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 - Familial Breast and Ovarian Cancer Syndrome

Debug Stats

### Total Build Time: 61 ms 53.347 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 384 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 452 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=1 ms Completed: 1 ms rowSize= 14 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=0 Completed: 0 ms rowSize= 7 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 15 bytes
CONCEPT_RELATIONSHIPS gt=10 ms Completed: 10 ms rowSize= 6.344 KB
CONCEPT_GENES gt=41 ms Completed: 41 ms rowSize= 44.939 KB
CONCEPT_XREFS gt=6 ms Completed: 6 ms rowSize= 1.177 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Familial Breast and Ovarian Cancer Syndrome C0677776

Definition (1)

An autosomal dominant inherited syndrome caused by mutations in the BRCA1 or BRCA2 genes. Patients are at high risk of developing breast cancer, particularly before the age of fifty, high risk of developing a second primary breast cancer, and high risk of developing both breast and ovarian cancer.

Relationships (11)

Relation Types:

diso_to_chem : 3

diso_to_diso : 7

diso_to_phen : 1

Relationships:

none : 3

gene_product_malfunction_associated_with_disease : 1

is_finding_of_disease : 1

isa : 2

mapped_to : 1

may_be_associated_disease_of_disease : 2

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	12		genetic aspects C0017399
DISO_to_CHEM	4		BRCA1 Protein C0259275
DISO_to_CHEM	4		BRCA2 Protein C0294028
DISO_to_CHEM		gene_product_malfunction_associated_with_disease	BRCA1 Protein C0259275
DISO_to_DISO		isa	BRCA1 Syndrome C1332442
DISO_to_DISO		isa	BRCA2 Syndrome C1332443
DISO_to_DISO		may_be_associated_disease_of_disease	Epithelial ovarian cancer C0677886
DISO_to_DISO		permuted_term_of	Familial Breast and Ovarian Cancer Syndrome C0677776
DISO_to_DISO		may_be_associated_disease_of_disease	Female Breast Carcinoma C0007104
DISO_to_DISO		is_finding_of_disease	Hereditary Lesion C1708351
DISO_to_DISO		mapped_to	Malignant neoplasm of breast C0006142

Genes (64)

Species:

human : 64

Page Size

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Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	BRCA1P1	394269	BRCA1 pseudogene 1	NCI, Score=801, Pubmed Id: 11880951, UMLKSK CUI: C0677776 In the two families with breast and ovarian cancer mentioned above, distinct homologous recombination events occurred between intron 2 of BRCA1 and intron 2 of PsiBRCA1, leading to 37-kb deletions.
Human	PEBP4	157310	phosphatidylethanolamine-binding protein 4	NCI, Score=801, Pubmed Id: 16865237, UMLKSK CUI: C0677776 Human phosphatidylethanolamine-binding protein 4 (hPEBP4) is a recently identified anti-apoptotic molecule and has been shown to be highly expressed in breast and ovarian cancer cells.
Human	CNKSR3	154043	CNKSR family member 3	NCI, Score=801, Pubmed Id: 9528852, UMLKSK CUI: C0677776 We have identified a novel protein, BAP1, which binds to the RING finger domain of the Breast/Ovarian Cancer Susceptibility Gene product, BRCA1.
Human	TUBA1C	84790	tubulin, alpha 1c	NCI, Score=801, Pubmed Id: 7553639, UMLKSK CUI: C0677776 Taxol stabilizes microtubules, prevents tubulin depolymerization, and promotes tubulin bundling and is one of the most effective drugs for the treatment of metastatic breast and ovarian cancer.
Human	BRIP1	83990	BRCA1 interacting protein C-terminal helicase 1	NCI, Score=801, Pubmed Id: 12872252, UMLKSK CUI: C0677776 Based on sequencing of ZBRK1 and BRIP1 in 21 BRCA1/2-negative probands from inherited breast/ovarian cancer families, it appears unlikely that mutations in these genes account for a significant fraction of inherited breast cancer. NCI, Score=801, Pubmed Id: 12565990, UMLKSK CUI: C0677776 No evidence of involvement of germline BACH1 mutations in Finnish breast and ovarian cancer families. NCI, Score=801, Pubmed Id: 14983014, UMLKSK CUI: C0677776 Mutations within the BRCT repeats disrupt the interaction between BRCA1 and BACH1, lead to defects in DNA repair, and result in breast and ovarian cancer. NCI, Score=801, Pubmed Id: 12872252, UMLKSK CUI: C0677776 Mutational analysis of the BRCA1-interacting genes ZNF350/ZBRK1 and BRIP1/BACH1 among BRCA1 and BRCA2-negative probands from breast-ovarian cancer families and among early-onset breast cancer cases and reference individuals. NCI, Score=801, Pubmed Id: 12565990, UMLKSK CUI: C0677776 Here, we screened 214 breast and ovarian cancer patients from 151 Finnish families for germline BACH1 mutations by utilising conformation-sensitive gel electrophoresis (CSGE) and genomic sequencing analysis. NCI, Score=801, Pubmed Id: 12565990, UMLKSK CUI: C0677776 Recently BACH1, a novel putative DNA helicase mapping to chromosome 17q22, was reported to interact specifically with BRCA1, and was suggested to be a candidate gene for predisposition to breast and ovarian cancers.
Human	ZNF350	59348	zinc finger protein 350	NCI, Score=801, Pubmed Id: 12872252, UMLKSK CUI: C0677776 Mutational analysis of the BRCA1-interacting genes ZNF350/ZBRK1 and BRIP1/BACH1 among BRCA1 and BRCA2-negative probands from breast-ovarian cancer families and among early-onset breast cancer cases and reference individuals. NCI, Score=801, Pubmed Id: 12872252, UMLKSK CUI: C0677776 Based on sequencing of ZBRK1 and BRIP1 in 21 BRCA1/2-negative probands from inherited breast/ovarian cancer families, it appears unlikely that mutations in these genes account for a significant fraction of inherited breast cancer.
Human	C11orf30	56946	chromosome 11 open reading frame 30	NCI, Score=801, Pubmed Id: 14651841, UMLKSK CUI: C0677776 EMSY is located within an amplicon in sporadic breast and ovarian cancers, suggesting that its overexpression may mimic the effects of BRCA2 inactivation. NCI, Score=801, Pubmed Id: 14651845, UMLKSK CUI: C0677776 EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. NCI, Score=801, Pubmed Id: 14651845, UMLKSK CUI: C0677776 The remarkable clinical overlap between sporadic EMSY amplification and familial BRCA2 deletion implicates a BRCA2 pathway in sporadic breast and ovarian cancer. NCI, Score=801, Pubmed Id: 14651845, UMLKSK CUI: C0677776 EMSY maps to chromosome 11q13.5, a region known to be involved in breast and ovarian cancer.
