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 - Low Grade Malignant Neoplasm

Debug Stats

### Total Build Time: 20 ms 38.403 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 354 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
Skipping details on: CONCEPT_DEFINITION gt=NONE 0 Completed: 0 ms rowSize= 0 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=2 ms Completed: 2 ms rowSize= 1.555 KB
CONCEPT_GENES gt=14 ms Completed: 14 ms rowSize= 35.271 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.162 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Low Grade Malignant Neoplasm C1334425

Relationships (2)

Relation Types:

diso_to_anat : 2

Relationships:

is_abnormal_cell_of_disease : 2

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_abnormal_cell_of_disease	Cancer Cell C0334227
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032

Genes (37)

Species:

human : 37

Page Size

Current 25

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Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	KLK9	284366	kallikrein-related peptidase 9	NCI, Score=801, Pubmed Id: 11691797, UMLKSK CUI: C1334425 When the Cox proportional hazard regression analysis was applied to subgroups of patients, KLK9 expression was found to be a significant predictor of progression-free survival in the subgroup of patients with low-grade tumors [hazard ratio (HR), 0.13; P = 0.0015], early stage (HR, 0.099; P = 0.031); and those with optimal debulking (HR, 0.26; P = 0.012).
Human	SLC17A7	57030	solute carrier family 17 (vesicular glutamate transporter), member 7	NCI, Score=801, Pubmed Id: 15961236, UMLKSK CUI: C1334425 We analyzed the distribution of vesicular glutamate transporter 1 in the peritumoral neocortex of patients with epilepsy secondary to low-grade tumors.
Human	KLK5	25818	kallikrein-related peptidase 5	NCI, Score=801, Pubmed Id: 11237385, UMLKSK CUI: C1334425 We conclude that KLK5 expression is associated with more aggressive forms of epithelial ovarian carcinoma and has indepdent prognostic value in low grade tumours.
Human	NRG3	10718	neuregulin 3	NCI, Score=801, Pubmed Id: 16261396, UMLKSK CUI: C1334425 High levels of expression of NRG2beta and NRG4 were associated with high-grade tumours (p_lt_/=0.005), NRG2beta staining was associated with tumour size >25 mm (p=0.005) while NRG3 nuclear staining was present more often in low-grade tumours (p=0.039).
Human	VCAM1	7412	vascular cell adhesion molecule 1	NCI, Score=801, Pubmed Id: 11192830, UMLKSK CUI: C1334425 Women with lymph node-positive and high-grade tumors had higher levels of serum VCAM-1 than women with lymph node-negative and low-grade tumors.
Human	TIMP3	7078	TIMP metallopeptidase inhibitor 3	NCI, Score=801, Pubmed Id: 12579314, UMLKSK CUI: C1334425 Some differences may be established regarding the methylation profiles of specific genes and tumor types: MGMT, THBS1, TIMP-3, and p16INK4A appear hypermethylated in low-grade tumors (at least in 45% of cases), whereas GSTP1, DAPK, and p14ARF are mostly changed in 15-50% of the higher grade forms versus <10% in low-grade tumors. NCI, Score=801, Pubmed Id: 10598711, UMLKSK CUI: C1334425 TIMP-2 and TIMP-3 were poorly expressed in high-grade tumors and strongly expressed in normal pituitary glands and in the majority of low-grade tumors.
Human	TIMP2	7077	TIMP metallopeptidase inhibitor 2	NCI, Score=801, Pubmed Id: 10598711, UMLKSK CUI: C1334425 TIMP-2 and TIMP-3 were poorly expressed in high-grade tumors and strongly expressed in normal pituitary glands and in the majority of low-grade tumors. NCI, Score=801, Pubmed Id: 10579795, UMLKSK CUI: C1334425 RESULTS: mRNA for MMP-2 and TIMP-2 was localized to the malignant epithelial cells of both high- and low-grade tumors in the periphery of the glands and in areas of extracapsular involvement, and to the glandular epithelium in the benign prostates. NCI, Score=801, Pubmed Id: 8369572, UMLKSK CUI: C1334425 The low grade tumors expressed low and relatively constant levels of TIMP-1, TIMP-2, and 92-kDa gelatinase transcripts, whereas high grade lymphomas displayed variable amounts of mRNAs for TIMPs and MMPs, with a trend toward elevated TIMP-1 and 92-kDa gelatinase mRNA levels.
Human	TIMP1	7076	TIMP metallopeptidase inhibitor 1	NCI, Score=801, Pubmed Id: 8369572, UMLKSK CUI: C1334425 The low grade tumors expressed low and relatively constant levels of TIMP-1, TIMP-2, and 92-kDa gelatinase transcripts, whereas high grade lymphomas displayed variable amounts of mRNAs for TIMPs and MMPs, with a trend toward elevated TIMP-1 and 92-kDa gelatinase mRNA levels.
Human	TFRC	7037	transferrin receptor (p90, CD71)	NCI, Score=801, Pubmed Id: 2899182, UMLKSK CUI: C1334425 The determination of membrane TfR expression appears to have little value in the diagnostic differentiation of leukemias, whereas Ki-67 is considered to be a useful supplementary investigation in defining high grade tumors, in the recognition of prognostically poor cases of otherwise well defined low grade malignancy, and of potential value in resolving discrepancies between morphological and immunophenotypic features in leukemias of ;intermediate; type.
