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 - Li-Fraumeni Syndrome

Debug Stats

### Total Build Time: 28 ms 33.633 KB
CONCEPT_NAME gt=11 ms Completed: 11 ms rowSize= 338 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 627 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= 187 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=4 ms Completed: 4 ms rowSize= 1,017 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 4.148 KB
CONCEPT_RELATIONSHIPS gt=8 ms Completed: 8 ms rowSize= 14.412 KB
CONCEPT_GENES gt=4 ms Completed: 4 ms rowSize= 11.765 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.154 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Li-Fraumeni Syndrome C0085390

Definition (1)

Rare autosomal dominant syndrome characterized by mesenchymal and epithelial neoplasms at multiple sites. MUTATION of the p53 tumor suppressor gene, a component of the DNA DAMAGE response pathway, apparently predisposes family members who inherit it to develop certain cancers. The spectrum of cancers in the syndrome was shown to include, in addition to BREAST CANCER and soft tissue sarcomas (SARCOMA); BRAIN TUMORS; OSTEOSARCOMA; LEUKEMIA; and ADRENOCORTICAL CARCINOMA.

Semantic Types (1)

Neoplastic Process (T191)

Parents (2)

C0027672

C1563696

Ancestral Roots

Root	Root Plus One	Depth	Parent
Neoplasms C0027651	Neoplastic Syndromes, Hereditary C0027672	3	Neoplastic Syndromes, Hereditary C0027672
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	4	Neoplastic Syndromes, Hereditary C0027672
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	4	DNA Repair-Deficiency Disorders C1563696

Relationships (29)

Relation Types:

diso_to_chem : 3

diso_to_diso : 17

diso_to_gene : 4

diso_to_phen : 2

diso_to_phys : 3

Relationships:

none : 10

allele_associated_with_disease : 2

associated_genetic_condition : 2

gene_product_malfunction_associated_with_disease : 1

is_finding_of_disease : 1

mapped_to : 1

may_be_associated_disease_of_disease : 9

may_be_molecular_abnormality_of_disease : 2

permuted_term_of : 1

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Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	88		genetic aspects C0017399
DISO_to_PHEN	53		genetic aspects C0017399
DISO_to_CHEM	37		Protein p53 C0080055
DISO_to_PHYS	28		Germ-Line Mutation C0206530
DISO_to_GENE	27		Genes, p53 C0079419
DISO_to_GENE	19		Genes, p53 C0079419
DISO_to_PHYS	17		Germ-Line Mutation C0206530
DISO_to_CHEM	12		Protein p53 C0080055
DISO_to_DISO	12		Complication Aspects C1171258
DISO_to_PHYS	12		GENET PREDISPOSITION C0314657
DISO_to_CHEM		gene_product_malfunction_associated_with_disease	Protein p53 C0080055
DISO_to_DISO		may_be_associated_disease_of_disease	ASTROCYTOMA C0004114
DISO_to_DISO		may_be_associated_disease_of_disease	Adrenocortical Carcinoma C0206686
DISO_to_DISO		associated_genetic_condition	Brain Neoplasms C0006118
DISO_to_DISO		may_be_molecular_abnormality_of_disease	CHEK2 Gene Mutation C1511442
DISO_to_DISO		may_be_associated_disease_of_disease	Choroid Plexus Neoplasms C0085138
DISO_to_DISO		may_be_associated_disease_of_disease	Colorectal Carcinoma C0009402
DISO_to_DISO		is_finding_of_disease	Hereditary Lesion C1708351
DISO_to_DISO		may_be_molecular_abnormality_of_disease	Inactivation of p53 Tumor-Suppressor Gene C1515171
DISO_to_DISO		mapped_to	LI-FRAUMENI SYNDROME 1 C1835398
DISO_to_DISO		permuted_term_of	Li-Fraumeni Syndrome C0085390
DISO_to_DISO		may_be_associated_disease_of_disease	Malignant neoplasm of breast C0006142
DISO_to_DISO		associated_genetic_condition	Malignant tumor of lymphoid hemopoietic and related tissue C0348393
DISO_to_DISO		may_be_associated_disease_of_disease	Medulloblastoma C0025149
DISO_to_DISO		may_be_associated_disease_of_disease	Osteosarcoma C0029463