Human	PMEPA1	56937	prostate transmembrane protein, androgen induced 1	NCI, Score=801, Pubmed Id: 14639658, UMLKSK CUI: C0677776 Finally, we have demonstrated that, besides prostate cancer and renal cell carcinoma, STAG1 was also overexpressed in breast and ovarian cancer cell lines and in breast primary tumors.
Human	WNT4	54361	wingless-type MMTV integration site family, member 4	NCI, Score=801, Pubmed Id: 15312687, UMLKSK CUI: C0677776 Their absence in cancer families, however, implies lack of involvement of WNT4 mutations in the etiology of hereditary susceptibility to breast and ovarian cancer. NCI, Score=801, Pubmed Id: 15312687, UMLKSK CUI: C0677776 Characterization and expression of the human WNT4; lack of associated germline mutations in high--to moderate--risk breast and ovarian cancer.
Human	UBR5	51366	ubiquitin protein ligase E3 component n-recognin 5	NCI, Score=801, Pubmed Id: 12902990, UMLKSK CUI: C0677776 AI is likely to represent amplification of the EDD gene locus rather than loss of heterozygosity, as quantitative RT-PCR and immunohistochemistry showed that EDD mRNA and protein are frequently overexpressed in breast and ovarian cancers, while among breast cancer cell lines EDD overexpression and increased gene copy number were correlated. NCI, Score=801, Pubmed Id: 12902990, UMLKSK CUI: C0677776 These results demonstrate that AI at the EDD locus is common in a diversity of carcinomas and that the EDD gene is frequently overexpressed in breast and ovarian cancer, implying a potential role in cancer progression.
Human	KLK14	43847	kallikrein-related peptidase 14	NCI, Score=801, Pubmed Id: 12645335, UMLKSK CUI: C0677776 To study KLK14 gene expression in endocrine-related cancers, we studied its hormonal regulation in breast and ovarian cancer cell lines. NCI, Score=801, Pubmed Id: 14695222, UMLKSK CUI: C0677776 Given that KLK14 is hormonally regulated, differentially expressed in endocrine-related cancers, and a prognostic marker for breast and ovarian cancer at the mRNA level, we hypothesize that its encoded protein, hK14, like hK3/prostate-specific antigen, may constitute a new biomarker for endocrine-related malignancies. NCI, Score=801, Pubmed Id: 12439719, UMLKSK CUI: C0677776 Similar to other kallikrein genes, KLK14 was found to be regulated by steroid hormones, particularly androgens and progestins, in breast and ovarian cancer cell lines.
Human	OSGIN1	29948	oxidative stress induced growth inhibitor 1	NCI, Score=801, Pubmed Id: 15217983, UMLKSK CUI: C0677776 To develop a rat model for further characterization of OKL38;s role in the initiation and progression of breast and ovarian cancer, we now report the cloning and characterization of three novel rat OKL38 cDNAs that are derived through alternative splicing and differential promoter usage.
Human	KLK5	25818	kallikrein-related peptidase 5	NCI, Score=801, Pubmed Id: 12873991, UMLKSK CUI: C0677776 KLK5 was shown to be differentially expressed at the mRNA level in breast and ovarian cancer. NCI, Score=801, Pubmed Id: 15627884, UMLKSK CUI: C0677776 KLK5-SV2 is a potential biomarker for breast and ovarian cancers. NCI, Score=801, Pubmed Id: 12873991, UMLKSK CUI: C0677776 Human kallikrein 5: a potential novel serum biomarker for breast and ovarian cancer. NCI, Score=801, Pubmed Id: 15004490, UMLKSK CUI: C0677776 We have previously reported regulation of the KLK5 gene by estrogens and progestins and its clinical value as a marker of poor prognosis in breast and ovarian cancers.
