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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.

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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/

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Script.aculo.us website

NOTE: Only the effects.js and dragdrop.js modules from Script.aculo.us are being used.

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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.

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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.

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tablesort website

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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 - Marginal Zone B-Cell Lymphoma

Debug Stats

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Disease (1)

Marginal Zone B-Cell Lymphoma C1367654

Definition (1)

A usually indolent mature B-cell lymphoma, arising from the marginal zone of lymphoid tissues. It is characterized by the presence of small to medium sized atypical lymphocytes. It comprises three entities, according to the anatomic sites involved: extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue, which affects extranodal sites (most often stomach, lung, skin, and ocular adnexa); nodal marginal zone B-cell lymphoma, which affects lymph nodes without evidence of extranodal disease; and splenic marginal zone B-cell lymphoma, which affects the spleen and splenic hilar lymph nodes, bone marrow, and often the peripheral blood.

Genes (37)

Species:

human : 36

mouse : 1

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Species	Gene	GeneId	Gene Name	Evidence
Mouse	GFI1	2672	growth factor independent 1 transcription repressor	NCI, Score=801, Pubmed Id: 15231650, UMLKSK CUI: C1367654 Heightened expression of Gfi1 distinguishes MZL from other lymphoma types.
Human	TNFRSF13C	115650	tumor necrosis factor receptor superfamily, member 13C	NCI, Score=801, Pubmed Id: 16025281, UMLKSK CUI: C1367654 BAFF-R expression was found only in B-cell lymphoma (44/80, positive cases/examined cases): B-lymphoblastic lymphoma 0/3, B-chronic lymphocytic leukemia/small lymphocytic lymphoma 4/4, mantle cell lymphoma 9/11, follicular lymphoma 10/14, diffuse large B-cell lymphoma (DLBCL) 11/25, marginal zone B-cell lymphoma 8/10, lymphoplasmacytic lymphoma 2/2, plasma cell myeloma 0/2, and Burkitt lymphoma 0/9, but not in T/NK cell lymphomas (0/19) or Hodgkin lymphoma (0/10).
Human	CARD11	84433	caspase recruitment domain family, member 11	NCI, Score=801, Pubmed Id: 17043017, UMLKSK CUI: C1367654 We analyzed the configuration of the CARMA1 gene, encoding a protein that closely interacts with BCL10 and MALT1, in a series of 120 extranodal marginal zone B-cell lymphomas of MALT-type and 35 diffuse large B-cell lymphomas. NCI, Score=801, Pubmed Id: 17043017, UMLKSK CUI: C1367654 CARMA1 and chromosomal translocations in extranodal marginal zone B-cell lymphomas of MALT type or diffuse large B-cell lymphomas.
Human	NUB1	51667	negative regulator of ubiquitin-like proteins 1	NCI, Score=801, Pubmed Id: 2364363, UMLKSK CUI: C1367654 Immunohistologic analysis of paraffin sections revealed the following characteristic immunophenotype of MZL: L26, LN2, NUB1 and T2/48 positive, and LN5, LN1, AF6 and UCHL1 negative.
Human	FOXP1	27086	forkhead box P1	NCI, Score=801, Pubmed Id: 15944719, UMLKSK CUI: C1367654 Further IHC and FISH studies performed on 98 cases of DLBCL and 93 cases of extranodal marginal zone lymphoma showed a high expression of FOXP1 in approximately 13 and 12% of cases, respectively.
Human	SWAP70	23075	SWAP switching B-cell complex 70kDa subunit	NCI, Score=801, Pubmed Id: 15163014, UMLKSK CUI: C1367654 SWAP-70 was strongly expressed in 59 of the 86 cases: 2 of 10 (20%) precursor B-cell lymphoblastic leukemias, 2 of 2 (100%) precursor B-cell lymphoblastic lymphomas, 2 of 4 (50%) mantle cell lymphomas, 7 of 9 (78%) Burkitt lymphomas, 9 of 9 (100%) diffuse large B-cell lymphomas, 8 of 8 (100%) follicular lymphomas, 6 of 6 (100%) nodular lymphocyte predominant Hodgkin lymphomas, 0 of 8 (0%) classic Hodgkin lymphomas, 12 of 13 (92%) chronic lymphocytic leukemias, 3 of 3 (100%) nodal marginal zone lymphomas, 5 of 5 (100%) extranodal marginal zone lymphomas, 1 of 2 (50%) splenic marginal zone lymphomas, 2 of 3 (66%) hairy cell leukemias, and 0 of 4 (0%) plasma cell neoplasms.
