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 - Enchondroma

Debug Stats

### Total Build Time: 13 ms 29.948 KB
CONCEPT_NAME gt=0 Completed: 0 ms rowSize= 320 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 263 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=6 ms Completed: 6 ms rowSize= 12.314 KB
CONCEPT_GENES gt=5 ms Completed: 5 ms rowSize= 15.849 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.146 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Enchondroma C1704356

Definition (1)

A benign (noncancerous) growth of cartilage in bones or in other areas where cartilage is not normally found.

Relationships (24)

Relation Types:

diso_to_anat : 14

diso_to_diso : 10

Relationships:

disease_has_associated_disease : 1

is_abnormal_cell_of_disease : 4

is_associated_anatomic_site_of : 1

is_finding_of_disease : 3

is_normal_cell_origin_of_disease : 3

is_normal_tissue_origin_of_disease : 2

is_not_normal_cell_origin_of_disease : 1

is_not_normal_tissue_origin_of_disease : 2

is_primary_anatomic_site_of_disease : 1

may_be_finding_of_disease : 5

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Cartilage C0007301
DISO_to_ANAT		is_normal_cell_origin_of_disease	Cartilage Cell C3161470
DISO_to_ANAT		is_normal_cell_origin_of_disease	Cell of connective tissue C0009781
DISO_to_ANAT		is_normal_cell_origin_of_disease	Chondrocyte C0225369
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Connective and Soft Tissue C1516798
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Medullary Bone C1708973
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cartilage Cell C1709167
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Chondrocyte C1513939
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Connective and Soft Tissue Cell C1513942
DISO_to_ANAT		is_not_normal_cell_origin_of_disease	Nerve Cell, Neuroepithelial Cell, and Supporting Cell of the Nervous System C1518293
DISO_to_ANAT		is_not_normal_tissue_origin_of_disease	Periosteum C0031110
DISO_to_ANAT		is_associated_anatomic_site_of	Skeletal bone C0262950
DISO_to_ANAT		is_not_normal_tissue_origin_of_disease	Synovial Membrane C0039099
DISO_to_DISO		may_be_finding_of_disease	Calcification C1533591
DISO_to_DISO		is_finding_of_disease	Cartilaginous Differentiation C1707309
DISO_to_DISO		disease_has_associated_disease	Chondrodysplasia with Hemangioma C0024454
DISO_to_DISO		permuted_term_of	Enchondroma C1704356
DISO_to_DISO		may_be_finding_of_disease	Fractures, Spontaneous C0016663
DISO_to_DISO		is_finding_of_disease	Hyaline Cartilage Differentiation C1708393
DISO_to_DISO		is_finding_of_disease	Indolent Clinical Course C1334168
DISO_to_DISO		may_be_finding_of_disease	Multinodular Pattern C1334823
DISO_to_DISO		may_be_finding_of_disease	Pain C0030193
DISO_to_DISO		may_be_finding_of_disease	Swelling C0038999

Genes (9)

Species:

human : 9

Species	Gene	GeneId	Gene Name	Evidence
Human	HMGA2	8091	high mobility group AT-hook 2	NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 Both skeletal chondromas expressed HMGA2. NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 Expression of HMGA2 could be assessed by RT-PCR in 8 chondromas and 13 chondrosarcomas. NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 Fusion, disruption, and expression of HMGA2 in bone and soft tissue chondromas. NCI, Score=801, Pubmed Id: 16133369, UMLKSK CUI: C1704356 For example, HMGA2/LPP has been reported in lipoma, pulmonary chondroid hamartoma, and soft tissue chondroma. NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 One soft tissue chondroma had a t(3;12)(q27;q15), and the RT-PCR analysis revealed an HMGA2-LPP fusion transcript, composed of HMGA2 exons 1-3 and LPP exons 9-11. NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 HMGA2 was expressed in 4 of six soft tissue chondromas, all displaying 12q-rearrangements at cytogenetic analysis.
Human	TIMP2	7077	TIMP metallopeptidase inhibitor 2	NCI, Score=801, Pubmed Id: 10473866, UMLKSK CUI: C1704356 The extent scores of MT1-MMP, MMP-2 and TIMP-2 in grade 2 chondrosarcoma were significantly higher than those in either enchondroma or grade 1 chondrosarcoma (P < 0.05).
Human	PTH1R	5745	parathyroid hormone 1 receptor	GENERIF, Score=812, Pubmed Id: 18559376, UMLKSK CUI: C1704356 PTHR1 functionally deleterious mutations have now been identified in five out 31 enchondromas from Ollier patients NCI, Score=801, Pubmed Id: 11850620, UMLKSK CUI: C1704356 We identified a mutant PTH/PTHrP type I receptor (PTHR1) in human enchondromatosis that signals abnormally in vitro and causes enchondroma-like lesions in transgenic mice. OMIM, Score=1000, UMLKSK CUI: C1704356 Enchondromata
Human	PPYR1	5540		NCI, Score=801, Pubmed Id: 7712113, UMLKSK CUI: C1704356 The expression of the two catalytic subunits of protein phosphatase (PP) type 1 PP1 gamma 1 and PP1 delta was examined in 4 cases of osteochondroma and 4 cases of enchondroma as a benign cartilaginous tumor, and 4 cases of chondrosarcoma as a malignant cartilaginous tumor using immunohistochemical analysis.
Human	LPP	4026	LIM domain containing preferred translocation partner in lipoma	NCI, Score=801, Pubmed Id: 14614053, UMLKSK CUI: C1704356 One soft tissue chondroma had a t(3;12)(q27;q15), and the RT-PCR analysis revealed an HMGA2-LPP fusion transcript, composed of HMGA2 exons 1-3 and LPP exons 9-11.
Human	HSPA8	3312	heat shock 70kDa protein 8	NCI, Score=801, Pubmed Id: 11079732, UMLKSK CUI: C1704356 In chondrosarcoma a decreased expression was found for hsp27 (62% positive, P<0.05) and hsp72 (43% positive, P<0.05), whereas no significant difference to chondromas was detected in the expression of hsp60 (49% positive), hsp73 and hsp90 (73% and 81% positive, respectively). NCI, Score=801, Pubmed Id: 11079732, UMLKSK CUI: C1704356 RESULTS: Chondromas showed a positive staining for hsp27 in 100%, for hsp60 in 30%, for hsp72 in 80%, for hsp73 in 80%, and for hsp90 in 90%.
Human	RUNX2	860	runt-related transcription factor 2	GENERIF, Score=1000, Pubmed Id: 17387386, UMLKSK CUI: C1704356 findings demonstrate that Runx2 expression is active in variable chondrosarcomas compared to enchondromas, suggesting its importance in growth and differentiation of neoplastic cartilage
Human	BRCA2	675	breast cancer 2, early onset	NCI, Score=801, Pubmed Id: 14661035, UMLKSK CUI: C1704356 This trait is most probably not associated with mutations in the two major hereditary breast cancer genes since no cases of enchondroma or chondrosarcoma were found in Dutch BRCA1 and BRCA2 families.
Human	ACTC1	70	actin, alpha, cardiac muscle 1	NCI, Score=801, Pubmed Id: 12874903, UMLKSK CUI: C1704356 The expression of alpha smooth muscle actin, muscle specific actin, desmin, h-caldesmon, and calponin was studied immunohistochemically in the following soft tissue and bone tumours and tumour-like lesions: muscle fibromatosis, inflammatory pseudotumours, chondroblastoma, enchondroma, chondrosarcoma, fibrous dysplasia, ossifying myositis, osteoblastoma, convential osteosarcoma, leiomyoma and leiomyosarcoma.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1704356	Enchondroma	0		self

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