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 - Ganglioneuroblastoma

Debug Stats

### Total Build Time: 37 ms 47.230 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 338 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 653 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= 549 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=4 ms Completed: 4 ms rowSize= 2.762 KB
CONCEPT_RELATIONSHIPS gt=15 ms Completed: 15 ms rowSize= 14.215 KB
CONCEPT_GENES gt=11 ms Completed: 11 ms rowSize= 27.378 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.154 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Ganglioneuroblastoma C0206718

Definition (1)

A moderately malignant neoplasm composed of primitive neuroectodermal cells dispersed in myxomatous or fibrous stroma intermixed with mature ganglion cells. It may undergo transformation into a neuroblastoma. It arises from the sympathetic trunk or less frequently from the adrenal medulla, cerebral cortex, and other locations. Cervical ganglioneuroblastomas may be associated with HORNER SYNDROME and the tumor may occasionally secrete vasoactive intestinal peptide, resulting in chronic diarrhea.

Semantic Types (1)

Neoplastic Process (T191)

Parents (1)

C0027819

Ancestral Roots

Root	Root Plus One	Depth	Parent
Neoplasms C0027651	Neoplasms by Histologic Type C0027652	9	Neuroblastoma C0027819
Neoplasms C0027651	Neoplasms by Histologic Type C0027652	8	Neuroblastoma C0027819

Relationships (34)

Relation Types:

diso_to_anat : 14

diso_to_diso : 18

diso_to_phen : 2

Relationships:

none : 11

is_abnormal_cell_of_disease : 5

is_finding_of_disease : 2

is_normal_cell_origin_of_disease : 4

is_normal_tissue_origin_of_disease : 4

is_not_finding_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 4

mapped_to : 1

permuted_term_of : 1

Page Size

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Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	13		Adrenal Gland Neoplasms C0001624
DISO_to_DISO	10		Complication Aspects C1171258
DISO_to_DISO	8		Neuroblastoma C0027819
DISO_to_DISO	7		Ganglioneuroma C0017075
DISO_to_PHEN	6		genetic aspects C0017399
DISO_to_DISO	5		Adrenal Gland Neoplasms C0001624
DISO_to_DISO	5		Neuroblastoma C0027819
DISO_to_PHEN	5		genetic aspects C0017399
DISO_to_DISO	4		Brain Neoplasms C0006118
DISO_to_DISO	4		MEDIASTINAL NEOPL C0025063
DISO_to_DISO	4		Spinal Cord Neoplasms C0037930
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 Ganglion Cell C1513970
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Neuroblast C1518268
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_primary_anatomic_site_of_disease	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

Genes (18)

Species:

human : 18

Species	Gene	GeneId	Gene Name	Evidence
Human	KIF1B	23095	kinesin family member 1B	OMIM, Score=1000, UMLKSK CUI: C0206718 Ganglioneuroblastoma
Human	WASF3	10810	WAS protein family, member 3	NCI, Score=801, Pubmed Id: 12856283, UMLKSK CUI: C0206718 We have identified the WAVE3 gene from Chromosome (Chr) 13q12, as being involved in one of the breakpoints of a t(1:13)(q21:q12) reciprocal translocation, in a patient with ganglioneuroblastoma (Sossey-Alaoui et al. 2002; Oncogene 21: 5967-5974). NCI, Score=801, Pubmed Id: 12185600, UMLKSK CUI: C0206718 WAVE3, an actin-polymerization gene, is truncated and inactivated as a result of a constitutional t(1;13)(q21;q12) chromosome translocation in a patient with ganglioneuroblastoma.
Human	PHOX2B	8929	paired-like homeobox 2b	OMIM, Score=1000, UMLKSK CUI: C0206718 Ganglioneuroblastoma
Human	TNFSF12	8742	tumor necrosis factor (ligand) superfamily, member 12	NCI, Score=801, Pubmed Id: 11750845, UMLKSK CUI: C0206718 The mean expression level of Apo-3L was significantly higher in ganglioneuromas/ganglioneuroblastomas compared with neuroblastomas (P=0.001) and in normal brain compared with PNET/medulloblastoma (P<0.0001).
Human	SYP	6855	synaptophysin	NCI, Score=801, Pubmed Id: 7959661, UMLKSK CUI: C0206718 The monoclonal antibody KP-1 that recognizes the lysosome-associated glycoprotein CD68 was used together with antibodies to other antigens (actin, glial fibrillary acidic protein, keratin, neurofilaments, chromogranin, synaptophysin, S-100 protein, HMB-45, lysozyme, and HLA-DR) in a labeled streptavidin biotin immunoperoxidase method to phenotypically characterize 27 granular cell tumors, five schwannomas, five neurofibromas, two ganglioneuromas, three ganglioneuroblastomas, five carcinoid tumors, five malignant melanomas, and five examples of histiocytosis X. NCI, Score=801, Pubmed Id: 2495784, UMLKSK CUI: C0206718 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: 2839087, UMLKSK CUI: C0206718 All the remaining tumors were neurogenic, showing either neurons and nerve fibers together with Schwann cells (ganglioneuromas and ganglioneuroblastomas) or endocrine cells (pheochromocytomas) reacting with VIP, PHM, NPY, enkephalin, somatostatin, neuron-specific enolase, synaptophysin, and MAP2 (but not cytokeratin, PP, or GRH) antibodies.
Human	SAG	6295	S-antigen; retina and pineal gland (arrestin)	NCI, Score=801, Pubmed Id: 2958128, UMLKSK CUI: C0206718 No S-antigen and opsin-like immunoreaction was found in malignant teratomas and germinomas of the pineal gland, oat cell tumors, astrocytomas, ependymomas, oligodendrogliomas, glioblastomas, gangliogliomas, gangliocytoma, ganglioneuroblastomas, neuroblastomas, and esthesioneuroblastoma.
Human	RAB3A	5864	RAB3A, member RAS oncogene family	NCI, Score=801, Pubmed Id: 1384950, UMLKSK CUI: C0206718 RESULTS. A high rab3A gene expression was observed in tumor samples derived from the neural tube (i.e., neuroblastomas, ganglioneuroblastomas, and adult nervous system neoplasms).
Human	PRPH	5630	peripherin	NCI, Score=801, Pubmed Id: 8078299, UMLKSK CUI: C0206718 CONCLUSIONS: The specificity of the peripherin labeling of NB and the ability of the peripherin antibody to label the entire spectrum of NBs, including ganglioneuroblastomas and ganglioneuromas, indicate that this intermediate filament protein has potential as a diagnostic marker for these related neural crest neoplasms. NCI, Score=801, Pubmed Id: 8078299, UMLKSK CUI: C0206718 The antibody specific for peripherin labeled all NBs, including immature NBs, composite ganglioneuroblastomas and ganglioneuromas.
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	OMIM, Score=1000, UMLKSK CUI: C0206718 Ganglioneuroblastoma
Human	NCAM1	4684	neural cell adhesion molecule 1	GENERIF, Score=1000, Pubmed Id: 18213713, UMLKSK CUI: C0206718 Ganglioneuromas and ganglioneuroblastomas express the adhesive 120 kDa NCAM isoform, while neuroblastomas preferentially express the 180 kDa isoform classically involved in cell motility