Human	MALT1	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1	NCI, Score=801, Pubmed Id: 15377491, UMLKSK CUI: C1367654 Absence of MALT1 translocations in primary cutaneous marginal zone B-cell lymphoma. NCI, Score=801, Pubmed Id: 14652825, UMLKSK CUI: C1367654 Two translocations involving the MALT1 gene have been described in extranodal marginal zone B-cell lymphomas of MALT type. NCI, Score=801, Pubmed Id: 12560219, UMLKSK CUI: C1367654 To determine if comparable events occurred in primary MALT and splenic MZL tumors, 40 cases were analyzed by FISH or QRT-PCR; genomic amplification and MALT1 overexpression were seen in 2 cases. NCI, Score=801, Pubmed Id: 10751367, UMLKSK CUI: C1367654 Recently we demonstrated that the t(11;18)(q21;q21) associated with extranodal marginal zone B cell lymphomas of MALT type results in the expression of a chimeric transcript fusing 5; API2 on chromosome 11 to 3; MLT on chromosome 18. NCI, Score=801, Pubmed Id: 12931213, UMLKSK CUI: C1367654 We conclude that the translocations t(11;18)(q21;q21) and t(14;18)(q21;q32) represent the main structural aberrations involving MLT/MALT1 in MALT lymphomas, whereas true amplifications of MLT/MALT1 occur rarely in MZBCL. NCI, Score=801, Pubmed Id: 10979968, UMLKSK CUI: C1367654 The translocation of chromosome 11, long arm, region 2, band 1, to chromosome 18, long arm, region 2, band 1 (t(11;18)(q21;q21)) represents a recurrent chromosomal abnormality in extranodal marginal zone B-cell lymphoma (MZBCL) of mucosa-associated lymphoid tissue (MALT) type and leads to a fusion of the apoptosis inhibitor-2 (API2) gene on chromosome 11 and the MALT lymphoma-associated translocation (MLT) gene on chromosome 18. NCI, Score=801, Pubmed Id: 12931213, UMLKSK CUI: C1367654 In 19 MALT lymphomas (26%), but in none of the nodal or splenic MZBCL, separated hybridization signals of the MLT/MALT1 flanking probes, were found. NCI, Score=801, Pubmed Id: 12560219, UMLKSK CUI: C1367654 First, 2 cases, one case of MALT lymphoma and another of aggressive marginal zone lymphoma (MZL) with t(14;18)(q32;q21), cytogenetically identical to the translocation involving BCL2, were shown by fluorescence in situ hybridization (FISH) to involve MALT1, which lies about 5 Mb centromeric of BCL2. NCI, Score=801, Pubmed Id: 14997743, UMLKSK CUI: C1367654 The disease entities are primarily exemplified by mantle cell lymphoma (the relative incidence, 3%, related with an aberrant expression of cyclin D1 activated by t(11;14) chromosomal translocation), follicular lymphoma (7%, with BCL2 by t(14;18) translocation), marginal zone B-cell lymphoma of MALT type (8%, with MALT1 by t(11;18) or t(14;18) translocation), adult T-cell leukemia/lymphoma (7%, but 20% in Kyushu, with human T-cell leukemia virus type 1 [HTLV1]), extranodal NK/T-cell lymphoma of nasal type (2%, with Epstein-Barr virus [EBV]), and anaplastic large cell lymphoma (2%, with ALK by t(2;5) translocation). NCI, Score=801, Pubmed Id: 11066071, UMLKSK CUI: C1367654 The t(11;18)(q21;q21) between the inhibitor of apoptosis API2 and the MLT gene is a distinct feature of marginal zone B-cell lymphomas of MALT-type. NCI, Score=801, Pubmed Id: 11066071, UMLKSK CUI: C1367654 Structure of the MLT gene and molecular characterization of the genomic breakpoint junctions in the t(11;18)(q21;q21) of marginal zone B-cell lymphomas of MALT type. NCI, Score=801, Pubmed Id: 15377491, UMLKSK CUI: C1367654 The implication of MALT1 gene in the pathogenesis of primary cutaneous marginal zone B-cell lymphomas (PCMZL) has been a matter of controversy.
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: C1367654 CD100 expression was not detectable in low-grade B-cell non-Hodgkin;s lymphomas, including cases of small lymphocytic lymphoma (18 cases), marginal zone lymphoma (10 cases), and mantle cell lymphoma (10 cases), as might be expected for these neoplasms that are not of follicular center cell origin. NCI, Score=801, Pubmed Id: 9665486, UMLKSK CUI: C1367654 CD100 expression was not detectable in low-grade B-cell non-Hodgkin;s lymphomas, including cases of small lymphocytic lymphoma (18 cases), marginal zone lymphoma (10 cases), and mantle cell lymphoma (10 cases), as might be expected for these neoplasms that are not of follicular center cell origin.
