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 - Breast Metastases

Debug Stats

### Total Build Time: 26 ms 52.691 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 332 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 288 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= 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=7 ms Completed: 7 ms rowSize= 11.405 KB
CONCEPT_GENES gt=15 ms Completed: 15 ms rowSize= 39.459 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.151 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Breast Metastases C0346993

Definition (1)

The spread of cancer to the breast. This may be from a primary breast cancer on the opposite side, or from a cancer at a distant site.

Relationships (24)

Relation Types:

diso_to_anat : 4

diso_to_diso : 20

Relationships:

classifies : 2

is_abnormal_cell_of_disease : 2

is_finding_of_disease : 1

is_metastatic_anatomic_site_of_disease : 1

isa : 3

location_of : 1

mapped_to : 14

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_metastatic_anatomic_site_of_disease	Breast C0006141
DISO_to_ANAT		is_abnormal_cell_of_disease	Cancer Cell C0334227
DISO_to_ANAT		location_of	Female breast C0222603
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_DISO		mapped_to	Breast Metastases C0346993
DISO_to_DISO		isa	Metastasis to breast of unknown primary C0563510
DISO_to_DISO		is_finding_of_disease	Metastatic Lesion C1513183
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to areola of female breast C0686297
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to areola of male breast C0686337
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to axillary tail of female breast C0686321
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to central portion of female breast C0686301
DISO_to_DISO		isa	Metastatic malignant neoplasm to ectopic female breast tissue C0686326
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to ectopic male breast tissue C0686342
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to lower inner quadrant of female breast C0686309
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to lower outer quadrant of female breast C0686317
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to male breast C0686329
DISO_to_DISO		isa	Metastatic malignant neoplasm to nipple of female breast C0686293
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to nipple of male breast C0686333
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to upper inner quadrant of female breast C0686305
DISO_to_DISO		mapped_to	Metastatic malignant neoplasm to upper outer quadrant of female breast C0686313
DISO_to_DISO		classifies	Other secondary malignancy C0810248
DISO_to_DISO		classifies	Secondary Neoplasm C2939419
DISO_to_DISO		mapped_to	Secondary malignant neoplasm of axillary tail of breast C1299236
DISO_to_DISO		mapped_to	pN3b: Metastasis in clinically apparent ipsilateral internal mammary nodes in the presence of 1 or more positive axillary nodes; or in >3 axillary nodes and in internal mammary nodes with microscopic disease in sentinel node but not clinically C1274009

Genes (39)

Species:

human : 38

mouse : 1

Page Size

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Current 1

Species	Gene	GeneId	Gene Name	Evidence
Mouse	EZR	7430	ezrin	NCI, Score=801, Pubmed Id: 15987432, UMLKSK CUI: C0346993 Together, these results suggest that blocking ezrin function may represent a novel and effective strategy for preventing breast cancer metastasis. NCI, Score=801, Pubmed Id: 15987432, UMLKSK CUI: C0346993 CONCLUSION : Our findings indicate that ezrin is required for breast cancer metastasis, and that c-Src and phosphatidylinositol 3-kinase/Akt are effectors of ezrin in the cell motility and invasion stages of the metastatic process.
Human	SCGB3A1	92304	secretoglobin, family 3A, member 1	NCI, Score=801, Pubmed Id: 15131050, UMLKSK CUI: C0346993 To characterize molecular alterations in breast cancer metastasis, we investigated the frequency of hypermethylation of five genes (Cyclin D2, RAR-beta, Twist, RASSF1A, and HIN-1) in metastasis to four common sites: lymph node, bone, brain, and lung.
Human	INHBE	83729	inhibin, beta E	NCI, Score=801, Pubmed Id: 12206515, UMLKSK CUI: C0346993 We, therefore, examined the gene expression pattern of the TGF-beta family members (inhibin/activin betaA subunit (activin betaA), inhibin alpha subunit, and bone morphogenetic protein-2 (BMP-2)), the TNF family members (receptor activator of NF-KB ligand (RANKL) and osteoprotegerin (OPG)), and osteopontin (OPN) in normal, non-invasive, invasive, and metastatic human breast cancer specimens.
Human	BRMS1	25855	breast cancer metastasis suppressor 1	NCI, Score=801, Pubmed Id: 15705865, UMLKSK CUI: C0346993 Taken together, these results implicate signaling through phosphoinositides in the regulation of breast cancer metastasis, specifically metastasis that can be suppressed by BRMS1. NCI, Score=801, Pubmed Id: 16006775, UMLKSK CUI: C0346993 Expression of the breast cancer metastasis suppressor gene, BRMS1, in human breast carcinoma: lack of correlation with metastasis to axillary lymph nodes. NCI, Score=801, Pubmed Id: 11751410, UMLKSK CUI: C0346993 Predisposition to efficient mammary tumor metastatic progression is linked to the breast cancer metastasis suppressor gene Brms1. NCI, Score=801, Pubmed Id: 15168732, UMLKSK CUI: C0346993 BRMS1 (breast cancer metastasis suppressor 1) was recently identified as a novel breast cancer metastasis suppressor gene. NCI, Score=801, Pubmed Id: 15252837, UMLKSK CUI: C0346993 We explored cell-to-cell communication between 435 carcinoma cells and a human osteoblastic cell line, hFOB1.19, to determine whether carcinoma cells can form gap junctions with bone cells and to explore the role of these heterotypic gap junctions and the BRMS1 gene in breast cancer metastasis to bone.
Human	WASL	8976	Wiskott-Aldrich syndrome-like	NCI, Score=801, Pubmed Id: 11865026, UMLKSK CUI: C0346993 Phosphoinositide 3-kinase (PI3K), small Rho GTPases, such as Cdc42 and Rac1, and neuronal Wiskott Aldrich syndrome protein (N-WASP) are key effectors that regulate dynamic changes in the actin cytoskeleton and cell migration. uPA- and EGF-stimulated chemotaxis, cytoskeletal rearrangements and activation of Cdc42, Rac1 and N-WASP were studied in the highly metastatic human breast cancer cell line MDA MB 231. NCI, Score=801, Pubmed Id: 11865026, UMLKSK CUI: C0346993 uPA- and EGF-stimulated chemotaxis, cytoskeletal rearrangements and activation of Cdc42, Rac1 and N-WASP were studied in the highly metastatic human breast cancer cell line MDA MB 231.
Human	TNFSF11	8600	tumor necrosis factor (ligand) superfamily, member 11	NCI, Score=801, Pubmed Id: 11516200, UMLKSK CUI: C0346993 BACKGROUND: Breast cancer metastasis to bone causes resorption of the mineralized matrix by osteoclasts.Macrophage colony stimulating factor (M-CSF)and receptor activator of the NF-kappaB ligand (RANKL) are produced by stromal cells and are essential for osteoclast formation. NCI, Score=801, Pubmed Id: 12206515, UMLKSK CUI: C0346993 We, therefore, examined the gene expression pattern of the TGF-beta family members (inhibin/activin betaA subunit (activin betaA), inhibin alpha subunit, and bone morphogenetic protein-2 (BMP-2)), the TNF family members (receptor activator of NF-KB ligand (RANKL) and osteoprotegerin (OPG)), and osteopontin (OPN) in normal, non-invasive, invasive, and metastatic human breast cancer specimens. GENERIF, Score=853, Pubmed Id: 15671541, UMLKSK CUI: C0346993 RANKL has a role in breast carcinoma metastasis
Human	CXCR4	7852	chemokine (C-X-C motif) receptor 4	Click here to display 17 evidence detail records.
Human	WNT5A	7474	wingless-type MMTV integration site family, member 5A	NCI, Score=801, Pubmed Id: 16880514, UMLKSK CUI: C0346993 We show here that NFAT1, a transcription factor connected with breast cancer metastasis, is activated by Wnt-5a through a Ca(2+) signaling pathway in human breast epithelial cells.
Human	EZR	7430	ezrin	NCI, Score=801, Pubmed Id: 15987432, UMLKSK CUI: C0346993 However, the role played by ezrin in breast cancer metastasis has not been clearly delineated.
Human	THBS1	7057	thrombospondin 1	GENERIF, Score=913, Pubmed Id: 11801541, UMLKSK CUI: C0346993 Increased expression is associated with breast tumor metastasis
