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 - M5b Acute differentiated monocytic leukemia

Debug Stats

### Total Build Time: 65 ms 35.115 KB
CONCEPT_NAME gt=6 ms Completed: 6 ms rowSize= 384 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 243 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= 106 bytes
CONCEPT_GENES gt=45 ms Completed: 45 ms rowSize= 33.152 KB
CONCEPT_XREFS gt=10 ms Completed: 10 ms rowSize= 1.177 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

M5b Acute differentiated monocytic leukemia C1318544

Definition (1)

A progressive, proliferative disease of blood cells, originating from immature monocytes.

Genes (53)

Species:

human : 52

mouse : 1

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Species	Gene	GeneId	Gene Name	Evidence
Mouse	FGR	2268	feline Gardner-Rasheed sarcoma viral oncogene homolog	NCI, Score=801, Pubmed Id: 8159769, UMLKSK CUI: C1318544 With an immune complex kinase assay in a monocytic leukemia cell line, 2H2 monoclonal antibody was shown to precipitate a 59-kDa protein that corresponds in molecular mass to murine Fgr.
Human	CCL3L3	414062	chemokine (C-C motif) ligand 3-like 3	NCI, Score=801, Pubmed Id: 2687328, UMLKSK CUI: C1318544 This protein was not found in culture supernatants or cell lysates of monocytic leukemia cells and HL-60 cells, although LD78 transcripts were found in those cells.
Human	RAB7B	338382	RAB7B, member RAS oncogene family	NCI, Score=801, Pubmed Id: 15144907, UMLKSK CUI: C1318544 RT-PCR or Western blot analysis of Rab7b expression shows that Rab7b is selectively expressed in monocytes, monocyte-derived immature dendritic cells (DCs), and promyeloid or monocytic leukemia cell lines.
Human	DIABLO	56616	diablo, IAP-binding mitochondrial protein	NCI, Score=801, Pubmed Id: 15767555, UMLKSK CUI: C1318544 Treatment of U937 monocytic leukemia cells with rapamycin (10 nmol/L) in conjunction with a minimally toxic concentration of UCN-01 (100 nmol/L) for 36 hours resulted in marked potentiation of mitochondrial injury (i.e., loss of mitochondrial membrane potential and cytosolic release of cytochrome c, AIF, and Smac/DIABLO), caspase activation, and apoptosis.
Human	MRAS	22808	muscle RAS oncogene homolog	NCI, Score=801, Pubmed Id: 15735740, UMLKSK CUI: C1318544 Expression of a constitutively active mutant of M-Ras in normal bone marrow is sufficient for induction of a malignant mastocytosis/mast cell leukemia, distinct from the histiocytosis/monocytic leukemia induced by expression of activated H-Ras.
Human	ABI1	10006	abl-interactor 1	GENERIF, Score=923, Pubmed Id: 12547160, UMLKSK CUI: C1318544 t(10;11)(p11.2;q23) involving MLL and this gene is associated with congenital acute monocytic leukemia
Human	MVP	9961	major vault protein	NCI, Score=801, Pubmed Id: 12801535, UMLKSK CUI: C1318544 In conclusion, we report that LRP is rather a marker of monocytic lineage than a prognostic index for MDR and we suggest that detection of LRP by ICC could be an argument for the diagnosis of monoblastic and monocytic leukemias.
Human	CD83	9308	CD83 molecule	NCI, Score=801, Pubmed Id: 11226522, UMLKSK CUI: C1318544 The efficient generation of CD83 positive immunocompetent dendritic cells from CD14 positive acute myelomonocytic or monocytic leukemia cells in vitro.
Human	AIFM1	9131	apoptosis-inducing factor, mitochondrion-associated, 1	NCI, Score=801, Pubmed Id: 15767555, UMLKSK CUI: C1318544 Treatment of U937 monocytic leukemia cells with rapamycin (10 nmol/L) in conjunction with a minimally toxic concentration of UCN-01 (100 nmol/L) for 36 hours resulted in marked potentiation of mitochondrial injury (i.e., loss of mitochondrial membrane potential and cytosolic release of cytochrome c, AIF, and Smac/DIABLO), caspase activation, and apoptosis.
Human	MLLT10	8028	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	NCI, Score=801, Pubmed Id: 12555219, UMLKSK CUI: C1318544 Monocytic leukemias with CALM/AF10 fusion are frequently associated with mediastinal invasion. NCI, Score=801, Pubmed Id: 12555219, UMLKSK CUI: C1318544 Monocytic leukemia with CALM/AF10 rearrangement showing mediastinal emphysema.
Human	MYST3	7994		NCI, Score=801, Pubmed Id: 15128673, UMLKSK CUI: C1318544 We show that a zebrafish ortholog of the human oncogenic histone acetyltransferase MOZ (monocytic leukemia zinc finger) is required for specifying segmental identity in the second through fourth pharyngeal arches. NCI, Score=801, Pubmed Id: 12619166, UMLKSK CUI: C1318544 In addition, fluorescence in situ hybridization analysis suggested a rearrangement in the monocytic leukemia zinc finger (MOZ) gene, located in the 8p11 region of chromosome 8.
