GP9, 173515.0001) C3278151
DISO_to_DISO		manifestation_of	Caused by mutation in the platelet glycoprotein Ib, alpha polypeptide, gene (GP1BA, 606672.0001) C3278149
DISO_to_DISO		manifestation_of	Caused by mutation in the platelet glycoprotein Ib, beta polypeptide, gene (GP1BB, 138720.0001) C3278150
DISO_to_DISO		manifestation_of	Congenital bleeding diathesis C1856452
DISO_to_DISO		alias_of	Deficiency of Platelet Glycoprotein 1b C2713537
DISO_to_DISO		manifestation_of	Epistaxis C0014591
DISO_to_DISO		manifestation_of	Hemorrhage C0019080
DISO_to_DISO		manifestation_of	Large platelets (finding) C1148412
DISO_to_DISO		manifestation_of	Menorrhagia C0025323
DISO_to_DISO		manifestation_of	Mild thrombocytopenia C1856453
DISO_to_DISO		manifestation_of	Normal platelet aggregation with ADP, collagen, epinephrine C1856450
DISO_to_DISO		manifestation_of	Purpura C0034150
DISO_to_DISO		manifestation_of	Reduced platelet glycoprotein Ib complex C1856449

Genes (4)

Species:

human : 4

Species	Gene	GeneId	Gene Name	Evidence
Human	GP9	2815	glycoprotein IX (platelet)	GENERIF, Score=1000, Pubmed Id: 17763149, UMLKSK CUI: C0005129 3 families from Iran with Bernard-Soulier syndrome were investigated; the presence of the same GpIX Phe55Ser missense mutation in two families and of a single base insertion (GP1BA C3221 ins) in the third family were demonstrated GENERIF, Score=1000, Pubmed Id: 12463594, UMLKSK CUI: C0005129 structure-activity relationship of mutations found in Bernard-Soulier syndrome GENERIF, Score=668, Pubmed Id: 17804902, UMLKSK CUI: C0005129 the first non-Caucasian Turkish Bernard-Soulier syndrome case due to GPIX N45S and is likely the result of a recurrent mutational event GENERIF, Score=1000, Pubmed Id: 12447957, UMLKSK CUI: C0005129 Novel nonsense mutation is associated with Bernard-Soulier syndrome GAD, Score=1000, Pubmed Id: 9163595, UMLKSK CUI: C0005129 Title:A phenylalanine-55 to serine amino-acid substitution in the human glycoprotein IX leucine-rich repeat is associated with Bernard-Soulier syndrome.\|Association:Y\|Conclusion:Not Found GAD, Score=1000, Pubmed Id: 9432024, UMLKSK CUI: C0005129 Title:\|Association:Y\|Conclusion:Not Found
Human	GP1BB	2812	glycoprotein Ib (platelet), beta polypeptide	GAD, Score=1000, Pubmed Id: 10928480, UMLKSK CUI: C0005129 Title:Homozygous Pro74-->Arg mutation in the platelet glycoprotein Ibbeta gene associated with Bernard-Soulier syndrome.\|Association:Y\|Conclusion:the mutation is responsible for a BSS phenotype observed in the patient. GENERIF, Score=1000, Pubmed Id: 11816714, UMLKSK CUI: C0005129 A GP1BB missense mutation suppresses GPIb/IX complex expression and is found to cause Bernard-Soulier Syndrome in the homozygous form and giant platelets in the heterozygous form GENERIF, Score=756, Pubmed Id: 12958615, UMLKSK CUI: C0005129 identified novel GPIbbeta mutation is responsible for the Bernard-Soulier syndrome phenotype and provide an explanation for the molecular mechanism underlying the reduced platelet content of GPIb-IX complex in the heterozygous individuals studied GENERIF, Score=1000, Pubmed Id: 12529755, UMLKSK CUI: C0005129 novel hemizygous variant of Bernard-Soulier Syndrome in which Pro29 in one GPIbbeta allele is substituted by a Leu GENERIF, Score=1000, Pubmed Id: 12463594, UMLKSK CUI: C0005129 structure-activity relationship of mutations found in Bernard-Soulier syndrome
Human	GP1BA	2811	glycoprotein Ib (platelet), alpha polypeptide	GAD, Score=1000, Pubmed Id: 7819107, UMLKSK CUI: C0005129 Title:Cys209 Ser mutation in the platelet membrane glycoprotein Ib alpha gene is associated with Bernard-Soulier syndrome.\|Association:Y\|Conclusion:The mutation identified in the family studied, responsible for the deficiency of the GP Ib/IX/V complex, suggests that the cysteine at amino acid position 209 may be involved in disulphide bonding. GAD, Score=1000, Pubmed Id: 2308962, UMLKSK CUI: C0005129 Title:Nonsense mutation in the glycoprotein Ib alpha coding sequence associated with Bernard-Soulier syndrome.\|Association:Y\|Conclusion:The molecular abnormality demonstrated in this family provides evidence that defective synthesis of GP Ib alpha alters the membrane expression of the GP Ib-IX complex and may be responsible for Bernard-Soulier syndrome. GENERIF, Score=1000, Pubmed Id: 11776304, UMLKSK CUI: C0005129 Two compound heterozygotes for the GPIbalpha gene(a maternal T insertion at position 1418 causing a translational frameshift and premature polypeptide termination, and a paternal T715A substitution changing Cys209 to Ser)had Bernard-Soulier syndrome GENERIF, Score=1000, Pubmed Id: 12463594, UMLKSK CUI: C0005129 structure-activity relationship of mutations found in Bernard-Soulier syndrome GENERIF, Score=1000, Pubmed Id: 18815197, UMLKSK CUI: C0005129 Sequencing analysis of the GPIbalpha gene revealed a novel heterozygous mutation, A169C, resulting in an N41H substitution in the protein in Bernard-Soulier syndrome OMIM, Score=1000, UMLKSK CUI: C0005129 Allelic with Giant Platelet Syndrome ({231200}) and Bernard-Soulier Syndrome, benign, autosomal dominant ({153670}) GAD, Score=1000, Pubmed Id: 11776304, UMLKSK CUI: C0005129 Title:\|Association:Y\|Conclusion:Not Found GENERIF, Score=1000, Pubmed Id: 17763149, UMLKSK CUI: C0005129 3 families from Iran with Bernard-Soulier syndrome were investigated; the presence of the same GpIX Phe55Ser missense mutation in two families and of a single base insertion (GP1BA C3221 ins) in the third family were demonstrated
Human	FBLN1	2192	fibulin 1	GENERIF, Score=851, Pubmed Id: 14635206, UMLKSK CUI: C0005129 mutations in the splice acceptor site of fibulin-1 exon 19, but no MYH9 mutations,were found in family individuals affected by autosomal-dominant giant platelet syndromes associated with aberrant antisense gene regulation of the fibulin-1 gene

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0005129	Bernard-Soulier Syndrome	0		self

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