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 - Anaplastic Oligodendroglioma

Debug Stats

### Total Build Time: 23 ms 34.950 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 354 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 310 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=9 ms Completed: 9 ms rowSize= 15.324 KB
CONCEPT_GENES gt=8 ms Completed: 8 ms rowSize= 17.745 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.162 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Anaplastic Oligodendroglioma C0334590

Definition (1)

A WHO grade III oligodendroglioma with focal or diffuse malignant morphologic features (prominent nuclear pleomorphism, mitoses, and increased cellularity).

Relationships (39)

Relation Types:

diso_to_anat : 16

diso_to_diso : 22

diso_to_phen : 1

Relationships:

is_abnormal_cell_of_disease : 6

is_associated_anatomic_site_of : 1

is_finding_of_disease : 4

is_normal_cell_origin_of_disease : 4

is_normal_tissue_origin_of_disease : 2

is_not_finding_of_disease : 3

is_primary_anatomic_site_of_disease : 1

isa : 2

location_of : 1

may_be_abnormal_cell_of_disease : 1

may_be_cytogenetic_abnormality_of_disease : 8

may_be_finding_of_disease : 5

permuted_term_of : 1

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Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		location_of	Brain C0006104
DISO_to_ANAT		is_abnormal_cell_of_disease	Cancer Cell C0334227
DISO_to_ANAT		is_normal_cell_origin_of_disease	Cell, Neuroepithelial C1449624
DISO_to_ANAT		is_associated_anatomic_site_of	Central Nervous System C0927232
DISO_to_ANAT		may_be_abnormal_cell_of_disease	Giant Cell, Neoplastic Multinucleated C1514030
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Glial Cell C1513978
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_abnormal_cell_of_disease	Neoplastic Oligodendrocyte C1514053
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_tissue_origin_of_disease	Neuroepithelial Tissue C1518281
DISO_to_ANAT		is_normal_cell_origin_of_disease	Neuroglia C0027836
DISO_to_ANAT		is_normal_cell_origin_of_disease	Oligodendrocyte C0028944
DISO_to_DISO		isa	Adult Undifferentiated Oligodendroglioma C0280790
DISO_to_DISO		is_finding_of_disease	Anaplasia C0002793
DISO_to_DISO		isa	Anaplastic Childhood Oligodendroglioma C1332943
DISO_to_DISO		permuted_term_of	Anaplastic Oligodendroglioma C0334590
DISO_to_DISO		may_be_cytogenetic_abnormality_of_disease	CDKN2A Gene Deletion C0805508
DISO_to_DISO		may_be_cytogenetic_abnormality_of_disease	Double Minutes C1512047
DISO_to_DISO		may_be_finding_of_disease	Extensive Necrosis C1517029
DISO_to_DISO		may_be_cytogenetic_abnormality_of_disease	Gain of Chromosome 7 C1517417
DISO_to_DISO		may_be_finding_of_disease	Headache C0018681

Genes (11)

Species:

human : 11

Species	Gene	GeneId	Gene Name	Evidence
Human	OLIG2	10215	oligodendrocyte lineage transcription factor 2	NCI, Score=801, Pubmed Id: 14575240, UMLKSK CUI: C0334590 The semiquantitative RT-PCR revealed that high levels of expression of Olig1 and Olig2 mRNAs were present in anaplastic oligodendrogliomas and anaplastic astrocytomas, while expression of these mRNAs in grade IV glioblastomas was lower than in grade II and grade III gliomas (p < 0.01). NCI, Score=801, Pubmed Id: 14575240, UMLKSK CUI: C0334590 Therefore, although OLIG2 expression was detected in a range of gliomas not specific for oligodendrogliomas, the expression level in anaplastic oligodendrogliomas was more uniform and intense than that in other glial tumors. NCI, Score=801, Pubmed Id: 14575240, UMLKSK CUI: C0334590 Immunohistochemical analyses demonstrated that the mean immunopositive proportion of OLIG2 was 82% in anaplastic oligodendrogliomas but only 34% in anaplastic astrocytomas. NCI, Score=801, Pubmed Id: 15198128, UMLKSK CUI: C0334590 Immunohistochemistry and microarray analyses demonstrate higher OLIG2 in anaplastic oligodendrogliomas versus glioblastomas, which are heterogeneous with respect to OLIG2 levels. NCI, Score=801, Pubmed Id: 14730454, UMLKSK CUI: C0334590 (2001) Lancet 358:298-300]. We investigated the mRNA expression of OLIG1 and OLIG2, as well as four other genes involved in oligodendrocyte development ( E2A, HEB, NKX2.2, and PDGFRA) in a panel of 70 gliomas, including 9 oligodendrogliomas, 11 anaplastic oligodendrogliomas, 5 oligoastrocytomas, 10 anaplastic oligoastrocytomas, 10 diffuse astrocytomas, 10 anaplastic astrocytomas, and 15 glioblastomas.
Human	TCF12	6938	transcription factor 12	NCI, Score=801, Pubmed Id: 14730454, UMLKSK CUI: C0334590 (2001) Lancet 358:298-300]. We investigated the mRNA expression of OLIG1 and OLIG2, as well as four other genes involved in oligodendrocyte development ( E2A, HEB, NKX2.2, and PDGFRA) in a panel of 70 gliomas, including 9 oligodendrogliomas, 11 anaplastic oligodendrogliomas, 5 oligoastrocytomas, 10 anaplastic oligoastrocytomas, 10 diffuse astrocytomas, 10 anaplastic astrocytomas, and 15 glioblastomas.
Human	TCF3	6929	transcription factor 3	NCI, Score=801, Pubmed Id: 14730454, UMLKSK CUI: C0334590 (2001) Lancet 358:298-300]. We investigated the mRNA expression of OLIG1 and OLIG2, as well as four other genes involved in oligodendrocyte development ( E2A, HEB, NKX2.2, and PDGFRA) in a panel of 70 gliomas, including 9 oligodendrogliomas, 11 anaplastic oligodendrogliomas, 5 oligoastrocytomas, 10 anaplastic oligoastrocytomas, 10 diffuse astrocytomas, 10 anaplastic astrocytomas, and 15 glioblastomas.
Human	SOX2	6657	SRY (sex determining region Y)-box 2	NCI, Score=801, Pubmed Id: 16077994, UMLKSK CUI: C0334590 SOX2 mRNA was expressed in ES cells, fetal brain, anaplastic oligodendroglioma, rhabdomyosarcoma, and small cell lung carcinoma.
Human	PIK3CA	5290	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	GENERIF, Score=1000, Pubmed Id: 15289301, UMLKSK CUI: C0334590 Mutations of PIK3CA is associated with anaplastic oligodendrogliomas, high-grade astrocytomas, and medulloblastomas
Human	MDM4	4194	Mdm4 p53 binding protein homolog (mouse)	NCI, Score=801, Pubmed Id: 10626796, UMLKSK CUI: C0334590 We investigated a series of 208 gliomas (106 glioblastomas, 46 anaplastic gliomas, and 56 low-grade gliomas) and identified 5 tumors (4 glioblastomas and 1 anaplastic oligodendroglioma) with MDM4 amplification and overexpression.
Human	STMN1	3925	stathmin 1	GENERIF, Score=673, Pubmed Id: 17440165, UMLKSK CUI: C0334590 Loss of heterozygosity for the stathmin gene may be associated with improved outcomes of patients with chromosome 1 anaplastic oligodendroglioma tumors
Human	IGFBP2	3485	insulin-like growth factor binding protein 2, 36kDa	NCI, Score=801, Pubmed Id: 10485462, UMLKSK CUI: C0334590 We carried out a gene expression profiling study using cDNA array technology with 24 primary glioma tissues of low-grade (oligodendroglioma), intermediate-grade (anaplastic oligodendroglioma and anaplastic astrocytoma), and high-grade (glioblastomas multiforme) tumors and found that insulin-like growth factor binding protein 2 (IGFBP2) was consistently overexpressed only in glioblastoma multiforme.
Human	GSTP1	2950	glutathione S-transferase pi 1	GENERIF, Score=1000, Pubmed Id: 15102663, UMLKSK CUI: C0334590 GSTP1 and GSTM1 polymorphisms have a role in survival from anaplastic astrocytoma, anaplastic oligodendroglioma, and anaplastic oligoastrocytoma
Human	GSTM1	2944	glutathione S-transferase mu 1	GENERIF, Score=1000, Pubmed Id: 15102663, UMLKSK CUI: C0334590 GSTP1 and GSTM1 polymorphisms have a role in survival from anaplastic astrocytoma, anaplastic oligodendroglioma, and anaplastic oligoastrocytoma
Human	CDKN2C	1031	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	NCI, Score=801, Pubmed Id: 10517502, UMLKSK CUI: C0334590 Homozygous deletions of the CDKN2C/p18INK4C gene on the short arm of chromosome 1 in anaplastic oligodendrogliomas. NCI, Score=801, Pubmed Id: 10515227, UMLKSK CUI: C0334590 We found 1 recurrent anaplastic oligodendroglioma that carried a somatic CDKN2C mutation at codon 113 (GAA ==> TAA: Glu ==> Stop). NCI, Score=801, Pubmed Id: 10994011, UMLKSK CUI: C0334590 A p18 mutation was found at an recurrence of an anaplastic oligodendroglioma, but not in the primary, low-grade tumor.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0334590	Anaplastic Oligodendroglioma	0		self

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