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 - Malignant Lymphoma, Large Cell Type

Debug Stats

### Total Build Time: 45 ms 48.581 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 368 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=14 ms Completed: 14 ms rowSize= 3.363 KB
CONCEPT_GENES gt=28 ms Completed: 28 ms rowSize= 43.619 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.169 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Malignant Lymphoma, Large Cell Type C1518189

Relationships (6)

Relation Types:

diso_to_anat : 1

diso_to_diso : 5

Relationships:

is_abnormal_cell_of_disease : 1

isa : 5

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_abnormal_cell_of_disease	Neoplastic Cell C0597032
DISO_to_DISO		isa	AIDS Associated Diffuse Large Cell Lymphoma C0281242
DISO_to_DISO		isa	Adult Diffuse Histiocytic Lymphoma C0278762
DISO_to_DISO		isa	Childhood Large Cell Lymphoma C0281710
DISO_to_DISO		isa	Malignant Lymphoma, Histiocytic, Diffuse C1521844
DISO_to_DISO		isa	Malignant Lymphoma, Large Cell, Cleaved and Non-Cleaved C1521845

Genes (37)

Species:

human : 35

mouse : 2

Page Size

Current 25

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Current 1

Species	Gene	GeneId	Gene Name	Evidence
Mouse	TLX1	3195	T-cell leukemia homeobox 1	NCI, Score=801, Pubmed Id: 9811890, UMLKSK CUI: C1518189 During their second year of life, all HOX11 transgenic mice became terminally ill with more than 75% developing large cell lymphomas in the spleen, which frequently disseminated to thymus, lymph nodes, and other nonhematopoietic tissues. NCI, Score=801, Pubmed Id: 9811890, UMLKSK CUI: C1518189 During their second year of life, all HOX11 transgenic mice became terminally ill with more than 75% developing large cell lymphomas in the spleen, which frequently disseminated to thymus, lymph nodes, and other nonhematopoietic tissues.
Mouse	ANXA2	302	annexin A2	NCI, Score=801, Pubmed Id: 8263043, UMLKSK CUI: C1518189 Extracellular annexin II is associated with divalent cation-dependent tumor cell-endothelial cell adhesion of metastatic RAW117 large-cell lymphoma cells.
Human	LUZP4	51213	leucine zipper protein 4	NCI, Score=801, Pubmed Id: 12538465, UMLKSK CUI: C1518189 In B-cell lymphomas, the most frequent expression of CT genes was observed in diffuse large-cell lymphomas (HOM-TES-14/SCP-1: 7 of 28; SSX-1: 5 of 28; CT-7: 2 of 28; and HOM-MEL-40/SSX-2 and HOM-TES-85: 1 of 28 positive cases).
Human	CHEK2	11200	checkpoint kinase 2	NCI, Score=801, Pubmed Id: 12393693, UMLKSK CUI: C1518189 However, 5 tumors, one typical MCL, 2 blastoid MCLs, and 2 large cell lymphomas, showed marked loss of protein expression, including 2 samples with complete absence of CHK2 protein. NCI, Score=801, Pubmed Id: 12393693, UMLKSK CUI: C1518189 However, 5 tumors, one typical MCL, 2 blastoid MCLs, and 2 large cell lymphomas, showed marked loss of protein expression, including 2 samples with complete absence of CHK2 protein.
Human	SEMA4D	10507	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	NCI, Score=801, Pubmed Id: 9665486, UMLKSK CUI: C1518189 Surprisingly, we found that the vast majority of follicular lymphomas (37 of 40 cases) as well as diffuse large-cell lymphomas of B-cell type (35 cases) did not express CD100.
Human	MAGEC1	9947	melanoma antigen family C, 1	NCI, Score=801, Pubmed Id: 12538465, UMLKSK CUI: C1518189 In B-cell lymphomas, the most frequent expression of CT genes was observed in diffuse large-cell lymphomas (HOM-TES-14/SCP-1: 7 of 28; SSX-1: 5 of 28; CT-7: 2 of 28; and HOM-MEL-40/SSX-2 and HOM-TES-85: 1 of 28 positive cases).
