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 - Carcinomatous Ascites

Debug Stats

### Total Build Time: 23 ms 50.275 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 340 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 280 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=1 ms Completed: 1 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= 1.566 KB
CONCEPT_GENES gt=16 ms Completed: 16 ms rowSize= 46.878 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.155 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Carcinomatous Ascites C0877550

Definition (1)

Accumulation of fluid in the peritoneal cavity resulting from the growth of primary or metastatic carcinoma in the peritoneum.

Relationships (2)

Relation Types:

diso_to_anat : 2

Relationships:

is_associated_anatomic_site_of : 2

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_associated_anatomic_site_of	Abdominal Cavity C0230168
DISO_to_ANAT		is_associated_anatomic_site_of	Peritoneum C0031153

Genes (47)

Species:

human : 36

mouse : 11

Page Size

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Species	Gene	GeneId	Gene Name	Evidence
Mouse	GLS2	27165	glutaminase 2 (liver, mitochondrial)	NCI, Score=801, Pubmed Id: 9929166, UMLKSK CUI: C0877550 The influence of progressive tumor growth on phosphate-activated glutaminase (PAG) expression in splenocytes from mice bearing Ehrlich ascites carcinoma cells was investigated. NCI, Score=801, Pubmed Id: 8137919, UMLKSK CUI: C0877550 Changes in phosphate-activated glutaminase activities determined in intact cells and isolated mitochondria have been followed during mouse Ehrlich ascites carcinoma development. NCI, Score=801, Pubmed Id: 9920404, UMLKSK CUI: C0877550 The pH dependence of the phosphate-activated glutaminase isolated from Ehrlich tumour cells suggests a functional role for two prototropic groups with apparent pKa of 9.3 and 7.7 at the active site of the protein; these pKa values are compatible with cysteine and histidine residues, respectively. NCI, Score=801, Pubmed Id: 10928057, UMLKSK CUI: C0877550 Changes in the relative mRNA levels of phosphate-activated glutaminase (PAG) and glutamine synthetase (GS) in the liver and kidney of mice bearing a highly malignant strain of Ehrlich ascites tumor cells were determined at different days after tumor transplantation.
Mouse	CACYBP	27101	calcyclin binding protein	NCI, Score=801, Pubmed Id: 9572262, UMLKSK CUI: C0877550 A protein target of mouse calcyclin, p30, which we call calcyclin-binding protein (CacyBP), was identified in mouse brain and Ehrlich ascites tumor (EAT) cells.
Mouse	PLA2G6	8398	phospholipase A2, group VI (cytosolic, calcium-independent)	NCI, Score=801, Pubmed Id: 12906892, UMLKSK CUI: C0877550 The cytotoxic activity of F3 and F4 against Ehrlich ascites carcinoma cells might be due to the presence of a cytotoxin rather than to the direct cytolytic effect of the PLA2 because the non-lethal F4 is free from PLA2.
Mouse	TIMP1	7076	TIMP metallopeptidase inhibitor 1	NCI, Score=801, Pubmed Id: 12704667, UMLKSK CUI: C0877550 Furthermore, TIMP-1 treatment did not affect the levels of matrix metalloproteinase (MMP)-2 and MMP-9 mRNA in the Ehrlich tumor cells in vitro, although these expressions in the tumor were markedly suppressed in the TIMP-Tg-mice, compared to the Cont-mice at the end of the experiment.
Mouse	SRM	6723	spermidine synthase	NCI, Score=801, Pubmed Id: 7332714, UMLKSK CUI: C0877550 The antitumor effect of dicyclohexylammonium sulfate (DCHA), a potent inhibitor of spermidine synthase, was tested on mice inoculated with Ehrlich ascites carcinoma, Ehrlich solid carcinoma and solid sarcoma-180.
Mouse	SLC9A1	6548	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	NCI, Score=801, Pubmed Id: 12202953, UMLKSK CUI: C0877550 The Na+/H+ exchanger isoforms NHE1, NHE2, and NHE3 were all found to be expressed in Ehrlich ascites tumor cells, as evaluated by Western blotting and confocal microscopy.
Mouse	SLC2A3	6515	solute carrier family 2 (facilitated glucose transporter), member 3	NCI, Score=801, Pubmed Id: 9328846, UMLKSK CUI: C0877550 We found that Ehrlich ascites tumor cells possess only glucose transporter 1 (GLUT1) and GLUT3 but not GLUT2, GLUT4, or GLUT5.
Mouse	MPST	4357	mercaptopyruvate sulfurtransferase	NCI, Score=801, Pubmed Id: 8094343, UMLKSK CUI: C0877550 1. The activity of cysteine aminotransferase (CAT), 3-mercaptopyruvate sulfurtransferase (MPST) and rhodanese is much lower in Ehrlich ascites tumor cells (EATC) than in mouse liver.