Human	TFF1	7031	trefoil factor 1	NCI, Score=801, Pubmed Id: 2153395, UMLKSK CUI: C0346993 The pNR-2 mRNA is regulated by oestrogens in cell lines established from metastatic human breast cancer cells.
Human	SPP1	6696	secreted phosphoprotein 1	GENERIF, Score=913, Pubmed Id: 11801541, UMLKSK CUI: C0346993 Increased expression is associated with breast tumor metastasis
Human	SNCG	6623	synuclein, gamma (breast cancer-specific protein 1)	NCI, Score=801, Pubmed Id: 11526506, UMLKSK CUI: C0346993 When over expressed, BCSG1 significantly stimulates breast cancer metastasis.
Human	CCL21	6366	chemokine (C-C motif) ligand 21	NCI, Score=801, Pubmed Id: 11242036, UMLKSK CUI: C0346993 Their respective ligands CXCL12/SDF-1alpha and CCL21/6Ckine exhibit peak levels of expression in organs representing the first destinations of breast cancer metastasis.
Human	S100A4	6275	S100 calcium binding protein A4	NCI, Score=801, Pubmed Id: 14710237, UMLKSK CUI: C0346993 S100A4 regulates cell motility and invasion in an in vitro model for breast cancer metastasis.
Human	MAP2K1	5604	mitogen-activated protein kinase kinase 1	NCI, Score=801, Pubmed Id: 10949153, UMLKSK CUI: C0346993 Using PD98059, an inhibitor of the ERK-kinase MEK1, we have here assessed the effects of ERK inhibition on the pattern of protein expression in the metastatic human breast cancer cell line MDA-MB-231.
Human	TNFRSF11B	4982	tumor necrosis factor receptor superfamily, member 11b	NCI, Score=801, Pubmed Id: 12206515, UMLKSK CUI: C0346993 We, therefore, examined the gene expression pattern of the TGF-beta family members (inhibin/activin betaA subunit (activin betaA), inhibin alpha subunit, and bone morphogenetic protein-2 (BMP-2)), the TNF family members (receptor activator of NF-KB ligand (RANKL) and osteoprotegerin (OPG)), and osteopontin (OPN) in normal, non-invasive, invasive, and metastatic human breast cancer specimens.
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	NCI, Score=801, Pubmed Id: 8347849, UMLKSK CUI: C0346993 We summarize published and recent research concerning the nm23 gene in breast cancer metastasis. NCI, Score=801, Pubmed Id: 14506169, UMLKSK CUI: C0346993 We searched for well-tolerated compounds that could elevate Nm23 metastasis suppressor expression in metastatic human breast cancer cell lines. NCI, Score=801, Pubmed Id: 8347849, UMLKSK CUI: C0346993 Nm23 and breast cancer metastasis. NCI, Score=801, Pubmed Id: 8620461, UMLKSK CUI: C0346993 The nm23-H1 and p53 genes have been involved in the development of breast cancer metastasis. NCI, Score=801, Pubmed Id: 14735469, UMLKSK CUI: C0346993 In the present investigation, we used cDNA microarrays to identify novel genes and functional pathways in nm23-mediated spontaneous breast metastasis.
Human	LOX	4015	lysyl oxidase	NCI, Score=801, Pubmed Id: 12154058, UMLKSK CUI: C0346993 We identified previously an up-regulation in lysyl oxidase (LOX) expression,an extracellular matrix remodeling enzyme, in a highly invasive/metastatic human breast cancer cell line, MDA-MB-231, compared with MCF-7, a poorly invasive/nonmetastatic breast cancer cell line.
Human	LASP1	3927	LIM and SH3 protein 1	NCI, Score=801, Pubmed Id: 7589475, UMLKSK CUI: C0346993 MLN 50 was previously identified in a cDNA library of breast cancer metastasis.
Human	KIF22	3835	kinesin family member 22	NCI, Score=801, Pubmed Id: 16764773, UMLKSK CUI: C0346993 [Expression and clinical significance of KNSL4 in breast cancer] BACKGROUND _amp_ OBJECTIVE: Previous screening of breast cancer metastasis-related genes found that the mRNA level of kinesin-like 4 (KNSL4) gene is down-regulated in metastatic lymph nodes as compared with the paired primary breast cancer.
Human	ITGAV	3685	integrin, alpha V	NCI, Score=801, Pubmed Id: 8727100, UMLKSK CUI: C0346993 Integrin alpha V beta 3 expression by bone-residing breast cancer metastases.
Human	INHA	3623	inhibin, alpha	NCI, Score=801, Pubmed Id: 12206515, UMLKSK CUI: C0346993 We, therefore, examined the gene expression pattern of the TGF-beta family members (inhibin/activin betaA subunit (activin betaA), inhibin alpha subunit, and bone morphogenetic protein-2 (BMP-2)), the TNF family members (receptor activator of NF-KB ligand (RANKL) and osteoprotegerin (OPG)), and osteopontin (OPN) in normal, non-invasive, invasive, and metastatic human breast cancer specimens.
Human	IGF1R	3480	insulin-like growth factor 1 receptor	NCI, Score=801, Pubmed Id: 10885804, UMLKSK CUI: C0346993 We found that the functional disruption of IGF-1R markedly influences breast cancer metastasis in nude mice by suppressing cellular adhesion, invasion, and metastasis of breast cancer cells to the lung, lymph nodes, and lymph vessels. NCI, Score=801, Pubmed Id: 15687676, UMLKSK CUI: C0346993 Finally, we consider the potential role of IGF-1R in regulating breast cancer metastases by facilitating angiogenesis and lymphangiogenesis.
Human	HIF1A	3091	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	NCI, Score=801, Pubmed Id: 10582706, UMLKSK CUI: C0346993 HIF-1alpha overexpression was detected in only 29% of primary breast cancers but in 69% of breast cancer metastases.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0346993	Breast Metastases	0		self

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