GATACA

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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,
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// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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// 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 - Oligodendroglial Neoplasm

Debug Stats

### Total Build Time: 22 ms 48.190 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 348 bytes
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CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 15 bytes
CONCEPT_RELATIONSHIPS gt=1 ms Completed: 1 ms rowSize= 106 bytes
CONCEPT_GENES gt=16 ms Completed: 16 ms rowSize= 46.240 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.159 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Oligodendroglial Neoplasm C1335110

Definition (1)

A rare, slow-growing tumor that begins in the oligodendrocytes (brain cells that provide support and nourishment for nerve cells).

Genes (23)

Species:

human : 23

Species	Gene	GeneId	Gene Name	Evidence
Human	CITED4	163732	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	GENERIF, Score=983, Pubmed Id: 17311001, UMLKSK CUI: C1335110 CITED4 is epigenetically silenced in the vast majority of oligodendroglial tumours with 1p and 19q deletions
Human	OLIG1	116448	oligodendrocyte transcription factor 1	NCI, Score=801, Pubmed Id: 12691627, UMLKSK CUI: C1335110 New oligodendrocytic lineage markers, such as OLIG1/2 gene, will probably help to define the real spectrum of oligodendroglial tumors, which may include a wide variety of tumors with very different prognoses. NCI, Score=801, Pubmed Id: 15164981, UMLKSK CUI: C1335110 Olig1 and Olig2 were expressed in 26/30 (87%) and 28/30 (93%) of oligodendroglial tumors respectively but in only 9% of glioblastomas (1/11). NCI, Score=801, Pubmed Id: 12924709, UMLKSK CUI: C1335110 Surprisingly, OLIG1 and OLIG2 expressionwas not limited to oligodendroglial tumors, but was observed in astrocytic lesions as well, independent of tumor grade.
Human	RTN4	57142	reticulon 4	GENERIF, Score=983, Pubmed Id: 17592524, UMLKSK CUI: C1335110 Nogo-A expression was negatively correlated with the malignancy grade of oligodendroglial tumors
Human	SOX6	55553	SRY (sex determining region Y)-box 6	NCI, Score=801, Pubmed Id: 15696972, UMLKSK CUI: C1335110 Immunohistochemical analysis revealed that astrocytic and oligodendroglial tumors expressed SOX6; neuronal-glial cell tumors (central neurocytoma) and embryonal tumors (medulloblastoma), which arise from multipotential stem cell precursors, also showed a high intensity of SOX6 staining.
Human	DEC1	50514	deleted in esophageal cancer 1	GENERIF, Score=844, Pubmed Id: 16136500, UMLKSK CUI: C1335110 DEC1 expression is found in the majority of 1p-aberrant oligodendroglial neoplasms; its immunohistochemical detection does not correlate with tisue hypoxia in this type of primary brain tumor NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 Materials and methods. 44 primary and 16 recurrent oligodendroglial neoplasms with 1p-aberrations were investigated immunohistochemically for the expression of DEC1, HIF-1alpha, and CA9. NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 DEC1 expression in 1p-aberrant oligodendroglial neoplasms. NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 In our study, we assessed the expression of DEC1 in 1p aberrant oligodendroglial neoplasms and its association with necrosis and expression of hypoxia-inducible factor 1alpha (HIF-1alpha), carbonic anhydrase-9 (CA9), and vascular endothelial growth factor-mRNA (VEGF).
Human	OLIG2	10215	oligodendrocyte lineage transcription factor 2	NCI, Score=801, Pubmed Id: 17257132, UMLKSK CUI: C1335110 Additionally, we analysed oligodendroglial neoplasms with numerous gliofibrillary and minigemistocytic oligodendrocytes for OLIG2/glial fibrillary acidic protein (GFAP) coexpression and central neurocytoma for coexpression of neurone-specific nuclear protein (NeuN) and OLIG2 using double immunofluorescent labelling and confocal laser scanning microscopy. NCI, Score=801, Pubmed Id: 11498220, UMLKSK CUI: C1335110 OLIG2 should prove a useful marker for the diagnosis of oligodendroglial tumours. NCI, Score=801, Pubmed Id: 16598485, UMLKSK CUI: C1335110 Ten antibodies [glial fibrillary acidic protein (GFAP), Olig2, vimentin, epithelial membrane antigen (EMA), cytokeratin (AE1/AE3), alpha-internexin, nestin, pinealocytes PP5, aquaporin-4 (AQP4) M13d and AQP4M13e] discriminated between astrocytomas and oligodendroglial tumors. NCI, Score=801, Pubmed Id: 11498220, UMLKSK CUI: C1335110 We investigated the expression of OLIG2 by in-situ hybridisation in 21 brain tumours: nine grade II and III