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 - Lymphangioleiomyomatosis

Debug Stats

### Total Build Time: 37 ms 40.259 KB
CONCEPT_NAME gt=4 ms Completed: 4 ms rowSize= 346 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 463 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= 187 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=2 ms Completed: 2 ms rowSize= 1,008 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=5 ms Completed: 5 ms rowSize= 5.344 KB
CONCEPT_RELATIONSHIPS gt=14 ms Completed: 14 ms rowSize= 14.209 KB
CONCEPT_GENES gt=9 ms Completed: 9 ms rowSize= 17.556 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)

Lymphangioleiomyomatosis C0751674

Definition (1)

A disease characterized by the progressive invasion of SMOOTH MUSCLE CELLS into the LYMPHATIC VESSELS, and the BLOOD VESSELS. The majority of the cases occur in the LUNGS of women of child-bearing age, eventually blocking the flow of air, blood, and lymph. The common symptom is shortness of breath (DYSPNEA).

Semantic Types (1)

Neoplastic Process (T191)

Parents (2)

C1300127

C0024223

Ancestral Roots

Relationships (39)

Relation Types:

diso_to_anat : 6

diso_to_chem : 3

diso_to_diso : 28

diso_to_phen : 2

Relationships:

none : 21

expanded_form_of : 1

is_abnormal_cell_of_disease : 2

is_associated_anatomic_site_of : 1

is_finding_of_disease : 6

is_normal_tissue_origin_of_disease : 1

is_not_finding_of_disease : 1

isa : 2

mapped_to : 2

may_be_associated_disease_of_disease : 1

may_be_molecular_abnormality_of_disease : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	107		Lung Neoplasms C0024121
DISO_to_DISO	100		Lung Neoplasms C0024121
DISO_to_DISO	66		Complication Aspects C1171258
DISO_to_DISO	58		Complication Aspects C1171258
DISO_to_DISO	35		Tuberous Sclerosis C0041341
DISO_to_PHEN	29		genetic aspects C0017399
DISO_to_CHEM	24		Sirolimus C0072980
DISO_to_DISO	24		Angiomyolipoma C0206633
DISO_to_PHEN	21		genetic aspects C0017399
DISO_to_DISO	19		Pneumothorax C0032326
DISO_to_DISO	18		Kidney Neoplasm C0022665
DISO_to_ANAT	15		Lung C0024109
DISO_to_DISO	15		Angiomyolipoma C0206633
DISO_to_DISO	15		Tuberous Sclerosis C0041341
DISO_to_CHEM	13		Proteins, Tumor Suppressor C0597611
DISO_to_DISO	13		Kidney Neoplasm C0022665
DISO_to_DISO	13		Neoplasm of retroperitoneum C0035358
DISO_to_DISO	11		Lung Diseases C0024115
DISO_to_ANAT	10		Lung C0024109
DISO_to_CHEM	10		Immunosuppressive Agents C0021081
DISO_to_DISO	10		NEOPL UTERINE C0042138
DISO_to_ANAT		is_associated_anatomic_site_of	Connective and Soft Tissue C1516798
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Perivascular Epithelioid Cell C1709193
DISO_to_ANAT		is_normal_tissue_origin_of_disease	soft tissue C0225317

Genes (13)

Species:

