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,
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// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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// 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 Lymphoma (neoplasm)

Debug Stats

### Total Build Time: 17 ms 46.362 KB
CONCEPT_NAME gt=0 Completed: 0 ms rowSize= 356 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 263 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=1 ms Completed: 1 ms rowSize= 3.897 KB
CONCEPT_GENES gt=12 ms Completed: 12 ms rowSize= 40.627 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.163 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Low Grade Lymphoma (neoplasm) C0079747

Definition (1)

A type of lymphoma that tends to grow and spread slowly, and has few symptoms. Also called indolent lymphoma.

Relationships (6)

Relation Types:

diso_to_anat : 1

diso_to_chem : 1

diso_to_diso : 4

Relationships:

is_abnormal_cell_of_disease : 1

isa : 3

may_treat : 1

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_CHEM		may_treat	IBRITUMOMAB TIUXETAN C0877880
DISO_to_DISO		isa	Low Grade Adult Non-Hodgkin's Lymphoma C0278885
DISO_to_DISO		isa	Low Grade B-Cell Non-Hodgkin's Lymphoma C1518004
DISO_to_DISO		permuted_term_of	Low Grade Lymphoma (neoplasm) C0079747
DISO_to_DISO		isa	Low Grade T-Cell Lymphoma C0456876

Genes (26)

Species:

human : 26

Page Size

Current 25

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Page 1 of 2

Prior Page

Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	MADCAM1	8174	mucosal vascular addressin cell adhesion molecule 1	NCI, Score=801, Pubmed Id: 11504840, UMLKSK CUI: C0079747 In this study, we examined the lymphocytic homing receptor alpha4beta7 integrin, L-selectin, and VLA-4 and mucosal addressin cell adhesion molecule-1 (MAdCAM-1) in low-grade lymphoma of the gastrointestinal tract and other organs such as the ocular adnexa and thyroid.
Human	XRCC5	7520	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	NCI, Score=801, Pubmed Id: 15215044, UMLKSK CUI: C0079747 Low-grade lymphoma, appearing as chronic lymphocytic leukaemia (CLL) displayed a significantly lower frequency of cells staining positive for DNA-PKcs and Ku86, but surprisingly not for Ku70, compared with acute lymphoblastic leukaemia (ALL) cells. NCI, Score=801, Pubmed Id: 15215044, UMLKSK CUI: C0079747 High-grade lymphoma lymph node samples showed an increased frequency of cells staining positive for DNA-PKcs, Ku86 and Ki-67 compared with lymph node samples from low-grade lymphoma patients.
Human	VEGFA	7422	vascular endothelial growth factor A	GENERIF, Score=1000, Pubmed Id: 12607599, UMLKSK CUI: C0079747 VEGF, but not bFGF, was associated with higher tumor grading of NHL and high-grade transformation of low-grade lymphoma
Human	TOP2A	7153	topoisomerase (DNA) II alpha 170kDa	NCI, Score=801, Pubmed Id: 9059350, UMLKSK CUI: C0079747 RESULTS: Levels of topoisomerase II alpha mRNA correlated strongly with the Ki-67 labelling index and were higher in high grade than in low grade lymphomas.
Human	TMPO	7112	thymopoietin	NCI, Score=801, Pubmed Id: 6198843, UMLKSK CUI: C0079747 Eight patients with cutaneous T-cell lymphomas (6 patients with mycosis fungoides, 1 patient with Sezary;s syndrome, 1 patient with low-grade malignant lymphoma, unclassified) were treated with TP-5, a synthetic pentapeptide having the same biologic activity as the thymic hormone thymopoietin.
Human	TGFBR3	7049	transforming growth factor, beta receptor III	GENERIF, Score=1000, Pubmed Id: 14704634, UMLKSK CUI: C0079747 expression values for TGF 1 and its receptors I, II, and III were twice as high in the group of patients with a diagnosis of high-grade lymphomas as in the group of patients diagnosed with low-grade lymphomas
Human	TGFBR2	7048	transforming growth factor, beta receptor II (70/80kDa)	GENERIF, Score=1000, Pubmed Id: 14704634, UMLKSK CUI: C0079747 expression values for TGF 1 and its receptors I, II, and III were twice as high in the group of patients with a diagnosis of high-grade lymphomas as in the group of patients diagnosed with low-grade lymphomas
Human	TGFBR1	7046	transforming growth factor, beta receptor 1	GENERIF, Score=1000, Pubmed Id: 14704634, UMLKSK CUI: C0079747 expression values for TGF 1 and its receptors I, II, and III were twice as high in the group of patients with a diagnosis of high-grade lymphomas as in the group of patients diagnosed with low-grade lymphomas
Human	TGFB1	7040	transforming growth factor, beta 1	GENERIF, Score=1000, Pubmed Id: 14704634, UMLKSK CUI: C0079747 expression values for TGF 1 and its receptors I, II, and III were twice as high in the group of patients with a diagnosis of high-grade lymphomas as in the group of patients diagnosed with low-grade lymphomas
Human	TFRC	7037	transferrin receptor (p90, CD71)	NCI, Score=801, Pubmed Id: 3355978, UMLKSK CUI: C0079747 However, transferrin receptor expression by certain histologic subtypes of lymphoma did not correlate with their morphologic grade: low-grade follicular lymphomas expressed the T9 antigen more frequently than diffuse low-grade lymphomas; diffuse small cleaved cell lymphomas were stained by OKT9 less often than other histologic subtypes of intermediate-grade lymphomas; and diffuse immunoblastic lymphomas expressed transferrin receptors less often than the other high-grade histologic subtypes of non-Hodgkins lymphoma. NCI, Score=801, Pubmed Id: 3106247, UMLKSK CUI: C0079747 Expression of the activation-associated 4F2 antigen, transferrin receptor and interleukin-2 (IL-2) receptor on suspended cells from 75 biopsied low-grade non-Hodgkin lymphomas (L-NHL) of B-cell origin was correlated to patient survival, clinical prognostic parameters and estimated DNA synthesis. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 CD antigens 5, 10, and 23 were expressed significantly more often by low grade lymphomas whereas CD38, 4F2 antigen, and transferrin receptor were more often expressed by high grade lymphomas. NCI, Score=801, Pubmed Id: 3549812, UMLKSK CUI: C0079747 In cutaneous lymphomas of high grade malignancy the TFR was expressed in virtually all cells compared to only 25-75% in low grade lymphomas. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 4F2 antigen and transferrin receptor may identify a poor prognostic group of cases in low grade lymphoma but we conclude that phenotyping B-cell NHL for many of the antigens expressed at various stages of B-cell differentiation and activation does not provide clinically useful information in addition to that obtained from standard histological classifications.
Human	SPN	6693	sialophorin	NCI, Score=801, Pubmed Id: 15256428, UMLKSK CUI: C0079747 Malignancy in these low-grade lymphomas is often inferred by immunoglobulin light-chain restriction and expression of CD43; molecular genetic evidence is sought only if these are in doubt.