oligodendrogliomas, three grade II oligoastrocytomas, and nine non-oligodendroglial tumours (four grade IV astrocytomas, two meningiomas, a dysembryoplastic neuroepithelial tumour, and two metastases). NCI, Score=801, Pubmed Id: 15111318, UMLKSK CUI: C1335110 The expression of Olig2 transcript has been demonstrated in human oligodendroglial tumors, although the protein expression has not been studied extensively. NCI, Score=801, Pubmed Id: 17257132, UMLKSK CUI: C1335110 CONCLUSIONS: Widespread OLIG2 expression discriminates oligodendroglial neoplasms or DNTs from other clear cell primary brain tumour types. GENERIF, Score=983, Pubmed Id: 17431671, UMLKSK CUI: C1335110 OLIG2 expression was predominant over ID2 expression in oligodendroglial tumors, while ID2 expression was predominant over OLIG2 expression in astrocytic tumors NCI, Score=801, Pubmed Id: 15164981, UMLKSK CUI: C1335110 Olig1 and Olig2 were expressed in 26/30 (87%) and 28/30 (93%) of oligodendroglial tumors respectively but in only 9% of glioblastomas (1/11). NCI, Score=801, Pubmed Id: 17257132, UMLKSK CUI: C1335110 METHODS AND RESULTS: We analysed OLIG2 expression in 60 oligodendroglial neoplasms (57 with and three without chromosome 1p aberration), 10 central neurocytomas, 10 clear cell ependymomas, nine dysembryoplastic neuroepithelial tumours (DNTs) and two clear cell meningiomas using immunohistochemistry. NCI, Score=801, Pubmed Id: 17257132, UMLKSK CUI: C1335110 All oligodendroglial neoplasms and DNTs showed widespread OLIG2 expression. NCI, Score=801, Pubmed Id: 11498220, UMLKSK CUI: C1335110 OLIG2 as a specific marker of oligodendroglial tumour cells. NCI, Score=801, Pubmed Id: 12924709, UMLKSK CUI: C1335110 Surprisingly, OLIG1 and OLIG2 expressionwas not limited to oligodendroglial tumors, but was observed in astrocytic lesions as well, independent of tumor grade.
Human	DIRAS3	9077	DIRAS family, GTP-binding RAS-like 3	GENERIF, Score=983, Pubmed Id: 18302158, UMLKSK CUI: C1335110 DIRAS3 is a novel, prognostically relevant candidate gene that is frequently methylated and silenced in oligodendroglial tumors with 1p deletion
Human	PROM1	8842	prominin 1	GENERIF, Score=844, Pubmed Id: 18371181, UMLKSK CUI: C1335110 cancer stem cells and expression of CD133 is predictive of prognosis in high-grade oligodendroglial tumors
Human	BHLHE40	8553	basic helix-loop-helix family, member e40	NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 In our study, we assessed the expression of DEC1 in 1p aberrant oligodendroglial neoplasms and its association with necrosis and expression of hypoxia-inducible factor 1alpha (HIF-1alpha), carbonic anhydrase-9 (CA9), and vascular endothelial growth factor-mRNA (VEGF). NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 DEC1 expression in 1p-aberrant oligodendroglial neoplasms. NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 DEC1 expression is found in the majority of 1p-aberrant oligodendroglial neoplasms and does not correlate with necrosis or expression of HIF-1alpha, CA9, VEGF.
Human	TP73	7161	tumor protein p73	GENERIF, Score=983, Pubmed Id: 11920588, UMLKSK CUI: C1335110 loss of reduced TP73 transcript expression through promoter hypermethylation may contribute to the tumorigenesis of oligodendroglial tumors
Human	TP53	7157	tumor protein p53	GENERIF, Score=983, Pubmed Id: 17854663, UMLKSK CUI: C1335110 findings suggest no association between oligodendroglial tumors and the SNP in codon 72 of TP53; also no correlation was found among the TP53 codon 72 polymorphism and prognosis, p53 expression, and chromosomes 1p and 19q status GENERIF, Score=983, Pubmed Id: 18262501, UMLKSK CUI: C1335110 MDM2 SNP309, alone or in combination with TP53 R72P, was not associated with oligodendroglial tumors
Human	SLC2A5	6518	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	NCI, Score=801, Pubmed Id: 15488021, UMLKSK CUI: C1335110 The number of GLUT5-positive microglia was significantly (P _lt_ 0.001) higher in astrocytic tumours than in oligodendroglial tumours.
Human	SLC2A1	6513	solute carrier family 2 (facilitated glucose transporter), member 1	GENERIF, Score=844, Pubmed Id: 18726700, UMLKSK CUI: C1335110 Expression of GLUT-1 is significantly reduced in low-grade oligodendroglial tumors harboring LOH 1p
Human	MMP10	4319	matrix metallopeptidase 10 (stromelysin 2)	NCI, Score=801, Pubmed Id: 14666700, UMLKSK CUI: C1335110 To determine the pattern of MMP expression in astrocytic and oligodendroglial tumors, sections of astrocytic and oligodendroglial differentiated glioblastomas (WHO grade IV), as well as of anaplastic oligodendrogliomas (WHO grade III) and anaplastic gemistocytic astrocytomas (WHO grade III) were immunostained for MMP-2, MMP-7, MMP-9, MMP-10 and MMP-11.