Human	VDR	7421	vitamin D (1,25- dihydroxyvitamin D3) receptor	GENERIF, Score=756, Pubmed Id: 15145445, UMLKSK CUI: C1318544 resistance of acute monocytic leukemia cells to calcitriol-induced differentiation correlates with impaired nuclear localization of vitamin D receptor, but not with its total expression in the cells
Human	TXN	7295	thioredoxin	NCI, Score=801, Pubmed Id: 10424449, UMLKSK CUI: C1318544 We therefore investigated the expression of redox-regulating proteins such as glutaredoxin (GRX) and thioredoxin (TRX) during the differentiation of murine monocytic leukemia cell line M1 cells and human monocytic leukemia cell line U937 cells.
Human	CCL3L1	6349	chemokine (C-C motif) ligand 3-like 1	NCI, Score=801, Pubmed Id: 2687328, UMLKSK CUI: C1318544 This protein was not found in culture supernatants or cell lysates of monocytic leukemia cells and HL-60 cells, although LD78 transcripts were found in those cells.
Human	SAA1	6288	serum amyloid A1	NCI, Score=801, Pubmed Id: 10886778, UMLKSK CUI: C1318544 Because SAA synthesis at the protein level in such cells has never been analyzed quantitatively, in this study an enzyme-linked immunosorbent assay was generated with a detection level sufficiently high to measure SAA concentrations in the culture supernatants of the human monocytic leukaemia cell line THP-1.
Human	SAA@	6287	serum amyloid A1 cluster	NCI, Score=801, Pubmed Id: 10886778, UMLKSK CUI: C1318544 Because SAA synthesis at the protein level in such cells has never been analyzed quantitatively, in this study an enzyme-linked immunosorbent assay was generated with a detection level sufficiently high to measure SAA concentrations in the culture supernatants of the human monocytic leukaemia cell line THP-1.
Human	S100A9	6280	S100 calcium binding protein A9	NCI, Score=801, Pubmed Id: 9706399, UMLKSK CUI: C1318544 Transcriptional regulation of the gene for the myeloid calcium binding protein, MRP14, was investigated in human monocytic leukemia cell lines.
Human	PLSCR1	5359	phospholipid scramblase 1	NCI, Score=801, Pubmed Id: 9712717, UMLKSK CUI: C1318544 These results provide new information on the possible roles of MmTRA1b/phospholipid scramblase and the truncated MmTRA1a in the leukemogenesis and differentiation of monocytic leukemia cells.
Human	PDGFB	5155	platelet-derived growth factor beta polypeptide	NCI, Score=801, Pubmed Id: 3165051, UMLKSK CUI: C1318544 In the present study, PDGF-1 and PDGF-2 gene expression was compared in HL-60 cells, human THP-1 monocytic leukemia cells, and human monocytes.
Human	PDGFA	5154	platelet-derived growth factor alpha polypeptide	NCI, Score=801, Pubmed Id: 3165051, UMLKSK CUI: C1318544 In the present study, PDGF-1 and PDGF-2 gene expression was compared in HL-60 cells, human THP-1 monocytic leukemia cells, and human monocytes.
Human	OLR1	4973	oxidized low density lipoprotein (lectin-like) receptor 1	NCI, Score=801, Pubmed Id: 11728449, UMLKSK CUI: C1318544 We investigated the effect of histamine on the expression of LOX-1 in cells of the human monocytic leukemia cell line THP-1. NCI, Score=801, Pubmed Id: 15016631, UMLKSK CUI: C1318544 Inhibition of NO synthesis in PMA-primed human monocytic leukemia HL-60 cells resulted in a twofold increase in expression of the receptor for oxidized LDL (OxLDL), termed the lectin-like OxLDL receptor (LOX-1).
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	NCI, Score=801, Pubmed Id: 9650453, UMLKSK CUI: C1318544 These findings are compatible with our previous report that nm23 gene is overexpressed in monocytic leukemia.
Human	CYTB	4519	cytochrome b	NCI, Score=801, Pubmed Id: 2839835, UMLKSK CUI: C1318544 In vitro treatment with interferon gamma substantially increases the level of phagocyte cytochrome b heavy chain gene transcripts in normal polymorphonuclear leukocytes, normal monocyte-derived macrophages, and the monocytic leukemia cell line THP-1.
Human	MLL	4297		GENERIF, Score=923, Pubmed Id: 12547160, UMLKSK CUI: C1318544 t(10;11)(p11.2;q23) involving this and ABI-1 genes is associated with congenital acute monocytic leukemia
Human	MC1R	4157	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	NCI, Score=801, Pubmed Id: 12177778, UMLKSK CUI: C1318544 Flow cytometry studies showed that melanocortin 1 receptor was expressed in in vitro activated monocytes/macrophages and in the THP-1 monocytic leukaemia line at levels of about 1 in 3 to 1 in 5 of that found in melanomas.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1318544	M5b Acute differentiated monocytic leukemia	0		self

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