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 - Childhood Leukemia

Debug Stats

### Total Build Time: 51 ms 43.233 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 334 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 1.165 KB
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=22 ms Completed: 22 ms rowSize= 10.354 KB
CONCEPT_GENES gt=22 ms Completed: 22 ms rowSize= 30.165 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.152 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Childhood Leukemia C1332977

Definition (1)

Leukemia is cancer of the white blood cells. It is the most common type of childhood cancer.

Your blood cells form in your bone marrow. White blood cells help your body fight infection. In leukemia, however, the bone marrow produces abnormal white blood cells. These cells crowd out the healthy blood cells, making it hard for blood to do its work. Leukemia can develop quickly or slowly. Acute leukemia is a fast growing type while chronic leukemia grows slowly. Children with leukemia usually have one of the acute types.

Risk factors for childhood leukemia include having a brother or sister with leukemia, having certain genetic disorders and having had radiation or chemotherapy. Treatment often cures childhood leukemia. Treatment options include chemotherapy, other drug therapy and radiation. In some cases bone marrow and blood stem cell transplantation might help.

NIH: National Cancer Institute

Relationships (21)

Relation Types:

diso_to_anat : 8

diso_to_diso : 13

Relationships:

is_abnormal_cell_of_disease : 4

is_associated_anatomic_site_of : 1

is_finding_of_disease : 1

is_normal_cell_origin_of_disease : 1

is_normal_tissue_origin_of_disease : 1

is_not_finding_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 5

related_to : 6

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Bone Marrow C0005953
DISO_to_ANAT		is_abnormal_cell_of_disease	Cancer Cell C0334227
DISO_to_ANAT		is_normal_tissue_origin_of_disease	HEMOLYMPHORETICULAR TISSUE C1512398
DISO_to_ANAT		is_associated_anatomic_site_of	Hematopoietic and Lymphatic System C1512394
DISO_to_ANAT		is_normal_cell_origin_of_disease	Hematopoietic and Lymphoid Cell C1512385
DISO_to_ANAT		is_abnormal_cell_of_disease	Leukemic Cell C1517806
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Hematopoietic and Lymphoid Cell C1513983
DISO_to_DISO		isa	AGL, childhood C0220621
DISO_to_DISO		isa	ALL, Childhood C0023452
DISO_to_DISO		isa	ALL, L3 childhood C0279582
DISO_to_DISO		related_to	Acute lymphocytic leukemia C0023449
DISO_to_DISO		related_to	Blood and Blood Disorders C1456636
DISO_to_DISO		isa	Childhood CML C1327920
DISO_to_DISO		is_finding_of_disease	Childhood Lesion C1880068
DISO_to_DISO		related_to	Chronic Lymphocytic Leukemia C0023434
DISO_to_DISO		isa	LEUKAEMIA NEONATAL C0235813
DISO_to_DISO		related_to	Leukemia C0023418
DISO_to_DISO		related_to	Leukemia, Myelocytic, Acute C0023467
DISO_to_DISO		related_to	Leukemia, Myelogenous, Chronic, BCR-ABL Positive C0023473
DISO_to_DISO		is_not_finding_of_disease	Solid Growth Pattern C1336028

Genes (21)

Species:

