GATACA

Credits

Hide Credits

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 - Neuroblastic Tumor

Debug Stats

### Total Build Time: 11 ms 31.860 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 334 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 373 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=2 ms Completed: 2 ms rowSize= 8.107 KB
CONCEPT_GENES gt=6 ms Completed: 6 ms rowSize= 21.840 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.152 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Neuroblastic Tumor C1334953

Definition (1)

A group of nervous system tumors which display neuronal differentiation. It includes tumors that are composed of immature round cells and tumors that display advanced differentiation and the formation of ganglion cells.

Relationships (16)

Relation Types:

diso_to_anat : 12

diso_to_diso : 4

Relationships:

is_abnormal_cell_of_disease : 3

is_associated_anatomic_site_of : 1

is_finding_of_disease : 1

is_normal_cell_origin_of_disease : 4

is_normal_tissue_origin_of_disease : 4

isa : 3

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_normal_cell_origin_of_disease	Cell, Neuroepithelial C1449624
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Ectomesenchyme C1518271
DISO_to_ANAT		is_normal_cell_origin_of_disease	Embryonic Cell C1947950
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Embryonic tissue C0920502
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Neuroepithelial Cell C1514048
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Neuroepithelial Cell and Neoplastic Perineural Cell C1514049
DISO_to_ANAT		is_normal_cell_origin_of_disease	Nerve Cell, Neuroepithelial Cell, and Supporting Cell of the Nervous System C1518293
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Nerve Tissue, Neuroepithelial Tissue, and Nerve Sheaths C1518250
DISO_to_ANAT		is_associated_anatomic_site_of	Nervous System C0027763
DISO_to_ANAT		is_normal_cell_origin_of_disease	Neuroectodermal Cell C1518272
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Neuroepithelial Tissue C1518281
DISO_to_DISO		isa	Ganglioneuroblastoma C0206718
DISO_to_DISO		isa	Ganglioneuroma C0017075
DISO_to_DISO		isa	Neuroblastoma C0027819
DISO_to_DISO		is_finding_of_disease	Neuroectodermal Differentiation C1709217

Genes (13)

Species:

human : 13

Species	Gene	GeneId	Gene Name	Evidence
Human	DLL1	28514	delta-like 1 (Drosophila)	GENERIF, Score=983, Pubmed Id: 15605081, UMLKSK CUI: C1334953 Dlk may regulate the endothelial function in neuroblastic tumors
Human	GALR2	8811	galanin receptor 2	GENERIF, Score=884, Pubmed Id: 11867941, UMLKSK CUI: C1334953 Elevated expression of galanin receptors in childhood neuroblastic tumors
Human	GALR3	8484	galanin receptor 3	GENERIF, Score=884, Pubmed Id: 11867941, UMLKSK CUI: C1334953 Elevated expression of galanin receptors in childhood neuroblastic tumors
Human	TP73	7161	tumor protein p73	GENERIF, Score=734, Pubmed Id: 11839584, UMLKSK CUI: C1334953 data establish a relationship between p73 gene expression and neuroblastic tumor differentiation and point out a role for the p73 gene in sympathetic neuronal differentiation
Human	TP53	7157	tumor protein p53	GENERIF, Score=983, Pubmed Id: 18561747, UMLKSK CUI: C1334953 Nuclear TP53 accumulation may be relevant in patient's prognosis in neuroblastic tumors
Human	SYP	6855	synaptophysin	NCI, Score=801, Pubmed Id: 2495784, UMLKSK CUI: C1334953 The presence and distribution of pan-neuroendocrine markers such as neuron-specific enolase (NSE), chromogranin (CG), and synaptophysin (SYP) were investigated by immunohistochemistry in 53 cases of neuroblastic tumors, including three cases of ganglioneuromas, 17 ganglioneuroblastomas, and 33 neuroblastomas. NCI, Score=801, Pubmed Id: 2495784, UMLKSK CUI: C1334953 Our observations conclude that antibodies against NSE and SYP are helpful as a diagnostic aid for neuroblastic tumors.
Human	MYCN	4613	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	NCI, Score=801, Pubmed Id: 11696453, UMLKSK CUI: C1334953 With this in view, we analyzed the different hTERT transcripts by reverse transcriptase-polymerase chain reaction in neuroblastic tumors and compared the results with the TA, the tumor growth fraction, and the MYCN status. NCI, Score=801, Pubmed Id: 12775732, UMLKSK CUI: C1334953 In neuroblastic tumors, amplification of the MYCN gene is an unequivocal marker that indicates aggressive tumor behavior and is consequently used for therapy stratification. NCI, Score=801, Pubmed Id: 11745206, UMLKSK CUI: C1334953 Histopathology (International Neuroblastoma Pathology Classification) and MYCN status in patients with peripheral neuroblastic tumors: a report from the Childrens Cancer Group. NCI, Score=801, Pubmed Id: 12907629, UMLKSK CUI: C1334953 Molecular mechanisms through which MYCN expression contributes to the malignant phenotype of neuroblastoma are unknown.We performed a genome-widegene expression analysis of 40 well-characterized neuroblastic tumors and 12 cell lines to identify genes and biological pathways associated with MYCN expression. GENERIF, Score=983, Pubmed Id: 19006223, UMLKSK CUI: C1334953 In neuroblastic tumors, MYCN amplification was detected in 35.3% of the cases, whereas 1p36 deletion and 17q23 gain was observed in 46.8% and 58.3% of the cases
Human	KIT	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	GENERIF, Score=983, Pubmed Id: 15671569, UMLKSK CUI: C1334953 c-kit may have a role in development of neuroblastic tumors
Human	ITGB1	3688	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	NCI, Score=801, Pubmed Id: 8623914, UMLKSK CUI: C1334953 Therefore, we compared the expression of integrin alphaVbeta3, a promiscuous receptor that binds with high affinity to numerous cell matrix proteins, with the expression of integrin alphaVbeta5 and the integrin beta 1 subunit (which pairs with multiple alpha subunits) in neuroblastic tumors at various stages of differentiation.
Human	ITGAV	3685	integrin, alpha V	NCI, Score=801, Pubmed Id: 9137089, UMLKSK CUI: C1334953 Vitronectin expression in differentiating neuroblastic tumors: integrin alpha v beta 5 mediates vitronectin-dependent adhesion of retinoic-acid-differentiated neuroblastoma cells.
Human	GALR1	2587	galanin receptor 1	NCI, Score=801, Pubmed Id: 11857022, UMLKSK CUI: C1334953 Galanin and galanin receptor expression in neuroblastic tumours: correlation with their differentiation status. NCI, Score=801, Pubmed Id: 16954604, UMLKSK CUI: C1334953 In neuroblastic tumors a relationship of differentiation of the tumor to galanin receptor expression and antiproliferative and apoptotic effects upon activation of galanin receptors in neuroblastoma cells was reported. NCI, Score=801, Pubmed Id: 11857022, UMLKSK CUI: C1334953 Galanin and galanin receptor expression in neuroblastic tumours: correlation with their differentiation status. NCI, Score=801, Pubmed Id: 11857022, UMLKSK CUI: C1334953 This study provides clear evidence for galanin and galanin receptor expression in human neuroblastic tumours. NCI, Score=801, Pubmed Id: 11857022, UMLKSK CUI: C1334953 This study provides clear evidence for galanin and galanin receptor expression in human neuroblastic tumours. NCI, Score=801, Pubmed Id: 11857022, UMLKSK CUI: C1334953 We investigated the expression and distribution of galanin and its three known receptors (Gal-R1, Gal-R2, Gal-R3) in 19 samples of neuroblastic tumours tissue by immunohistochemistry, in situ hybridization and fluorescent-ligand binding.
Human	CASP3	836	caspase 3, apoptosis-related cysteine peptidase	NCI, Score=801, Pubmed Id: 9377572, UMLKSK CUI: C1334953 We studied 52 neuroblastic tumors to test whether the cell death-related proteases, interleukin-1 beta converting enzyme (ICE), CPP32, and Ich-1, were involved in the regression of the tumors.
Human	CASP2	835	caspase 2, apoptosis-related cysteine peptidase	NCI, Score=801, Pubmed Id: 9377572, UMLKSK CUI: C1334953 We studied 52 neuroblastic tumors to test whether the cell death-related proteases, interleukin-1 beta converting enzyme (ICE), CPP32, and Ich-1, were involved in the regression of the tumors.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1334953	Neuroblastic Tumor	0		self

Gataca is supported by...