Human	TNFRSF4	7293	tumor necrosis factor receptor superfamily, member 4	NCI, Score=801, Pubmed Id: 10233901, UMLKSK CUI: C1518189 In contrast, large numbers of OX40/CD134(+) tumors cells were typical of angioimmunoblastic lymphoma (15/16 [94%]), angiocentric lymphoma (4/4), a subset of large-cell lymphomas (10/21 [48%]), and lymphomas with a prominent histiocytic component (6/7 [86%]).
Human	TFRC	7037	transferrin receptor (p90, CD71)	NCI, Score=801, Pubmed Id: 11100630, UMLKSK CUI: C1518189 Cytomorphological studies disclosed a large-cell lymphoma with a population of cells demonstrating intermediate CD45 expression and partial coexpression of CD20 and CD23 markers, as well as universal expression of HLA-DR, CD71, CD38, and CD-30.
Human	TAL1	6886	T-cell acute lymphocytic leukemia 1	NCI, Score=801, Pubmed Id: 11781220, UMLKSK CUI: C1518189 Among the quiescent genes activated by rearrangement, expression of cyclin D1 (due to rearrangement of the CCND1 [BCL-1] gene) is a near-specific marker of t(11;14) in mantle cell lymphoma; BCL-2 expression distinguishes follicular lymphoma cells from their nonneoplastic counterparts in reactive germinal centers and appears to be an independent prognostic marker in diffuse large cell lymphoma; and TAL-1 (SCL) expression identifies T-cell acute lymphoblastic neoplasms in which this gene is activated.
Human	SYCP1	6847	synaptonemal complex protein 1	NCI, Score=801, Pubmed Id: 12538465, UMLKSK CUI: C1518189 In B-cell lymphomas, the most frequent expression of CT genes was observed in diffuse large-cell lymphomas (HOM-TES-14/SCP-1: 7 of 28; SSX-1: 5 of 28; CT-7: 2 of 28; and HOM-MEL-40/SSX-2 and HOM-TES-85: 1 of 28 positive cases).
Human	SSX1	6756	synovial sarcoma, X breakpoint 1	NCI, Score=801, Pubmed Id: 12538465, UMLKSK CUI: C1518189 In B-cell lymphomas, the most frequent expression of CT genes was observed in diffuse large-cell lymphomas (HOM-TES-14/SCP-1: 7 of 28; SSX-1: 5 of 28; CT-7: 2 of 28; and HOM-MEL-40/SSX-2 and HOM-TES-85: 1 of 28 positive cases).
Human	SPN	6693	sialophorin	NCI, Score=801, Pubmed Id: 7801900, UMLKSK CUI: C1518189 Coexpression of the T-cell marker CD43 (Leu-22) was the most common immunophenotypic abnormality, seen in 60% of mantle cell lymphomas (MCL), 39% of CLL/small lymphocytic lymphomas, 16% of diffuse large cell lymphomas (DLCL), but only 5% of follicular lymphomas (FL).
Human	SELL	6402	selectin L	NCI, Score=801, Pubmed Id: 3310610, UMLKSK CUI: C1518189 Subclassification of the lymphomas with the use of the International Working Formulation showed that most small lymphocytic, intermediate lymphocytic, and diffuse large cell lymphomas and about half of diffuse small cleaved, diffuse mixed, and follicular lymphomas expressed Leu-8. NCI, Score=801, Pubmed Id: 3310610, UMLKSK CUI: C1518189 These results indicate that Leu-8 is expressed on a wide variety of B-cell lymphomas and that differences in Leu-8 expression may be useful in the diagnostic separation of small lymphocytic lymphoma with plasmacytoid features from multiple myeloma/plasmacytoma, and diffuse large cell lymphoma from Burkitts lymphoma.
Human	SDC1	6382	syndecan 1	NCI, Score=801, Pubmed Id: 15507667, UMLKSK CUI: C1518189 To explore the possibility for giving accurate real time quantitative RT-PCR results, cDNA obtained from matched frozen, Bouin-fixed and formalin-fixed neoplastic samples (two diffuse large cell lymphomas, one plasmacytoma) was tested for the following target genes: CD40, Aquaporin-3, BLIMP1, IRF4, Syndecan-1.