Genes (4)

Species:

human : 4

Species	Gene	GeneId	Gene Name	Evidence
Human	CHEK2	11200	checkpoint kinase 2	GENERIF, Score=1000, Pubmed Id: 18004398, UMLKSK CUI: C0085390 Parallel studies of the human CHEK2 gene have also highlighted its role as a candidate multiorgan tumour susceptibility gene rather than a highly penetrant predisposition gene for Li-Fraumeni syndrome GENERIF, Score=1000, Pubmed Id: 18178638, UMLKSK CUI: C0085390 We believe that CHEK2 mutations are not associated with the cancer types seen in the LFS or LFL (other than breast cancer) and it is no longer reasonable to consider CHEK2 mutations to be a cause of LFS (Li-Fraumeni syndrome) GENERIF, Score=1000, Pubmed Id: 11719428, UMLKSK CUI: C0085390 Destabilization of CHK2 by a missense mutation associated with Li-Fraumeni Syndrome
Human	TP53	7157	tumor protein p53	GENERIF, Score=1000, Pubmed Id: 14656244, UMLKSK CUI: C0085390 A novel germline mutation in p53 gene was found in a patient with Li-Fraumeni syndrome GENERIF, Score=1000, Pubmed Id: 15942083, UMLKSK CUI: C0085390 Alterations of the TP53 gene occur not only as somatic mutations in human malignancies, but also as germline mutations in some cancer-prone families with Li-Fraumeni syndrome GENERIF, Score=1000, Pubmed Id: 16912210, UMLKSK CUI: C0085390 germ-line p53 mutations and sex had significant effects on cancer risk in patients with Li-Fraumeni syndrome GENERIF, Score=694, Pubmed Id: 18937320, UMLKSK CUI: C0085390 the identification and functional characterization of a novel TP53 germinal mutant allele (Cys275Phe c.824G > T p.C275F) in a large Italian Li-Fraumeni syndrome family GENERIF, Score=1000, Pubmed Id: 17427234, UMLKSK CUI: C0085390 R248W may predispose to composite tumors and to neuroblastoma in individuals with Li-Fraumeni syndrome GENERIF, Score=1000, Pubmed Id: 12584563, UMLKSK CUI: C0085390 TP53 rearrangements in families with the Li-Fraumeni syndrome reveals a complete deletion of the TP53 gene GENERIF, Score=1000, Pubmed Id: 15381368, UMLKSK CUI: C0085390 germline mutations in the TP53 gene in five index cases of German and Swiss origin with cancers typical of Li-Fraumeni syndrome GENERIF, Score=1000, Pubmed Id: 18511570, UMLKSK CUI: C0085390 These results represent a definitive argument demonstrating that Li-Fraumeni syndrome results from TP53 haplodeficiency GENERIF, Score=1000, Pubmed Id: 17318340, UMLKSK CUI: C0085390 a family with Li-Fraumeni syndrome in which initially a novel germline TP53 intron 5 splice site mutation was found
Human	MDM2	4193	MDM2 oncogene, E3 ubiquitin protein ligase	GENERIF, Score=717, Pubmed Id: 17003841, UMLKSK CUI: C0085390 TP53 germline mutation carriers with SNP309 G allele have earlier onset of tumours; higher prevalence of MDM2 SNP309 homozygous carriers in TP53-negative group suggests allele contributes to cancer susceptibility in Li-Fraumeni syndrome & related families
Human	BAX	581	BCL2-associated X protein	GENERIF, Score=679, Pubmed Id: 15298965, UMLKSK CUI: C0085390 Alteriations of BAX are not responsible for cancers in TP53 wild-type Li-Fraumeni syndrome families

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0085390	Li-Fraumeni Syndrome	0		self

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