human : 21

Species	Gene	GeneId	Gene Name	Evidence
Human	PRAME	23532	preferentially expressed antigen in melanoma	GENERIF, Score=913, Pubmed Id: 16860864, UMLKSK CUI: C1332977 Overexpression of PRAME was associated with childhood acute leukemia
Human	MVP	9961	major vault protein	NCI, Score=801, Pubmed Id: 9490695, UMLKSK CUI: C1332977 Relationship between major vault protein/lung resistance protein, multidrug resistance-associated protein, P-glycoprotein expression, and drug resistance in childhood leukemia. NCI, Score=801, Pubmed Id: 16086885, UMLKSK CUI: C1332977 BACKGROUND : Previous studies revealed that lung resistance protein (LRP) and multidrug resistance-associated protein (MRP) relate to drug resistance of childhood leukemia, which is not caused by only one mechanism.
Human	AKR1C3	8644	aldo-keto reductase family 1, member C3	GENERIF, Score=734, Pubmed Id: 18339682, UMLKSK CUI: C1332977 The maternal methylenetetrahydrofolate reductase A1298C polymorphism was found to be an effect modifier of the maternal intron 4 polymorphism of the AKR1C3 gene and the childhood leukemia risk
Human	WT1	7490	Wilms tumor 1	GENERIF, Score=913, Pubmed Id: 16876863, UMLKSK CUI: C1332977 High levels of WT1 expression is associated with childhood acute leukemia
Human	TPMT	7172	thiopurine S-methyltransferase	NCI, Score=801, Pubmed Id: 10997970, UMLKSK CUI: C1332977 These results indicate that polymerase chain reaction-based assays give reliable and robust results for the detection of TPMT deficiency, but that caution should be exercised in relying exclusively on DNA obtained from lymphoblasts in childhood leukaemia. NCI, Score=801, Pubmed Id: 12021625, UMLKSK CUI: C1332977 This study examined the role of thiopurine methyltransferase (TPMT) polymorphism in the metabolism and clinical effects of azathioprine and 6-mercaptopurine in the treatment of inflammatory bowel disease and childhood leukemia.
Human	TP53	7157	tumor protein p53	GENERIF, Score=983, Pubmed Id: 11764099, UMLKSK CUI: C1332977 higher expression in childhood leukemias with poor prognosis compared to long-term survivors
Human	TCF3	6929	transcription factor 3	NCI, Score=801, Pubmed Id: 7894030, UMLKSK CUI: C1332977 Our observations suggest that there could be heterogeneity in the molecular events among adult leukemias carrying the t(1;19) and that the E2A/PBX1 fusion formation might also be associated with an adverse treatment outcome in adult leukemias as in childhood leukemias. NCI, Score=801, Pubmed Id: 10086727, UMLKSK CUI: C1332977 Identification of a novel molecular partner of the E2A gene in childhood leukemia.
Human	PTPN11	5781	protein tyrosine phosphatase, non-receptor type 11	NCI, Score=801, Pubmed Id: 15116097, UMLKSK CUI: C1332977 Recent identification of SHP-2 mutations in childhood leukemia further emphasizes the importance of SHP-2 regulation in hematopoietic cells.
Human	PBX1	5087	pre-B-cell leukemia homeobox 1	NCI, Score=801, Pubmed Id: 7894030, UMLKSK CUI: C1332977 Our observations suggest that there could be heterogeneity in the molecular events among adult leukemias carrying the t(1;19) and that the E2A/PBX1 fusion formation might also be associated with an adverse treatment outcome in adult leukemias as in childhood leukemias.
Human	NBN	4683	nibrin	GENERIF, Score=1000, Pubmed Id: 18691878, UMLKSK CUI: C1332977 The TT genotype of c.2071-30A>T polymorphism was higher in leukaemia patients than in controls. results suggest that some specific haplotypes of the NBS1 gene may be associated with childhood leukaemia
Human	MTRR	4552	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	GENERIF, Score=913, Pubmed Id: 18610829, UMLKSK CUI: C1332977 polymorphic variants of genes GSTT1, GSTM1, NAT2 and MTRR can modulate the risk of childhood acute leukemia, residents of European part of Russia
Human	MTHFR	4524	methylenetetrahydrofolate reductase (NAD(P)H)	GENERIF, Score=734, Pubmed Id: 18339682, UMLKSK CUI: C1332977 The maternal methylenetetrahydrofolate reductase A1298C polymorphism was found to be an effect modifier of the maternal intron 4 polymorphism of the aldo-keto reductase family 1 member C3 gene and the childhood leukemia risk