Mouse	MPI	4351	mannose phosphate isomerase	NCI, Score=801, Pubmed Id: 2775533, UMLKSK CUI: C0877550 In contrast, Ehrlich ascites tumor cells obtained from the peritoneum of BALB/c mice had low MPI activity (half of the HKM activity and, therefore, a ratio of 2).
Mouse	GLS	2744	glutaminase	NCI, Score=801, Pubmed Id: 11169963, UMLKSK CUI: C0877550 Our results suggest that inhibition of glutaminase expression using anti-sense technology induces phenotypic changes in Ehrlich ascites tumor cells that allow the development of an effective anti-tumor immune response, which makes the cells unable to develop in vivo tumors. NCI, Score=801, Pubmed Id: 11169963, UMLKSK CUI: C0877550 Ehrlich ascites tumor cells expressing anti-sense glutaminase mRNA lose their capacity to evade the mouse immune system. NCI, Score=801, Pubmed Id: 11169963, UMLKSK CUI: C0877550 Using anti-sense technology, an Ehrlich ascites tumor cell line (0.28AS-2) with reduced glutaminase activity has been obtained.
Mouse	FH	2271	fumarate hydratase	NCI, Score=801, Pubmed Id: 729708, UMLKSK CUI: C0877550 Ehrlich ascites carcinoma induced significant changes in liver fumarase (activation) and aconitase (inhibition). NCI, Score=801, Pubmed Id: 729708, UMLKSK CUI: C0877550 Changes induced by Ehrlich ascites carcinoma in hepatic fumarase and aconitase activities.
Human	TUBA1C	84790	tubulin, alpha 1c	NCI, Score=801, Pubmed Id: 6832357, UMLKSK CUI: C0877550 Preparations of cycled tubulin from Ehrlich ascites tumor cells contain several accessory proteins; once or twice cycled microtubule preparations are usually composed of fibers 10 nm in diameter, but lack vimentin. NCI, Score=801, Pubmed Id: 3934153, UMLKSK CUI: C0877550 Tubulin was phosphorylated mainly at tyrosine residues by membranes from mouse liver and Ehrlich ascites tumor with ATP in the presence of MnCl2, ZnCl2, NaVO3, and Nonidet P-40 in an epidermal growth factor (EGF)- and insulin-independent manner. NCI, Score=801, Pubmed Id: 6251907, UMLKSK CUI: C0877550 Catecholamine-induced stimulation of adenylate cyclase in parallel with a change in tubulin assembly in Ehrlich ascites tumor cells. NCI, Score=801, Pubmed Id: 6832357, UMLKSK CUI: C0877550 In vitro formation of different tubulin polymers from purified tubulin of Ehrlich ascites tumor cells. NCI, Score=801, Pubmed Id: 435479, UMLKSK CUI: C0877550 The results demonstrate that the in vitro assembly of tubulin from Ehrlich ascites tumor cells does not require high molecular weight proteins or gamma-like factor(s) as has been proposed for the neurotubulin system. NCI, Score=801, Pubmed Id: 889806, UMLKSK CUI: C0877550 In vitro assembly of tubulin from nonneural cells (Ehrlich ascites tumor cells). NCI, Score=801, Pubmed Id: 3880702, UMLKSK CUI: C0877550 In vivo TriEL also caused MT depolymerization in interphase and mitotic PtK-1 and Ehrlich ascites tumor (EAT) cells as monitored by indirect immuno-fluorescent staining of tubulin and electron microscopy.
Human	CACYBP	27101	calcyclin binding protein	NCI, Score=801, Pubmed Id: 12042313, UMLKSK CUI: C0877550 Co-immunoprecipitation of CacyBP/SIP with S100B from brain and with S100A6 from Ehrlich ascites tumor cells suggests that these interactions are physiologically relevant and that the ubiquitinylation complex involving CacyBP/SIP might be regulated by S100 proteins.
Human	VAT1	10493	vesicle amine transport 1	NCI, Score=801, Pubmed Id: 9581869, UMLKSK CUI: C0877550 Mammalian protein homologous to VAT-1 of Torpedo californica: isolation from Ehrlich ascites tumor cells, biochemical characterization, and organization of its gene. NCI, Score=801, Pubmed Id: 9581869, UMLKSK CUI: C0877550 This VAT-1 homolog was isolated from a murine breast cancer cell line (Ehrlich ascites tumor) and identified by sequencing of cleavage peptides. NCI, Score=801, Pubmed Id: 9581869, UMLKSK CUI: C0877550 The isolated VAT-1 homolog protein displays an ATPase activity and exists in two isoforms with isoelectric points of 5.7 and 5.8. cDNA was prepared from Ehrlich ascites tumor cells, and the murine VAT-1 homolog sequence was amplified by polymerase chain reaction and partially sequenced.