Human	CHEK2	11200	checkpoint kinase 2	NCI, Score=801, Pubmed Id: 14507240, UMLKSK CUI: C0677776 This is the first study from South India, on BRCA1, BRCA2 (1100 del C) mutations in patients with a family history of breast and/or ovarian cancer and early onset breast/ovarian cancer, using the sensitive DHPLC approach. NCI, Score=801, Pubmed Id: 15280181, UMLKSK CUI: C0677776 Most women with a family history of breast/ovarian cancer have tumors characterized by alterations in particular genes, mainly BRCA1 and BRCA2, but also CHK2, ATM, STK11 and others. NCI, Score=801, Pubmed Id: 14507240, UMLKSK CUI: C0677776 BRCA1, BRCA2 and CHEK2 (1100 del C) germline mutations in hereditary breast and ovarian cancer families in South India. NCI, Score=801, Pubmed Id: 15217503, UMLKSK CUI: C0677776 INTRODUCTION: Mutations in BRCA1, BRCA2, ATM, TP53, CHK2 and PTEN account for many, but not all, multiple-case breast and ovarian cancer families.
Human	WFDC2	10406	WAP four-disulfide core domain 2	NCI, Score=801, Pubmed Id: 16080959, UMLKSK CUI: C0677776 Amplification of 20q is frequently implicated in both breast and ovarian cancer; this region contains a number of oncogenes including MDM2, ZNF217, and the ovarian tumor marker WFDC2 (alias HE4).
Human	HMG20B	10362	high mobility group 20B	NCI, Score=801, Pubmed Id: 12083780, UMLKSK CUI: C0677776 Because of the high incidence of genetic links of prostate cancer to breast and ovarian cancers, we investigated the BRAF25 expression in the prostate specimens.
Human	RAD50	10111	RAD50 homolog (S. cerevisiae)	NCI, Score=801, Pubmed Id: 14684699, UMLKSK CUI: C0677776 Mutation screening of Mre11 complex genes: indication of RAD50 involvement in breast and ovarian cancer susceptibility.
Human	C1orf38	9473		NCI, Score=801, Pubmed Id: 16219472, UMLKSK CUI: C0677776 Expression of icb-1 gene is interferon-gamma inducible in breast and ovarian cancer cell lines and affects the IFNgamma-response of SK-OV-3 ovarian cancer cells.
Human	DIRAS3	9077	DIRAS family, GTP-binding RAS-like 3	Click here to display 10 evidence detail records.
Human	BECN1	8678	beclin 1, autophagy related	NCI, Score=801, Pubmed Id: 11309306, UMLKSK CUI: C0677776 Beclin 1 encodes a Bcl-2-interacting coiled-coil protein with autophagy and tumor suppressor function and is monoallelically deleted in 40-75% of sporadic human breast and ovarian cancers.
Human	CXCR4	7852	chemokine (C-X-C motif) receptor 4	NCI, Score=801, Pubmed Id: 12414661, UMLKSK CUI: C0677776 Recently, SDF-1alpha and CXCR4 have been shown to be important regulators of migration and metastasis in breast and ovarian cancer.
Human	ZNF217	7764	zinc finger protein 217	NCI, Score=801, Pubmed Id: 16080959, UMLKSK CUI: C0677776 Amplification of 20q is frequently implicated in both breast and ovarian cancer; this region contains a number of oncogenes including MDM2, ZNF217, and the ovarian tumor marker WFDC2 (alias HE4).
Human	CLEC3B	7123	C-type lectin domain family 3, member B	NCI, Score=801, Pubmed Id: 7998355, UMLKSK CUI: C0677776 [Tetranectin, a plasma and tissue protein--a prognostic marker of breast and ovarian cancer]
Human	THRA	7067	thyroid hormone receptor, alpha	NCI, Score=801, Pubmed Id: 8460637, UMLKSK CUI: C0677776 Gene mapping in extended families with inherited, early-onset breast and ovarian cancer indicates that BRCA1 is distal to THRA1 and proximal to D17S183 (SCG43), an interval of < 4 cM. NCI, Score=801, Pubmed Id: 8460637, UMLKSK CUI: C0677776 In order to pinpoint the locale of the gene for early-onset familial breast and ovarian cancer (BRCA1), polymorphisms were developed within the locus for thyroid hormone receptor alpha (THRA1) and for several anonymous sequences at chromosome 17q12-q21. NCI, Score=801, Pubmed Id: 8460637, UMLKSK CUI: C0677776 THRA1 and D17S183 flank an interval of < 4 cM for the breast-ovarian cancer gene (BRCA1) on chromosome 17q21.
Human	TFF1	7031	trefoil factor 1	NCI, Score=801, Pubmed Id: 2178364, UMLKSK CUI: C0677776 Prognostic value of pS2 protein and receptors for epidermal growth factor (EGF-R), insulin-like growth factor-1 (IGF-1-R) and somatostatin (SS-R) in patients with breast and ovarian cancer.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0677776	Familial Breast and Ovarian Cancer Syndrome	0		self

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