Human	PRIM1	5557	primase, DNA, polypeptide 1 (49kDa)	NCI, Score=801, Pubmed Id: 1429873, UMLKSK CUI: C1518189 The deoxyribonucleoprotein-ribonucleoprotein complexes contain RNA and DNA polymerase and primase activities and were isolated from nuclei of murine RAW117 large-cell lymphoma cells by restriction digestion with Msp-I, gentle extraction with solutions containing MgCl2, but without chelating agents, and low ionic strength gel electrophoresis.
Human	SERPINB9	5272	serpin peptidase inhibitor, clade B (ovalbumin), member 9	NCI, Score=801, Pubmed Id: 11756176, UMLKSK CUI: C1518189 In nodal T-anaplastic large cell lymphomas and peripheral T-cell lymphomas (not otherwise specified), PI9 expression occurred less frequently.
Human	PAX5	5079	paired box 5	NCI, Score=801, Pubmed Id: 10350329, UMLKSK CUI: C1518189 Thus, an understanding of the PAX-5 gene;s physiological role in B-cell development and the pathological role in tumorigenesis may lead to the optimal clinical treatment strategy for LPL and LPL-derived diffuse large cell lymphoma (DLCL). NCI, Score=801, Pubmed Id: 8650231, UMLKSK CUI: C1518189 Deregulation of PAX-5 by translocation of the Emu enhancer of the IgH locus adjacent to two alternative PAX-5 promoters in a diffuse large-cell lymphoma. NCI, Score=801, Pubmed Id: 8650231, UMLKSK CUI: C1518189 The human PAX-5 gene is located on chromosome 9 in region p13, which is involved in t(9;14)(pl3;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype and in derived large-cell lymphomas. NCI, Score=801, Pubmed Id: 9694719, UMLKSK CUI: C1518189 The high levels of BSAP, especially those found in large-cell lymphomas and in some follicular lymphomas, may be a consequence of deregulated gene expression and suggest a possible involvement of PAX-5 in certain B-cell malignancies. NCI, Score=801, Pubmed Id: 11460166, UMLKSK CUI: C1518189 Here we report that an aberrant hypermutation activity targets multiple loci, including the proto-oncogenes PIM1, MYC, RhoH/TTF (ARHH) and PAX5, in more than 50% of diffuse large-cell lymphomas (DLCLs), which are tumours derived from germinal centres.
Human	NPM1	4869	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	NCI, Score=801, Pubmed Id: 10779993, UMLKSK CUI: C1518189 The tumor cells expressed the CD30 antigen and reacted with the ALK1 antibody, suggesting the presence of the nucleophosmin-anaplastic large cell lymphoma kinase (NPM/ALK) fusion protein.
Human	MTAP	4507	methylthioadenosine phosphorylase	NCI, Score=801, Pubmed Id: 9591637, UMLKSK CUI: C1518189 Codeletion of CDKN2 and MTAP genes in a subset of non-Hodgkin;s lymphoma may be associated with histologic transformation from low-grade to diffuse large-cell lymphoma.
Human	SMAD1	4086	SMAD family member 1	NCI, Score=801, Pubmed Id: 15470494, UMLKSK CUI: C1518189 This study focuses on Smad1 signaling pathway in non-Hodgkin lymphoma cells including follicular or large-cell lymphoma cells.
Human	ITGB2	3689	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	NCI, Score=801, Pubmed Id: 2887833, UMLKSK CUI: C1518189 Furthermore, in an initial survey, the tumours from 5 of 7 patients with non-relapsing large cell lymphomas expressed LFA-1 whereas only 3 of 18 patients with relapsing lymphomas had tumours that did so. NCI, Score=801, Pubmed Id: 2642732, UMLKSK CUI: C1518189 However, we found no correlation between LFA-1 expression and clinical course in a series of 64 patients with diffuse large cell lymphomas. NCI, Score=801, Pubmed Id: 1974938, UMLKSK