Human	SLC3A2	6520	solute carrier family 3 (amino acid transporter heavy chain), member 2	NCI, Score=801, Pubmed Id: 3106247, UMLKSK CUI: C0079747 Expression of the activation-associated 4F2 antigen, transferrin receptor and interleukin-2 (IL-2) receptor on suspended cells from 75 biopsied low-grade non-Hodgkin lymphomas (L-NHL) of B-cell origin was correlated to patient survival, clinical prognostic parameters and estimated DNA synthesis. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 CD antigens 5, 10, and 23 were expressed significantly more often by low grade lymphomas whereas CD38, 4F2 antigen, and transferrin receptor were more often expressed by high grade lymphomas. NCI, Score=801, Pubmed Id: 1698116, UMLKSK CUI: C0079747 For example, in the intermediate-grade category less than one half of diffuse small cleaved cell lymphomas were 4F2 positive, and expression was weak, similar to that of low-grade lymphomas. NCI, Score=801, Pubmed Id: 1698116, UMLKSK CUI: C0079747 Approximately one half of all low-grade lymphomas, two thirds of intermediate-grade lymphomas, and all high-grade lymphomas were 4F2 positive. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 CD antigens 5, 10, and 23 were expressed significantly more often by low grade lymphomas whereas CD38, 4F2 antigen, and transferrin receptor were more often expressed by high grade lymphomas. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 4F2 antigen and transferrin receptor may identify a poor prognostic group of cases in low grade lymphoma but we conclude that phenotyping B-cell NHL for many of the antigens expressed at various stages of B-cell differentiation and activation does not provide clinically useful information in addition to that obtained from standard histological classifications. NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 4F2 antigen and transferrin receptor may identify a poor prognostic group of cases in low grade lymphoma but we conclude that phenotyping B-cell NHL for many of the antigens expressed at various stages of B-cell differentiation and activation does not provide clinically useful information in addition to that obtained from standard histological classifications.
Human	SKP2	6502	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	NCI, Score=801, Pubmed Id: 12351407, UMLKSK CUI: C0079747 Our data provide evidence for p27(Kip1) degradative function of Skp2 in low-grade lymphomas.
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	NCI, Score=801, Pubmed Id: 8956779, UMLKSK CUI: C0079747 Besides this heterogeneity, a general trend towards highly malignant samples expressing higher nm23-H1/NDPK-A, levels than the low-grade lymphomas was observed.
Human	MME	4311	membrane metallo-endopeptidase	GENERIF, Score=923, Pubmed Id: 17296585, UMLKSK CUI: C0079747 MUM1 expression dichotomises follicular lymphoma (FL) into low-grade FL of CD10+/Bcl-6+/MUM1-/Ki-67low phenotype, and high-grade FL of CD10+/- /Bcl-6+/weak/MUM1+/ Ki-67high phenotype
Human	MKI67	4288	antigen identified by monoclonal antibody Ki-67	GENERIF, Score=923, Pubmed Id: 17296585, UMLKSK CUI: C0079747 MUM1 expression dichotomises follicular lymphoma (FL) into low-grade FL of CD10+/Bcl-6+/MUM1-/Ki-67low phenotype, and high-grade FL of CD10+/- /Bcl-6+/weak/MUM1+/ Ki-67high phenotype
Human	ITGB2	3689	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	NCI, Score=801, Pubmed Id: 2642732, UMLKSK CUI: C0079747 Eighty percent of initial biopsy specimens of low-grade lymphoma exhibited LFA-1 expression, whereas only 8% of recurrent specimens retained expression of both LFA-1 subunits.
Human	ITGAL	3683	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	NCI, Score=801, Pubmed Id: 2642732, UMLKSK CUI: C0079747 Eighty percent of initial biopsy specimens of low-grade lymphoma exhibited LFA-1 expression, whereas only 8% of recurrent specimens retained expression of both LFA-1 subunits.
Human	IRF4	3662	interferon regulatory factor 4	GENERIF, Score=923, Pubmed Id: 17296585, UMLKSK CUI: C0079747 MUM1 expression dichotomizes follicular lymphoma (FL) into low-grade FL of CD10+/Bcl-6+/MUM1-/Ki-67low phenotype, and high-grade FL of CD10+/- /Bcl-6+/weak/MUM1+/ Ki-67high phenotype
Human	IL1A	3552	interleukin 1, alpha	NCI, Score=801, Pubmed Id: 11423389, UMLKSK CUI: C0079747 Subgroup analyses according to histology [diffuse large B-cell lymphoma (DLBL), follicular lymphoma, low-grade lymphoma of mucosa associated lymphoid tissue, and others] failed to illustrate differences except for DLBL which showed a possible association with IL-1A and IL-1B polymorphisms.
Human	ICAM3	3385	intercellular adhesion molecule 3	NCI, Score=801, Pubmed Id: 8946680, UMLKSK CUI: C0079747 ICAM-3 expression in endothelial cells of NHL was significantly more frequent in high grade (40%) than in low grade lymphomas (14%) (p = 0.012). NCI, Score=801, Pubmed Id: 8946680, UMLKSK CUI: C0079747 ICAM-3 expression in endothelial cells of NHL was significantly more frequent in high grade (40%) than in low grade lymphomas (14%) (p = 0.012).
Human	XRCC6	2547	X-ray repair complementing defective repair in Chinese hamster cells 6	NCI, Score=801, Pubmed Id: 15215044, UMLKSK CUI: C0079747 Low-grade lymphoma, appearing as chronic lymphocytic leukaemia (CLL) displayed a significantly lower frequency of cells staining positive for DNA-PKcs and Ku86, but surprisingly not for Ku70, compared with acute lymphoblastic leukaemia (ALL) cells.
Human	CD38	952	CD38 molecule	NCI, Score=801, Pubmed Id: 2593045, UMLKSK CUI: C0079747 CD antigens 5, 10, and 23 were expressed significantly more often by low grade lymphomas whereas CD38, 4F2 antigen, and transferrin receptor were more often expressed by high grade lymphomas.
Human	MS4A1	931	membrane-spanning 4-domains, subfamily A, member 1	NCI, Score=801, Pubmed Id: 11830481, UMLKSK CUI: C0079747 Flow cytometric analysis demonstrated that B-CLL cells express CD20 with a fluorescence intensity that is significantly weaker than that of normal CD5(+) and CD5(-) B cells and that of malignant CD5(-) low-grade non-Hodgkin lymphoma cells.
Human	CCND3	896	cyclin D3	NCI, Score=801, Pubmed Id: 9376597, UMLKSK CUI: C0079747 In other B-cell lymphomas (n = 55), including chronic lymphocytic leukemia, low-grade lymphomas of mucosa-associated lymphatic tissue, follicular lymphomas, and diffuse large B-cell lymphomas, no cyclin D1 expression could be detected and 89% of these cases displayed cyclin D3 positivity.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0079747	Low Grade Lymphoma (neoplasm)	0		self

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