Human	MLLT4	4301	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	NCI, Score=801, Pubmed Id: 12067721, UMLKSK CUI: C1332977 AF6 is a recurrent fusion partner of MLL, the human homolog of Drosophila trithorax chromatin remodeling protein that is involved in childhood leukemia and mixed lineage leukemia.
Human	MDM2	4193	MDM2 oncogene, E3 ubiquitin protein ligase	GENERIF, Score=983, Pubmed Id: 11764099, UMLKSK CUI: C1332977 higher expression in childhood leukemias with poor prognosis compared to long-term survivors
Human	IGFBP3	3486	insulin-like growth factor binding protein 3	NCI, Score=801, Pubmed Id: 11340377, UMLKSK CUI: C1332977 OBJECTIVE: To investigate whether the three principal components of the insulin-like growth factor (IGF) system, IGF-1, IGF-2 and IGF binding protein-3 (IGFBP-3), are associated with survival from childhood leukemia. NCI, Score=801, Pubmed Id: 9935146, UMLKSK CUI: C1332977 Because IGFBP-3 is essentially a binding protein, we interpret our findings as indicating that bioavailable IGF-I may play an important role in the aetiology of childhood leukaemia. NCI, Score=801, Pubmed Id: 9935146, UMLKSK CUI: C1332977 Since insulin-like growth factor-I (IGF-I) mediates the effect of growth hormone and has been positively associated with prostate cancer, we have evaluated the role of this hormone and its principal binding protein, IGFBP-3, in the aetiology of childhood leukaemia. NCI, Score=801, Pubmed Id: 11340377, UMLKSK CUI: C1332977 Insulin-like growth factor binding protein-3 predicts survival from acute childhood leukemia. NCI, Score=801, Pubmed Id: 11065014, UMLKSK CUI: C1332977 OBJECTIVE: Insulin-like growth factor-1 (IGF-1) and its principal binding protein-3 (IGFBP-3) are central in the mediation of the effect of growth hormone, and the IGF system has been reported to play a role in the pathogenesis of childhood leukemia. NCI, Score=801, Pubmed Id: 11340377, UMLKSK CUI: C1332977 CONCLUSION: The presented empirical evidence in conjunction with the fact that IGFBP-3 modulates IGF-1 and IGF-2 bioavailability and is likely to have proapoptotic effects makes this compound a plausible independent predictor of survival from childhood leukemia. NCI, Score=801, Pubmed Id: 9935146, UMLKSK CUI: C1332977 There was no significant association between IGF-I and the likelihood of childhood leukaemia, but an increment of 1 microg/ml of IGFBP-3 was associated with a substantial and statistically significant reduction of childhood leukaemia by 28% (95% confidence interval 7% to 45%).
Human	HFE	3077	hemochromatosis	GAD, Score=1000, Pubmed Id: 10627122, UMLKSK CUI: C1332977 Title:The C282Y mutation of HFE is another male-specific risk factor for childhood acute lymphoblastic leukemia\|Association:Y\|Conclusion:
Human	ERCC1	2067	excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)	NCI, Score=801, Pubmed Id: 9827920, UMLKSK CUI: C1332977 This is the first report describing a mutation at the ERCC1 gene in acute childhood leukaemia.
Human	NQO1	1728	NAD(P)H dehydrogenase, quinone 1	GENERIF, Score=1000, Pubmed Id: 17332311, UMLKSK CUI: C1332977 This is the first study showing robust (to bias due to population structure) evidence that the NQO1 C609T variant is a risk factor for childhood leukemia
Human	CYP1A1	1543	cytochrome P450, family 1, subfamily A, polypeptide 1	GENERIF, Score=1000, Pubmed Id: 15298960, UMLKSK CUI: C1332977 The risk of childhood leukemia showed no evidence of association between cytochrome P-450 1A1 genotype frequencys and case control status
Human	CDKN1B	1027	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	GENERIF, Score=1000, Pubmed Id: 16526056, UMLKSK CUI: C1332977 Mutations in the 3' untranslated region of Kip1 could provide an additional tool for risk classification in childhood leukemia
Human	RUNX1	861	runt-related transcription factor 1	GENERIF, Score=902, Pubmed Id: 14523475, UMLKSK CUI: C1332977 Amplification of this gene in childhood acute lymphoblsatic leukemia is associatd with poor outcome

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1332977	Childhood Leukemia	0		self

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