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 - Mastocytosis, Systemic

Debug Stats

### Total Build Time: 24 ms 40.838 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 342 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 361 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= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 548 bytes
CONCEPT_CHILDREN gt=2 ms Completed: 2 ms rowSize= 557 bytes
CONCEPT_ANCESTRAL_ROOTS gt=2 ms Completed: 2 ms rowSize= 4.058 KB
CONCEPT_RELATIONSHIPS gt=6 ms Completed: 6 ms rowSize= 14.657 KB
CONCEPT_GENES gt=8 ms Completed: 8 ms rowSize= 18.990 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.156 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Mastocytosis, Systemic C0221013

Definition (1)

A variant of mastocytosis characterized by multifocal, dense infiltrates of mast cells (15 or more mast cells in aggregates) detected in the bone marrow and/or other extracutaneous sites. (WHO, 2001) -- 2003

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0024899

Children (1)

C0023461

Ancestral Roots

Root	Root Plus One	Depth	Parent
Skin and Connective Tissue Diseases C0175166	Skin Diseases C0037274	4	Mastocytosis C0024899
Neoplasms C0027651	Neoplasms by Histologic Type C0027652	6	Mastocytosis C0024899
Skin and Connective Tissue Diseases C0175166	Connective Tissue Diseases C0009782	5	Mastocytosis C0024899

Relationships (46)

Relation Types:

diso_to_anat : 17

diso_to_chem : 9

diso_to_diso : 16

diso_to_phen : 3

diso_to_phys : 1

Relationships:

none : 22

is_abnormal_cell_of_disease : 5

is_associated_anatomic_site_of : 1

is_finding_of_disease : 1

is_normal_cell_origin_of_disease : 3

is_normal_tissue_origin_of_disease : 2

is_not_finding_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 6

may_be_finding_of_disease : 1

may_be_molecular_abnormality_of_disease : 2

permuted_term_of : 1

Page Size

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Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	88		Complication Aspects C1171258
DISO_to_PHEN	74		genetic aspects C0017399
DISO_to_ANAT	51		Mast Cells C0024880
DISO_to_DISO	44		Complication Aspects C1171258
DISO_to_PHEN	39		genetic aspects C0017399
DISO_to_CHEM	32		Proto-Oncogene Protein c-kit C0072470
DISO_to_CHEM	20		Pyrimidines C0034289
DISO_to_ANAT	18		Mast Cells C0024880
DISO_to_CHEM	17		Pyrimidines C0034289
DISO_to_ANAT	16		In Blood C0005768
DISO_to_CHEM	16		Proto-Oncogene Protein c-kit C0072470
DISO_to_DISO	16		Anaphylaxis C0002792
DISO_to_CHEM	14		Piperazines C0031958
DISO_to_ANAT	13		Bone Marrow C0005953
DISO_to_ANAT	12		Bone Marrow C0005953
DISO_to_CHEM	12		Antineoplastic Agents C0003392
DISO_to_CHEM	12		Piperazines C0031958
DISO_to_CHEM	9		Antineoplastic Agents C0003392
DISO_to_PHYS	9		Mutation C0026882
DISO_to_CHEM	8		Protein Kinase Inhibitors C1449702
DISO_to_DISO	8		Hypereosinophilic Syndrome C1540912
DISO_to_DISO	8		Leukemia, Myelocytic, Acute C0023467
DISO_to_ANAT		is_associated_anatomic_site_of	Bone Marrow C0005953
DISO_to_ANAT		is_normal_cell_origin_of_disease	Bone Marrow Stem Cell C1511246
DISO_to_ANAT		is_abnormal_cell_of_disease	Cancer Cell C0334227

Genes (16)

Species:

human : 16

Species	Gene	GeneId	Gene Name	Evidence
Human	RASGRP4	115727	RAS guanyl releasing protein 4	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	FIP1L1	81608	factor interacting with PAPOLA and CPSF1	GENERIF, Score=901, Pubmed Id: 15284118, UMLKSK CUI: C0221013 FIP1L1-PDGFRA is a relatively infrequent but treatment-relevant mutation in primary eosinophilia that is indicative of an underlying systemic mastocytosis
Human	CHIC2	26511	cysteine-rich hydrophobic domain 2	NCI, Score=801, Pubmed Id: 12842979, UMLKSK CUI: C0221013 CHIC2 deletion, a surrogate for FIP1L1-PDGFRA fusion, occurs in systemic mastocytosis associated with eosinophilia and predicts response to imatinib mesylate therapy. GENERIF, Score=1000, Pubmed Id: 12842979, UMLKSK CUI: C0221013 used fluorescence in situ hybridization to detect deletion of the CHIC2 locus at 4q12 as a surrogate for the FIP1L1-PDGFRA fusion and was observed in bone marrow cells for 3 of 5 patients with systemic mast cell disease associated with eosinophilia
Human	MRAS	22808	muscle RAS oncogene homolog	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	SLC18A2	6571	solute carrier family 18 (vesicular monoamine transporter), member 2	NCI, Score=801, Pubmed Id: 16116033, UMLKSK CUI: C0221013 Vesicular Monoamine Transporter 2 (VMAT2) Expression in Hematopoietic Cells and in Patients with Systemic Mastocytosis.
Human	SERPINB9	5272	serpin peptidase inhibitor, clade B (ovalbumin), member 9	NCI, Score=801, Pubmed Id: 15739160, UMLKSK CUI: C0221013 In addition, in 80% of all cases of cutaneous and systemic mastocytosis tested the majority of the mast cells expressed PI9.
Human	ENPP3	5169	ectonucleotide pyrophosphatase/phosphodiesterase 3	NCI, Score=801, Pubmed Id: 16110150, UMLKSK CUI: C0221013 Several of these antigens (CD2, CD25, CD35, CD88, CD203c) appear to be upregulated on MCs in patients with systemic mastocytosis and therefore are used as diagnostic markers.
Human	PDGFRA	5156	platelet-derived growth factor receptor, alpha polypeptide	NCI, Score=801, Pubmed Id: 12676775, UMLKSK CUI: C0221013 Although bone marrow biopsies in these patients showed increased numbers of CD25+ mast cells and atypical spindle-shaped mast cells, patients with HES and elevated serum tryptase could be distinguished from patients with systemic mastocytosis and eosinophilia by their clinical manifestations, the absence of mast cell aggregates, the lack of a somatic KIT mutation, and the presence of the recently described fusion of the Fip1-like 1 (FIP1L1) gene to the platelet-derived growth factor receptor alpha gene (PDGFRA).
Human	NTRK3	4916	neurotrophic tyrosine kinase, receptor, type 3	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	KIT	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	NCI, Score=801, Pubmed Id: 11381374, UMLKSK CUI: C0221013 Immunohistochemical properties of bone marrow mast cells in systemic mastocytosis: evidence for expression of CD2, CD117/Kit, and bcl-x(L). GENERIF, Score=1000, Pubmed Id: 18165278, UMLKSK CUI: C0221013 These data suggest that KIT(D816V+) systemic mastocytosis (SM) can co-exist with JAK2(V617F+) chronic idiopathic myelofibrosis (CIMF) and in some of these SM-CIMF cases, the two mutations are present in the neoplastic cells of both disease components GENERIF, Score=1000, Pubmed Id: 17691909, UMLKSK CUI: C0221013 Dysregulated kit function is an important component of oncogenesis in a large number of neoplastic disorders, including systemic mastocytosis GENERIF, Score=1000, Pubmed Id: 16597595, UMLKSK CUI: C0221013 rapamycin induction of apoptosis appears specific to the C-Kit D816V mutation in systemic mastocytosis GENERIF, Score=1000, Pubmed Id: 12091362, UMLKSK CUI: C0221013 Evidence for the involvement of a hematopoietic progenitor cell in systemic mastocytosis from single-cell analysis of mutations in the c-kit gene
Human	ITGB1	3688	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	ITGAV	3685	integrin, alpha V	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	IL2RA	3559	interleukin 2 receptor, alpha	GENERIF, Score=1000, Pubmed Id: 18059223, UMLKSK CUI: C0221013 Immunoreactivity for CD25 in gastrointestinal mucosal mast cells is specific for systemic mastocytosis and can be used to confirm the diagnosis
Human	CSF1	1435	colony stimulating factor 1 (macrophage)	NCI, Score=801, Pubmed Id: 11703299, UMLKSK CUI: C0221013 We report the in vitro and in vivo effects of granulocyte macrophage colony stimulating factor (GM-CSF), a known inhibitor of in vitro mast cell differentiation, in a patient with benign, adult-onset systemic mastocytosis.
Human	BTK	695	Bruton agammaglobulinemia tyrosine kinase	INFERRED, Score=800, UMLKSK CUI: C0221013
Human	BCL2L1	598	BCL2-like 1	NCI, Score=801, Pubmed Id: 12937123, UMLKSK CUI: C0221013 In contrast to the skin lesions, bone marrow infiltrates of patients with systemic mastocytosis showed only low or absent immunoreactivity for bcl-2, but marked expression of bcl-xL.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0221013	Mastocytosis, Systemic	0		self

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