Human	MGMT	4255	O-6-methylguanine-DNA methyltransferase	GENERIF, Score=983, Pubmed Id: 15455350, UMLKSK CUI: C1335110 Frequent promoter hypermethylation and low expression of the MGMT gene is associated with oligodendroglial tumors
Human	MAP2	4133	microtubule-associated protein 2	NCI, Score=801, Pubmed Id: 11589429, UMLKSK CUI: C1335110 Our findings demonstrate MAP2 expression in astrocytic and oligodendroglial neoplasms.
Human	HIF1A	3091	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 Materials and methods. 44 primary and 16 recurrent oligodendroglial neoplasms with 1p-aberrations were investigated immunohistochemically for the expression of DEC1, HIF-1alpha, and CA9. NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 In our study, we assessed the expression of DEC1 in 1p aberrant oligodendroglial neoplasms and its association with necrosis and expression of hypoxia-inducible factor 1alpha (HIF-1alpha), carbonic anhydrase-9 (CA9), and vascular endothelial growth factor-mRNA (VEGF). NCI, Score=801, Pubmed Id: 16136500, UMLKSK CUI: C1335110 DEC1 expression is found in the majority of 1p-aberrant oligodendroglial neoplasms and does not correlate with necrosis or expression of HIF-1alpha, CA9, VEGF.
Human	EMP3	2014	epithelial membrane protein 3	GENERIF, Score=983, Pubmed Id: 17187361, UMLKSK CUI: C1335110 EMP3 overexpression is associated with oligodendroglial tumors
Human	EGFR	1956	epidermal growth factor receptor	GENERIF, Score=844, Pubmed Id: 17143531, UMLKSK CUI: C1335110 Mutations and amplification/overdose in the EGFR gene are present in low-grade oligodendroglial tumours, and may contribute to the development of these brain neoplasms
Human	DMBT1	1755	deleted in malignant brain tumors 1	NCI, Score=801, Pubmed Id: 12672033, UMLKSK CUI: C1335110 Mutation analysis of DMBT1 in glioblastoma, medulloblastoma and oligodendroglial tumors. NCI, Score=801, Pubmed Id: 12672033, UMLKSK CUI: C1335110 We also assessed homozygous deletions of the DMBT1 gene in the series and found that 16 of 95 (5 glioblastomas, 5 medulloblastomas, 6 oligodendroglial tumors; total 17%) tumors harbor such alteration. NCI, Score=801, Pubmed Id: 15099021, UMLKSK CUI: C1335110 We characterized 138 of 189 (73%) available primary and recurrent oligodendroglial neoplasms from 80 patients, utilizing paired FISH probes for 1p32/1q42, 19p13/19q13, CEP7/EGFR, CEP9/p16, and PTEN/DMBT1. NCI, Score=801, Pubmed Id: 12672033, UMLKSK CUI: C1335110 A total of 102 primary brain tumors, consisting of 25 glioblastoma multiforme, 24 medulloblastoma and 53 oligodendroglial tumors, were analyzed by conformation-sensitive gel electrophoresis in all 54 coding exons of DMBT1.
Human	CDKN2C	1031	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	NCI, Score=801, Pubmed Id: 10515227, UMLKSK CUI: C1335110 Our data thus provide evidence for more than a single oligodendroglioma-associated tumor suppressor gene on 1p and implicate CDKN2C as a candidate tumor suppressor gene altered in a low fraction of oligodendroglial tumors. NCI, Score=801, Pubmed Id: 10994011, UMLKSK CUI: C1335110 Loss of heterozygosity on 1p, mutation(s), homozygous deletion(s), and expression of p18 in 30 oligodendroglial tumors were investigated. NCI, Score=801, Pubmed Id: 10515227, UMLKSK CUI: C1335110 Identification of two distinct deleted regions on the short arm of chromosome 1 and rare mutation of the CDKN2C gene from 1p32 in oligodendroglial tumors.
Human	CDKN2B	1030	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	NCI, Score=801, Pubmed Id: 11764089, UMLKSK CUI: C1335110 Oligodendroglial tumors frequently demonstrate hypermethylation of the CDKN2A (MTS1, p16INK4a), p14ARF, and CDKN2B (MTS2, p15INK4b) tumor suppressor genes. NCI, Score=801, Pubmed Id: 11764089, UMLKSK CUI: C1335110 Taken together, our results indicate that hypermethylation of CDKN2A, p14ARF, and CDKN2B is an important epigenetic mechanism by which oligodendroglial tumors may escape from p53- and pRb-dependent growth control. NCI, Score=801, Pubmed Id: 11764089, UMLKSK CUI: C1335110 We investigated 34 oligodendroglial tumors (7 oligodendrogliomas, 11 anaplastic oligodendrogliomas, 8 oligoastrocytomas, and 8 anaplastic oligoastrocytomas) for deletion, mutation, hypermethylation, and expression of the CDKN2A (MTS1, p16INK4a), p14ARF, and CDKN2B (MTS2, p15INK4b) tumor suppressor genes at 9p21.
Human	CA9	768	carbonic anhydrase IX	GENERIF, Score=896, Pubmed Id: 18173856, UMLKSK CUI: C1335110 CA IX was proved to be an independent prognostic indicator in oligodendroglial brain tumors, and it also correlates reversely with cell proliferation

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1335110	Oligodendroglial Neoplasm	0		self

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