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 - Oligodendroglioma

Debug Stats

### Total Build Time: 20 ms 34.615 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 332 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 843 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= 187 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 542 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 2.748 KB
CONCEPT_RELATIONSHIPS gt=1 ms Completed: 1 ms rowSize= 106 bytes
CONCEPT_GENES gt=12 ms Completed: 12 ms rowSize= 28.718 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.151 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Oligodendroglioma C0028945

Definition (1)

A relatively slow-growing glioma that is derived from oligodendrocytes and tends to occur in the cerebral hemispheres, thalamus, or lateral ventricle. They may present at any age, but are most frequent in the third to fifth decades, with an earlier incidence peak in the first decade. Histologically, these tumors are encapsulated, relatively avascular, and tend to form cysts and microcalcifications. Neoplastic cells tend to have small round nuclei surrounded by unstained nuclei. The tumors may vary from well-differentiated to highly anaplastic forms. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2052; Adams et al., Principles of Neurology, 6th ed, p655)

Semantic Types (1)

Neoplastic Process (T191)

Parents (1)

C0017638

Ancestral Roots

Root	Root Plus One	Depth	Parent
Neoplasms C0027651	Neoplasms by Histologic Type C0027652	7	Glioma C0017638
Neoplasms C0027651	Neoplasms by Histologic Type C0027652	6	Glioma C0017638

Genes (26)

Species:

human : 26

Page Size

Current 25

100

250

ALL

Page 1 of 2

Prior Page

Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	ATAD3B	83858	ATPase family, AAA domain containing 3B	GENERIF, Score=1000, Pubmed Id: 18639545, UMLKSK CUI: C0028945 These results demonstrate the potential for ATAD 3B as a putative marker in discriminating astrocytomas from oligodendrogliomas
Human	PARVG	64098	parvin, gamma	GENERIF, Score=694, Pubmed Id: 15993274, UMLKSK CUI: C0028945 INI1hSNF5 and PARVG do not seem to be the tumor suppressor genes involved in oligodendroglioma development and progression
Human	MIB1	57534	mindbomb E3 ubiquitin protein ligase 1	GENERIF, Score=861, Pubmed Id: 17390041, UMLKSK CUI: C0028945 Comparative genomic hybridization and immunohistochemical assessment of EGFR, PTEN, p53, and MIB-1 expression in 13 oligodendrogliomas, one oligoastrocytoma and 23 high-grade astrocytomas is reported
Human	RTN4	57142	reticulon 4	GENERIF, Score=1000, Pubmed Id: 18685489, UMLKSK CUI: C0028945 Nogo-a expression in glial CNS tumors may be a marker to differentiate between oligodendrogliomas and other gliomas
Human	AJAP1	55966	adherens junctions associated protein 1	GENERIF, Score=1000, Pubmed Id: 16410724, UMLKSK CUI: C0028945 While a mutation was not detected in the coding region of the SHREW1 gene in oligodendrogliomas, SHREW1 expression restoration resulted in suppression of cell adhesion and migration, thus, SHREW1 inactivation may lead to oligodendroglial tumorigenesis
Human	ATAD3A	55210	ATPase family, AAA domain containing 3A	GENERIF, Score=1000, Pubmed Id: 18639545, UMLKSK CUI: C0028945 We also have shown that the loss of ATAD 3A/3B may be involved in the transformation pathway and the chemosensitivity of oligodendrogliomas
Human	GLTSCR1	29998	glioma tumor suppressor candidate region gene 1	GENERIF, Score=1000, Pubmed Id: 15834925, UMLKSK CUI: C0028945 Polymorphisms in GLTSCR1 are associated with the development of oligodendrogliomas
Human	OLIG2	10215	oligodendrocyte lineage transcription factor 2	GENERIF, Score=694, Pubmed Id: 16103065, UMLKSK CUI: C0028945 Overexpression of OLIG2 was not only found in oligodendroglioma samples and normal neural tissue but also in a wide spectrum of malignant cell lines including leukemia, non-small cell lung carcinoma, melanoma, and breast cancer cell lines
Human	PRDX6	9588	peroxiredoxin 6	GENERIF, Score=1000, Pubmed Id: 17653765, UMLKSK CUI: C0028945 overexpression of peroxiredoxin 6 is associated with oligodendroglioma
Human	SMARCB1	6598	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	GENERIF, Score=694, Pubmed Id: 15993274, UMLKSK CUI: C0028945 INI1hSNF5 and PARVG do not seem to be the tumor suppressor genes involved in oligodendroglioma development and progression
Human	PTPRZ1	5803	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	GENERIF, Score=660, Pubmed Id: 18003890, UMLKSK CUI: C0028945 results from the immunohistochemical analyses of rPTPbeta/zeta expression should prompt further evaluation of this protein as a novel oligodendroglioma marker
Human	PTGS2	5743	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	GENERIF, Score=827, Pubmed Id: 15484698, UMLKSK CUI: C0028945 Immunohistochemical results are compared with patient survival in order to verify COX-2 prognostic significance in 32 primary oligodendrogliomas
Human	PMS2	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	OMIM, Score=1000, UMLKSK CUI: C0028945 Oligodendroglioma
Human	NOTCH2	4853	notch 2	GENERIF, Score=694, Pubmed Id: 19119320, UMLKSK CUI: C0028945 Results suggest that the NOTCH2 gene is not physically rearranged by t(1;19) translocation of oligodendroglioma tumors, and that the t(1;19) translocation arises from complex intra and interchromosomal rearrangements
Human	MSH2	4436	mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)	OMIM, Score=1000, UMLKSK CUI: C0028945 Oligodendroglioma
Human	MLH1	4292	mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)	OMIM, Score=1000, UMLKSK CUI: C0028945 Oligodendroglioma
Human	KCNA5	3741	potassium voltage-gated channel, shaker-related subfamily, member 5	GENERIF, Score=1000, Pubmed Id: 12850541, UMLKSK CUI: C0028945 Kv1.5 potassium channel mRNA expression correlates with glioma entities and malignancy grades; expression is high in astrocytomas, moderate in oligodendrogliomas, and low in glioblastomas
Human	IDH1	3417	isocitrate dehydrogenase 1 (NADP+), soluble	GENERIF, Score=1000, Pubmed Id: 18985363, UMLKSK CUI: C0028945 Data show that the very high frequency of IDH1 mutations occurrs in diffuse astrocytomas, oligodendrogliomas, oligoastrocytomas and secondary glioblastomas
Human	MSH6	2956	mutS homolog 6 (E. coli)	OMIM, Score=1000, UMLKSK CUI: C0028945 Oligodendroglioma
Human	ERCC2	2068	excision repair cross-complementing rodent repair deficiency, complementation group 2	GENERIF, Score=1000, Pubmed Id: 15834925, UMLKSK CUI: C0028945 Polymorphisms in ERCC2 are associated with the development of oligodendrogliomas
Human	EDNRB	1910	endothelin receptor type B	GENERIF, Score=1000, Pubmed Id: 15950764, UMLKSK CUI: C0028945 These data point to ET-1 as a possible survival factor for oligodendrogliomas via ET(B)-R activation and suggest that ET(B)-R-specific antagonists might constitute a potential therapeutic alternative for oligodendrogliomas
Human	DFFB	1677	DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)	GENERIF, Score=694, Pubmed Id: 16156899, UMLKSK CUI: C0028945 DFFB haploinsufficiency from 1p allelic loss is a contributing factor in oligodendroglioma development
Human	CDKN2A	1029	cyclin-dependent kinase inhibitor 2A	GAD, Score=1000, Pubmed Id: 14507338, UMLKSK CUI: C0028945 Title:Tumour necrosis and microvascular proliferation are associated with 9p deletion and CDKN2A alterations in 1p/19q-deleted oligodendrogliomas.\|Association:Y\|Conclusion:Not Found
Human	CD44	960	CD44 molecule (Indian blood group)	GENERIF, Score=1000, Pubmed Id: 12635659, UMLKSK CUI: C0028945 expressed by cells of the oligodendrocyte lineage in vitro and by oligodendrogliomas in vivo; could play a role in migration of tumor cells in oligodendrocytic tumors
Human	ARHGDIA	396	Rho GDP dissociation inhibitor (GDI) alpha	GENERIF, Score=1000, Pubmed Id: 17653765, UMLKSK CUI: C0028945 Underexpression of rho GDP dissociation inhibitor alpha is associated with oligodendroglioma

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0028945	Oligodendroglioma	0		self

Gataca is supported by...