human : 13

Species	Gene	GeneId	Gene Name	Evidence
Human	PDPN	10630	podoplanin	GENERIF, Score=1000, Pubmed Id: 17377811, UMLKSK CUI: C0751674 Data showed podoplanin (D2-40 monoclonal antibody) was positive in thin-wall branching vessels and confirmed the current concept of lymphangiogenic origin of the tumor vessels in lymphangioleiomyoma/lymphangioleiomyomatosis
Human	HMGA2	8091	high mobility group AT-hook 2	GENERIF, Score=1000, Pubmed Id: 17332316, UMLKSK CUI: C0751674 HMGA2 plays a central role in the pathogenesis of Lymphangiomyomatosis NCI, Score=801, Pubmed Id: 17332316, UMLKSK CUI: C0751674 Here, we show that HMGA2 is misexpressed in pulmonary lymphangiomyomatosis (LAM), a severe disorder of unknown etiology consisting of lymphatic smooth muscle cell proliferation that results in the obstruction of airways, lymphatics, and vessels. NCI, Score=801, Pubmed Id: 17332316, UMLKSK CUI: C0751674 Identification of the benign mesenchymal tumor gene HMGA2 in lymphangiomyomatosis.
Human	TSC2	7249	tuberous sclerosis 2	GENERIF, Score=1000, Pubmed Id: 17114346, UMLKSK CUI: C0751674 These findings suggest a link between tuberin nuclear localization and a variety of intracellular signaling events that have direct implications with respect to the role of tuberin in the pathology of tuberous sclerosis and lymphangioleiomyomatosis OMIM, Score=1000, UMLKSK CUI: C0751674 Lymphangiomyomatosis, rare
Human	TSC1	7248	tuberous sclerosis 1	OMIM, Score=1000, UMLKSK CUI: C0751674 Lymphangiomyomatosis, rare
Human	TIMP3	7078	TIMP metallopeptidase inhibitor 3	NCI, Score=801, Pubmed Id: 12654640, UMLKSK CUI: C0751674 Tissue inhibitor of metalloproteinase-3 downregulation in lymphangioleiomyomatosis: potential consequence of abnormal serum response factor expression. NCI, Score=801, Pubmed Id: 12707009, UMLKSK CUI: C0751674 Lymphangioleiomyomatosis: a complex tale of serum response factor-mediated tissue inhibitor of metalloproteinase-3 regulation. GENERIF, Score=1000, Pubmed Id: 12654640, UMLKSK CUI: C0751674 This protein is downregulated in lymphangioleiomyomatosis as a consequence of abnormal serum response factor expression
Human	SRF	6722	serum response factor (c-fos serum response element-binding transcription factor)	GENERIF, Score=1000, Pubmed Id: 12654640, UMLKSK CUI: C0751674 Tissue inhibitor of metalloproteinase-3 is downregulated in lymphangioleiomyomatosis as a consequence of abnormal SRF expression
Human	RHEB	6009	Ras homolog enriched in brain	NCI, Score=801, Pubmed Id: 16575396, UMLKSK CUI: C0751674 These data suggest that activation of the Rheb/mTOR/p70 S6 kinase pathway is related to the pathogenesis of lymphangioleiomyomatosis-associated and sporadic angiomyolipomas lacking TSC1/TSC2 loss of heterozygosity.
Human	IGFBP2	3485	insulin-like growth factor binding protein 2, 36kDa	NCI, Score=801, Pubmed Id: 11523698, UMLKSK CUI: C0751674 METHODS: To evaluate the role of the IGF system in lymphangioleiomyomatosis (LAM), we used immunohistochemical and in situ hybridization techniques to characterize the expression of IGF-1, IGF-2, IGF-1R, and IGFBP-2, -4, -5, and -6 in lung tissue from 18 LAM patients.
Human	IGF1R	3480	insulin-like growth factor 1 receptor	NCI, Score=801, Pubmed Id: 11523698, UMLKSK CUI: C0751674 METHODS: To evaluate the role of the IGF system in lymphangioleiomyomatosis (LAM), we used immunohistochemical and in situ hybridization techniques to characterize the expression of IGF-1, IGF-2, IGF-1R, and IGFBP-2, -4, -5, and -6 in lung tissue from 18 LAM patients.
Human	IFNG	3458	interferon, gamma	OMIM, Score=1000, UMLKSK CUI: C0751674 Lymphangiomyomatosis, rare
Human	MLANA	2315	melan-A	NCI, Score=801, Pubmed Id: 9720495, UMLKSK CUI: C0751674 Comparison of melanoma antigen recognized by T cells (MART-1) to HMB-45: additional evidence to support a common lineage for angiomyolipoma, lymphangiomyomatosis, and clear cell sugar tumor.
Human	FIGF	2277	c-fos induced growth factor (vascular endothelial growth factor D)	GENERIF, Score=1000, Pubmed Id: 17034294, UMLKSK CUI: C0751674 Serum VEGF-D levels may be a valuable surrogate marker for evaluating the disease severity in lymphangioleiomyomatosis
Human	COMT	1312	catechol-O-methyltransferase	NCI, Score=801, Pubmed Id: 10856317, UMLKSK CUI: C0751674 Oestrogen metabolism in lymphangioleiomyomatosis: catechol-O-methyltransferase pathway is not involved.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0751674	Lymphangioleiomyomatosis	0		self

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