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 - Pinealoma

Debug Stats

### Total Build Time: 50 ms 37.380 KB
CONCEPT_NAME gt=18 ms Completed: 18 ms rowSize= 367 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 890 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
CONCEPT_NAMESPACE gt=NONE 1 ms Completed: 1 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 995 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=2 ms Completed: 2 ms rowSize= 6.602 KB
CONCEPT_RELATIONSHIPS gt=18 ms Completed: 18 ms rowSize= 13.258 KB
CONCEPT_GENES gt=7 ms Completed: 7 ms rowSize= 13.960 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.144 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (2)

Pinealoma C0031941

Pineal Gland Neoplasm

Definition (1)

Neoplasms which originate from pineal parenchymal cells that tend to enlarge the gland and be locally invasive. The two major forms are pineocytoma and the more malignant pineoblastoma. Pineocytomas have moderate cellularity and tend to form rosette patterns. Pineoblastomas are highly cellular tumors containing small, poorly differentiated cells. These tumors occasionally seed the neuroaxis or cause obstructive HYDROCEPHALUS or Parinaud's syndrome. GERMINOMA; CARCINOMA, EMBRYONAL; GLIOMA; and other neoplasms may arise in the pineal region with germinoma being the most common pineal region tumor. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2064; Adams et al., Principles of Neurology, 6th ed, p670)

Semantic Types (1)

Neoplastic Process (T191)

Parents (2)

C0006118

C0206715

Ancestral Roots

Relationships (47)

Relation Types:

diso_to_anat : 19

diso_to_diso : 26

diso_to_phen : 2

Relationships:

none : 21

is_abnormal_cell_of_disease : 4

is_associated_anatomic_site_of : 5

is_normal_cell_origin_of_disease : 3

is_normal_tissue_origin_of_disease : 3

isa : 9

mapped_to : 1

permuted_term_of : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT	106		Pineal Gland C0031939
DISO_to_DISO	96		Brain Neoplasms C0006118
DISO_to_DISO	62		Brain Neoplasms C0006118
DISO_to_ANAT	56		Pineal Gland C0031939
DISO_to_DISO	29		Germinoma C0206660
DISO_to_DISO	25		Germinoma C0206660
DISO_to_DISO	22		Complication Aspects C1171258
DISO_to_DISO	22		GERM CELL EMBRYONAL NEOPL C0027658
DISO_to_DISO	19		Carcinoma, Papillary C0007133
DISO_to_DISO	16		Complication Aspects C1171258
DISO_to_PHEN	11		genetic aspects C0017399
DISO_to_PHEN	9		genetic aspects C0017399
DISO_to_ANAT	6		In Blood C0005768
DISO_to_DISO	6		ASTROCYTOMA C0004114
DISO_to_DISO	6		Teratoma C0039538
DISO_to_ANAT	5		Third Ventricle C0149555
DISO_to_DISO	5		LOCAL NEOPL RECURRENCE C0027643
DISO_to_DISO	5		METACHRONOUS NEOPL C0085183
DISO_to_DISO	5		NEOPL RETINAL C0524801
DISO_to_DISO	5		Pituitary Neoplasms C0032019
DISO_to_DISO	5		Retinoblastoma C0035335
DISO_to_ANAT		is_associated_anatomic_site_of	Brain C0006104
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		is_abnormal_cell_of_disease	Neoplastic Cell C0597032

Genes (6)

Species:

human : 6

Species	Gene	GeneId	Gene Name	Evidence
Human	SYP	6855	synaptophysin	NCI, Score=801, Pubmed Id: 12701886, UMLKSK CUI: C0031941 Pineal parenchymal tumor (PPT) differentiation was confirmed by immunohistochemical detection of neuroendocrine markers (synaptophysin, neurofilaments, and chromogranin A).
Human	SAG	6295	S-antigen; retina and pineal gland (arrestin)	NCI, Score=801, Pubmed Id: 2709107, UMLKSK CUI: C0031941 Immunoreactive S-antigen in cerebrospinal fluid: a marker of pineal parenchymal tumors? NCI, Score=801, Pubmed Id: 3541480, UMLKSK CUI: C0031941 S-antigen immunoreactivity in human pineal glands and pineal parenchymal tumors. NCI, Score=801, Pubmed Id: 2709107, UMLKSK CUI: C0031941 This investigation evaluated the possibility that the occurrence of S-antigen in cerebrospinal fluid (CSF) might be used as a preoperative marker of pineal parenchymal tumors (pineoblastoma and pineocytoma). NCI, Score=801, Pubmed Id: 3541480, UMLKSK CUI: C0031941 Using a four-step immunoperoxidase (PAP) method and the monoclonal antibody MAbA9-C6 (MAbA9-C6), which defines an epitope of the retinal S-antigen (S-Ag), we investigated the S-Ag immunoreactivity in human fetal, newborn, infantile and adult pineal glands and in 13 human pineal parenchymal tumors. NCI, Score=801, Pubmed Id: 2709107, UMLKSK CUI: C0031941 These preliminary results suggest that testing for S-antigen in CSF might be useful in characterizing and treating tumors of the pineal region and, when identified in conjunction with other markers, it might also help to better define pineal parenchymal tumors. NCI, Score=801, Pubmed Id: 8360704, UMLKSK CUI: C0031941 Pineal parenchymal tumors demonstrate a highly variable and incomplete photosensory differentiation evidenced by specific cytoarchitectural features and the expression of photosensory retinal S-Antigen (S-Ag). NCI, Score=801, Pubmed Id: 3541632, UMLKSK CUI: C0031941 S-antigen immunoreactivity was observed in two pineal gland tumors but not the remaining nine primary intracranial neoplasms or the two intraocular medulloepitheliomas.
Human	RBP3	5949	retinol binding protein 3, interstitial	NCI, Score=801, Pubmed Id: 8360704, UMLKSK CUI: C0031941 In this study, a pineal parenchymal tumor of the ;mixed pineoblastoma/pineocytoma; type was examined for the expression of several photoreceptor, glial and neuronal proteins including: interphotoreceptor retinoid-binding protein (IRBP), rod opsin, cone opsin, S-Ag and cellular retinaldehyde-binding protein (CRA1BP). NCI, Score=801, Pubmed Id: 8360704, UMLKSK CUI: C0031941 The analysis of IRBP expression may facilitate the diagnostic recognition of primitive pineal neoplasms and further define the neuroretinal differentiation which occurs in pineal parenchymal tumors.
Human	MAP2	4133	microtubule-associated protein 2	NCI, Score=801, Pubmed Id: 15146346, UMLKSK CUI: C0031941 Immunohistochemical analysis led to the following conclusions: (1) specific pattern of MAP2-positive tumor cells can be identified in 95% of glial neoplasms; (2) ependymal tumors do not express MAP2 in their rosette-forming cell component; (3) tumors of the pineal gland as well as malignant embryonic tumors are also characterized by abundant MAP2 immunoreactivity; (4) virtually no MAP2 expression can be observed in the neoplastic glial component of glio-neuronal tumors, i.e. gangliogliomas; (5) malignant glial tumor variants (WHO grade III or IV) exhibit different and less specific MAP2 staining patterns compared to their benign counterparts (WHO grade I or II); (6) with the exception of melanomas and small cell lung cancers, MAP2 expression is very rare in metastatic and non-neuroepithelial tumors; (7) glial MAP2 expression was not detected in 56 non-neoplastic lesions.
Human	CHM	1121	choroideremia (Rab escort protein 1)	GAD, Score=1000, Pubmed Id: 9349950, UMLKSK CUI: C0031941 Title:A hemizygous A to CC base change of the CHM gene causing choroideremia associated with pinealoma.\|Association:Y\|Conclusion:The hemizygous mutation was detected in a patient and the heterozygous pattern in his mother, the carrier, suggesting that this mutation caused the disease.
Human	ASMT	438	acetylserotonin O-methyltransferase	NCI, Score=801, Pubmed Id: 10831155, UMLKSK CUI: C0031941 Demonstration of hydroxyindole-O-methyltransferase (HIOMT) mRNA expression in pineal parenchymal tumors: histochemical in situ hybridization. NCI, Score=801, Pubmed Id: 10831155, UMLKSK CUI: C0031941 These results suggest that the neoplastic cells of pineoblastomas and pineocytomas often retain the ability to express HIOMT mRNA, as in normal pinealocytes, and that HIOMT is a useful tumor marker for the diagnosis of pineal parenchymal tumors.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0031941	Pinealoma	0		self

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