Human	SPN	6693	sialophorin	NCI, Score=801, Pubmed Id: 7552415, UMLKSK CUI: C1334425 CONCLUSIONS: Morphological appearance together with immunophenotypic results (positivity of CD20 and Ki-B5, negativity of CD3, CD43, CD45RO, and of lysozyme, negativity of CD30) are considered to represent sufficient diagnostic criteria of MBCL, including its differential diagnosis of other B-cell low grade malignancies.
Human	SKP2	6502	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	NCI, Score=801, Pubmed Id: 15305377, UMLKSK CUI: C1334425 Cyclin D3, skp2 and Ki-67 IR significantly increased from grade I to grade III FL (p = 0.0003, p = 0.0001 and p < 0.0001, respectively), while p27 IR was significantly (p < 0.0001) more prevalent in low-grade tumors.
Human	S100A2	6273	S100 calcium binding protein A2	NCI, Score=801, Pubmed Id: 10956408, UMLKSK CUI: C1334425 S100A2 was detected in 18/19 (95%) low-grade tumors and in 22/43 (51%) high-grade tumors, which were partially keratinizing.
Human	KLK6	5653	kallikrein-related peptidase 6	NCI, Score=801, Pubmed Id: 15305183, UMLKSK CUI: C1334425 More significantly, high level of kallikrein 6 expression was found in many early-stage and low-grade tumours, and elevated hK6 proteins were found in benign epithelia coexisting with borderline and invasive tissues, suggesting that overexpression of hK6 is an early phenomenon in the development of ovarian cancer.
Human	KLK7	5650	kallikrein-related peptidase 7	NCI, Score=801, Pubmed Id: 12633763, UMLKSK CUI: C1334425 KLK7 expression is an independent predictor of both disease-free and overall survival for patients with low grade tumors.
Human	PRKCA	5578	protein kinase C, alpha	NCI, Score=801, Pubmed Id: 9676858, UMLKSK CUI: C1334425 When analyzed in freshly frozen samples from human gliomas, the expression of PKC alpha was at similar levels in high- and low-grade tumors and was also similar to the levels in normal brain tissue controls.
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	NCI, Score=801, Pubmed Id: 12926065, UMLKSK CUI: C1334425 RESULTS: High-grade tumours significantly overexpressed nm23 (including both nm23-H1 and nm23-H2) compared with both intermediate and low-grade tumours (ANOVA and Tukey, all p < 0.05). NCI, Score=801, Pubmed Id: 7780979, UMLKSK CUI: C1334425 A significant relationship between nm23-H1 mRNA expression and lymph node metastasis was observed in high-grade tumors, which are intrinsically more invasive than are low-grade tumors.
Human	LDHA	3939	lactate dehydrogenase A	NCI, Score=801, Pubmed Id: 1117520, UMLKSK CUI: C1334425 In neoplastic urothelium the LDH-I per cent was increased in low grade tumors, while the LDH-V per cent and LDH-V/I ratio was increased in high grade tumors.
Human	KRT13	3860	keratin 13	NCI, Score=801, Pubmed Id: 8840999, UMLKSK CUI: C1334425 Grade IV tumors lacked or expressed reduced levels of keratin 13 but most resembled low-grade tumors.
Human	GNB3	2784	guanine nucleotide binding protein (G protein), beta polypeptide 3	NCI, Score=801, Pubmed Id: 15019160, UMLKSK CUI: C1334425 We conclude that the GNB3 825C>T polymorphism does not appear to be associated with breast cancer risk, but may influence development of metastasis in low-grade tumors.
Human	FGF7	2252	fibroblast growth factor 7	NCI, Score=801, Pubmed Id: 11061946, UMLKSK CUI: C1334425 There was no association between KGF and tumor grade or stage but there was a strong positive linear relationship between PSA and KGF (p = 0.006, R(2) = 68.3%) in low grade tumors.
Human	FABP4	2167	fatty acid binding protein 4, adipocyte	NCI, Score=801, Pubmed Id: 8840999, UMLKSK CUI: C1334425 In addition, low-grade tumors contained more A-FABP than their high-grade counterparts.
Human	EZH2	2146	enhancer of zeste homolog 2 (Drosophila)	NCI, Score=801, Pubmed Id: 17138155, UMLKSK CUI: C1334425 In addition, EZH2 mRNA expression was noted in 100% (16 of 16) of high-grade bladder tumors versus 50% (4 of 8) of low-grade tumors (P = 0.01). NCI, Score=801, Pubmed Id: 16361539, UMLKSK CUI: C1334425 In addition, EZH2 mRNA expression was noted in 100% (16 of 16) of high-grade bladder tumors versus 50% (4 of 8) of low-grade tumors (P=0.01). NCI, Score=801, Pubmed Id: 16361539, UMLKSK CUI: C1334425 In addition, EZH2 mRNA expression was noted in 100% (16 of 16) of high-grade bladder tumors versus 50% (4 of 8) of low-grade tumors (P = 0.01).
Human	ERCC6	2074	excision repair cross-complementing rodent repair deficiency, complementation group 6	NCI, Score=801, Pubmed Id: 8876669, UMLKSK CUI: C1334425 Here we have extended these studies to compare low-grade tumors to high-grade tumors and to include ERCC3 (which links DNA repair with DNA transcription) and ERCC6 (which is essential for gene-specific repair).
Human	ERCC3	2071	excision repair cross-complementing rodent repair deficiency, complementation group 3	NCI, Score=801, Pubmed Id: 8876669, UMLKSK CUI: C1334425 Here we have extended these studies to compare low-grade tumors to high-grade tumors and to include ERCC3 (which links DNA repair with DNA transcription) and ERCC6 (which is essential for gene-specific repair).
Human	EP300	2033	E1A binding protein p300	NCI, Score=801, Pubmed Id: 8367495, UMLKSK CUI: C1334425 Cluster analysis revealed the markers fell into three independent groups: (i) G-actin and EGFR; (ii) ploidy, cytology, and p185 (HER-2/neu oncoprotein) (ERBB2); and (iii) p300, a low-grade tumor antigen.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1334425	Low Grade Malignant Neoplasm	0		self

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