Human	EIF2S2	8894	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa	NCI, Score=801, Pubmed Id: 8099583, UMLKSK CUI: C0877550 Purification and characterization of eukaryotic initiation factor (eIF)-2 alpha kinases from Ehrlich ascites tumor cells. NCI, Score=801, Pubmed Id: 6551177, UMLKSK CUI: C0877550 With complexes formed by using a partially purified preparation of eIF-2 from Ehrlich ascites tumor cells, it is possible to reverse the 40S subunit induced inhibition by creating conditions which eliminate free GDP from the system. NCI, Score=801, Pubmed Id: 6498200, UMLKSK CUI: C0877550 Translation of exogenous mRNAs in micrococcal nuclease-treated extracts from Ehrlich ascites tumor cells is greatly stimulated by the addition of crude initiation factors or initiation factors eIF-2B and eIF-2 containing eIF-2B. NCI, Score=801, Pubmed Id: 3402451, UMLKSK CUI: C0877550 Previously, we have shown that phosphorylation of the eukaryotic initiation factor eIF-2 alpha increases under several physiological stresses in which protein synthesis is inhibited in Ehrlich ascites tumor cells.
Human	EIF2B4	8890	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	NCI, Score=801, Pubmed Id: 6498200, UMLKSK CUI: C0877550 Translation of exogenous mRNAs in micrococcal nuclease-treated extracts from Ehrlich ascites tumor cells is greatly stimulated by the addition of crude initiation factors or initiation factors eIF-2B and eIF-2 containing eIF-2B.
Human	TKT	7086	transketolase	NCI, Score=801, Pubmed Id: 6127634, UMLKSK CUI: C0877550 Thiamine pyrophosphate (TPP) content, activities of thiamine pyrophosphokinase (TPKase), thiamine pyrophosphatase, transketolase (TK), pyruvate (PDG) and oxoglutarate dehydrogenases (OGDG) were measured in the liver and cells of Ehrlich ascites carcinoma (EAC) on the 5th, 10th and 15th day after transplantation of the tumor to mice fed a thiamine-deficient diet.
Human	SSTR1	6751	somatostatin receptor 1	NCI, Score=801, Pubmed Id: 2476562, UMLKSK CUI: C0877550 It is suggested that the LTD4-induced activation of K and Cl transporting systems in Ehrlich ascites tumor cells is mediated via a G-protein coupled receptor and that LTD4 might exert its effect through another lipoxygenase product.
Human	SIGLEC1	6614	sialic acid binding Ig-like lectin 1, sialoadhesin	NCI, Score=801, Pubmed Id: 10602886, UMLKSK CUI: C0877550 The aim of this study was to assess whether Ehrlich tumor (ET) - a murine mammary carcinoma - growth may modify the sialoadhesin expression by bone marrow macrophages and/or sialoadhesin-inducing activity in ET-bearing sera.
Human	SLC12A1	6557	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	NCI, Score=801, Pubmed Id: 8006960, UMLKSK CUI: C0877550 The Na-K-2Cl cotransporter is in a permanently activated state in cytoplasts from Ehrlich ascites tumor cells.
Human	SLC9A3	6550	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	NCI, Score=801, Pubmed Id: 12202953, UMLKSK CUI: C0877550 The Na+/H+ exchanger isoforms NHE1, NHE2, and NHE3 were all found to be expressed in Ehrlich ascites tumor cells, as evaluated by Western blotting and confocal microscopy.
Human	SLC2A5	6518	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	NCI, Score=801, Pubmed Id: 9328846, UMLKSK CUI: C0877550 We found that Ehrlich ascites tumor cells possess only glucose transporter 1 (GLUT1) and GLUT3 but not GLUT2, GLUT4, or GLUT5.
Human	SLC2A2	6514	solute carrier family 2 (facilitated glucose transporter), member 2	NCI, Score=801, Pubmed Id: 9328846, UMLKSK CUI: C0877550 We found that Ehrlich ascites tumor cells possess only glucose transporter 1 (GLUT1) and GLUT3 but not GLUT2, GLUT4, or GLUT5.
Human	RPS6	6194	ribosomal protein S6	NCI, Score=801, Pubmed Id: 208946, UMLKSK CUI: C0877550 After mengovirus infection of Ehrlich ascites tumor cells, an increased incorporation of radioactive phosphate into ribosomal protein S6 was detected. NCI, Score=801, Pubmed Id: 7317434, UMLKSK CUI: C0877550 Phosphorylation of ribosomal protein S6 in the Ehrlich ascites tumor cell. NCI, Score=801, Pubmed Id: 208946, UMLKSK CUI: C0877550 Enhanced phosphorylation of ribosomal protein s6 and other cytoplasmic proteins after mengovirus infection of Ehrlich ascites tumor cells.
Human	PRIM1	5557	primase, DNA, polypeptide 1 (49kDa)	NCI, Score=801, Pubmed Id: 3191193, UMLKSK CUI: C0877550 The effect of a single-stranded DNA-binding protein (SSB-protein) form Ehrlich ascites tumour cells (EAT) on the activity of homologous purified DNA-polymerases alpha and beta, DNA-replicase, primase and DNA-polymerases from phage T4 and Bacillus stearothermophillus was studied.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0877550	Carcinomatous Ascites	0		self

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