CUI: C1518189 Adhesion molecules in the prognosis of diffuse large-cell lymphoma: expression of a lymphocyte homing receptor (CD44), LFA-1 (CD11a/18), and ICAM-1 (CD54). NCI, Score=801, Pubmed Id: 1974938, UMLKSK CUI: C1518189 To investigate whether lymphocyte adhesion molecules involved in the migration of normal lymphocytes, i.e., CD44 homing receptor, LFA-1 (CD11a/18), and ICAM-1 (CD54), also play a role in the spread and hence in the disease course of non-Hodgkin;s lymphomas (NHL), expression of these molecules was examined in 78 cases of diffuse large-cell lymphoma. NCI, Score=801, Pubmed Id: 1546685, UMLKSK CUI: C1518189 Large cell lymphomas often involve the stomach; commonly express the lymphocyte adhesion molecules CD44, LFA-1 (CD11a and CD18), and CD54; and may express monotypic cytoplasmic immunoglobulin in approximately one third of cases.
Human	ITGAL	3683	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	NCI, Score=801, Pubmed Id: 2887833, UMLKSK CUI: C1518189 Furthermore, in an initial survey, the tumours from 5 of 7 patients with non-relapsing large cell lymphomas expressed LFA-1 whereas only 3 of 18 patients with relapsing lymphomas had tumours that did so. NCI, Score=801, Pubmed Id: 1546685, UMLKSK CUI: C1518189 Large cell lymphomas often involve the stomach; commonly express the lymphocyte adhesion molecules CD44, LFA-1 (CD11a and CD18), and CD54; and may express monotypic cytoplasmic immunoglobulin in approximately one third of cases. NCI, Score=801, Pubmed Id: 2642732, UMLKSK CUI: C1518189 However, we found no correlation between LFA-1 expression and clinical course in a series of 64 patients with diffuse large cell lymphomas. NCI, Score=801, Pubmed Id: 1974938, UMLKSK CUI: C1518189 Adhesion molecules in the prognosis of diffuse large-cell lymphoma: expression of a lymphocyte homing receptor (CD44), LFA-1 (CD11a/18), and ICAM-1 (CD54). NCI, Score=801, Pubmed Id: 1974938, UMLKSK CUI: C1518189 To investigate whether lymphocyte adhesion molecules involved in the migration of normal lymphocytes, i.e., CD44 homing receptor, LFA-1 (CD11a/18), and ICAM-1 (CD54), also play a role in the spread and hence in the disease course of non-Hodgkin;s lymphomas (NHL), expression of these molecules was examined in 78 cases of diffuse large-cell lymphoma.
Human	HLA-G	3135		NCI, Score=801, Pubmed Id: 14708718, UMLKSK CUI: C1518189 Our investigations in lymphoproliferative disorders show (i) a frequent and variable distribution of alternatively spliced HLA-G mRNA isoforms, (ii) a rare cell surface expression in diffuse large cell lymphomas with HLA class I loss in half of cases, and (iii) an increased serum level of sHLA-G in half of cases.
Human	FLT4	2324	fms-related tyrosine kinase 4	NCI, Score=801, Pubmed Id: 10590384, UMLKSK CUI: C1518189 Nonvascular tumors (including perivascular tumors, other sarcomas, melanomas, carcinomas, and large cell lymphomas) consistently were negative whereas tumor neovascularization commonly was VEGFR-3 positive.
Human	FCER2	2208	Fc fragment of IgE, low affinity II, receptor for (CD23)	NCI, Score=801, Pubmed Id: 11100630, UMLKSK CUI: C1518189 Cytomorphological studies disclosed a large-cell lymphoma with a population of cells demonstrating intermediate CD45 expression and partial coexpression of CD20 and CD23 markers, as well as universal expression of HLA-DR, CD71, CD38, and CD-30.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1518189	Malignant Lymphoma, Large Cell Type	0		self

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