Human	MYCN	4613	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	NCI, Score=801, Pubmed Id: 12709798, UMLKSK CUI: C0206718 In conclusion, ganglioneuroblastoma, intermixed subtype, lack of MYCN amplification, aneuploid DNA content and presence of lymphoid infiltrates may contribute to favorable prognosis in NTs associated with OMS. NCI, Score=801, Pubmed Id: 9353827, UMLKSK CUI: C0206718 Heterogeneity of MYCN amplification in a child with stroma-rich neuroblastoma (ganglioneuroblastoma). NCI, Score=801, Pubmed Id: 11745206, UMLKSK CUI: C0206718 METHODS: A total of 628 NTs (535 neuroblastomas [NBs]); 21 ganglioneuroblastoma, intermixed [GNBi]; 9 ganglioneuromas [GN]; and 63 ganglioneuroblastoma, nodular [GNBn]) from the Children;s Cancer Group studies were evaluated histologically (favorable histology [FH] tumors vs. unfavorable histology [UH] tumors) according to the International Classification and were tested molecularly for MYCN status (amplified vs. nonamplified). NCI, Score=801, Pubmed Id: 9353827, UMLKSK CUI: C0206718 We report a child with stage III favorable histology stroma-rich neuroblastoma (ganglioneuroblastoma) and a poor outcome with an apparent change in MYCN gene amplification by Southern blot.
Human	MAP2	4133	microtubule-associated protein 2	NCI, Score=801, Pubmed Id: 2839087, UMLKSK CUI: C0206718 All the remaining tumors were neurogenic, showing either neurons and nerve fibers together with Schwann cells (ganglioneuromas and ganglioneuroblastomas) or endocrine cells (pheochromocytomas) reacting with VIP, PHM, NPY, enkephalin, somatostatin, neuron-specific enolase, synaptophysin, and MAP2 (but not cytokeratin, PP, or GRH) antibodies.
Human	ITGAV	3685	integrin, alpha V	NCI, Score=801, Pubmed Id: 9137089, UMLKSK CUI: C0206718 Cell adhesion may play a role in metastasis, and we have shown recently that expression of integrin alpha v beta 5 protein and mRNA is up-regulated in ganglioneuroblastomas in vivo.
Human	ID2	3398	inhibitor of DNA binding 2, dominant negative helix-loop-helix protein	NCI, Score=801, Pubmed Id: 16549780, UMLKSK CUI: C0206718 Finally, the differentiated neural crest-derived tumor ganglioneuroblastoma coexpresses Id2 and ENH in the cytoplasm of ganglionic cells.
Human	HMGA1	3159	high mobility group AT-hook 1	NCI, Score=801, Pubmed Id: 15650238, UMLKSK CUI: C0206718 In contrast, HMGA1 expression is readily detectable in all NB cell lines and tumors, but its expression is consistently higher in less differentiated NBs compared with ganglioneuromas and ganglioneuroblastomas.
Human	FGF8	2253	fibroblast growth factor 8 (androgen-induced)	NCI, Score=801, Pubmed Id: 11532426, UMLKSK CUI: C0206718 In accordance with these in vitro findings, the immunohistochemical analysis on human neurological diseases showed that FGF8 expression is evident in differentiating histological types of neuroblastoma and ganglioneuroblastoma, and that the levels of FGF8 immunoreactivity in the substantia nigra from Parkinsons disease are significantly lower than those in age-matched controls.
Human	ENO1	2023	enolase 1, (alpha)	NCI, Score=801, Pubmed Id: 6793214, UMLKSK CUI: C0206718 The presence of the two forms of enolase, neuron-specific enolase (NSE) and non-neuronal enolase (NNE), have been examined in biopsy material of human neuroblastoma, ganglioneuroblastoma, ganglioneuroma and cultured neuroblastoma cells, after separation with ion exchange chromatography.
Human	CD68	968	CD68 molecule	NCI, Score=801, Pubmed Id: 7959661, UMLKSK CUI: C0206718 The neoplastic cells in all 27 of the granular cell tumors and four of the five schwannomas strongly stained for CD68, whereas none of the neurofibromas, ganglioneuromas, ganglioneuroblastomas, or carcinoid tumors contained CD68-positive tumor cells. NCI, Score=801, Pubmed Id: 7959661, UMLKSK CUI: C0206718 The monoclonal antibody KP-1 that recognizes the lysosome-associated glycoprotein CD68 was used together with antibodies to other antigens (actin, glial fibrillary acidic protein, keratin, neurofilaments, chromogranin, synaptophysin, S-100 protein, HMB-45, lysozyme, and HLA-DR) in a labeled streptavidin biotin immunoperoxidase method to phenotypically characterize 27 granular cell tumors, five schwannomas, five neurofibromas, two ganglioneuromas, three ganglioneuroblastomas, five carcinoid tumors, five malignant melanomas, and five examples of histiocytosis X.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0206718	Ganglioneuroblastoma	0		self

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