Human	BCL10	8915	B-cell CLL/lymphoma 10	NCI, Score=801, Pubmed Id: 10803524, UMLKSK CUI: C1367654 BCL10, a gene involved in apoptosis signalling, has recently been identified through the cloning of chromosomal breakpoints in extranodal (MALT-type) marginal zone lymphomas carrying the t(1;14)(p22;q32) translocation. NCI, Score=801, Pubmed Id: 11748643, UMLKSK CUI: C1367654 Initially, one case with a novel t(1;2)(p22;p12) translocation involving the BCL10 gene was identified, in a marginal zone lymphoma of the MALT type, and was reported elsewhere. NCI, Score=801, Pubmed Id: 12883238, UMLKSK CUI: C1367654 These data suggest that 1) B. burgdorferi infection may not play an important role in developing cutaneous marginal zone B-cell lymphoma in Asian cases, 2) neither API2-MALT1 fusion nor BCL10 mutation is closely associated with the pathogenesis, 3) aberrant nuclear BCL10 may frequently be expressed in the absence of these genetic abnormalities, and 4) nuclear BCL10 expression may be clinically important because it was observed in locally aggressive tumors. NCI, Score=801, Pubmed Id: 17043017, UMLKSK CUI: C1367654 We analyzed the configuration of the CARMA1 gene, encoding a protein that closely interacts with BCL10 and MALT1, in a series of 120 extranodal marginal zone B-cell lymphomas of MALT-type and 35 diffuse large B-cell lymphomas. NCI, Score=801, Pubmed Id: 12883238, UMLKSK CUI: C1367654 We examined 24 Asian cases of cutaneous marginal zone B-cell lymphoma for B. burgdorferi involvement, API2-MALT1 fusion, BCL10 cellular expression, and BCL10 mutation. NCI, Score=801, Pubmed Id: 16784987, UMLKSK CUI: C1367654 Aberrant nuclear BCL10 expression and lack of t(11;18)(q21;q21) in primary cutaneous marginal zone B-cell lymphoma. NCI, Score=801, Pubmed Id: 10803524, UMLKSK CUI: C1367654 BCL10, a gene involved in apoptosis signalling, has recently been identified through the cloning of chromosomal breakpoints in extranodal (MALT-type) marginal zone lymphomas carrying the t(1;14)(p22;q32) translocation. NCI, Score=801, Pubmed Id: 17274374, UMLKSK CUI: C1367654 [Expression of BCL-10 protein and the relationship with API2-MALT1 fusion gene in extranodal marginal zone B-cell lymphoma of mucosa associated lymphoid tissue] OBJECTIVE: To investigate the relationship of BCL-10 protein and API2-MALT1 fusion gene in MALT lymphoma. NCI, Score=801, Pubmed Id: 16636680, UMLKSK CUI: C1367654 Aberrant nuclear expression of BCL-10 occurs in a subset of extranodal marginal zone B-cell lymphomas (MALT lymphomas), primarily those with the t(1;14)(p22;q32) or t(11;18)(q21;q21). NCI, Score=801, Pubmed Id: 11748643, UMLKSK CUI: C1367654 Initially, one case with a novel t(1;2)(p22;p12) translocation involving the BCL10 gene was identified, in a marginal zone lymphoma of the MALT type, and was reported elsewhere.
Human	TCL1A	8115	T-cell leukemia/lymphoma 1A	NCI, Score=801, Pubmed Id: 10786666, UMLKSK CUI: C1367654 Conversely, TCL1 was not expressed in Hodgkin/Reed-Sternberg cells, multiple myelomas, marginal zone B-cell lymphomas, CD30+ anaplastic large cell lymphoma, lymphoblastic T-cell lymphoma, peripheral T-cell lymphoma, and mycosis fungoides.
Human	D13S25	8101	Disrupted in B-cell neoplasia	NCI, Score=801, Pubmed Id: 10913669, UMLKSK CUI: C1367654 Analysis of the P53, RB/D13S25, and P16 tumor suppressor genes in marginal zone B-cell lymphoma: An interphase fluorescence in situ hybridization study. NCI, Score=801, Pubmed Id: 10913669, UMLKSK CUI: C1367654 Heterozygous deletions of the RB gene (nodal MZBCL) and D13S25 (splenic MZBCL) were found in one case each.
Human	WRN	7486	Werner syndrome, RecQ helicase-like	NCI, Score=801, Pubmed Id: 16738949, UMLKSK CUI: C1367654 WRN Cys1367Arg was associated with decreased risk of NHL overall (OR: 0.71; 95% CI: 0.56-0.91; P = 0.007) and DLBCL (OR: 0.66; 95% CI: 0.45-0.95; P = 0.024), as well as follicular and marginal zone lymphomas.
Human	TNFAIP3	7128	tumor necrosis factor, alpha-induced protein 3	GENERIF, Score=913, Pubmed Id: 17886247, UMLKSK CUI: C1367654 May act as a tumor suppressor gene in ocular adnexal marginal zone B cell lymphoma; loss of this gene may play an important role in lymphomagenesis
Human	SPN	6693	sialophorin	NCI, Score=801, Pubmed Id: 10191768, UMLKSK CUI: C1367654 Three categories of CD43 positivity were found: (1) more than 90% of T-cell lymphoma, mantle cell lymphoma, B-cell small lymphocytic lymphoma, and Burkitt lymphoma cases were positive; (2) 20% to 40% of nodal and extranodal marginal zone lymphoma (MZL), diffuse large B-cell lymphoma, Burkitt-like B-cell lymphoma, and lymphoplasmacytoid lymphoma cases were positive; and (3) 0% to 6% of primary splenic MZL and various types of follicular lymphoma cases were positive. NCI, Score=801, Pubmed Id: 15185428, UMLKSK CUI: C1367654 Six lymphomas were CD43 positive and five of them were extranodal marginal zone B-cell lymphomas. NCI, Score=801, Pubmed Id: 15185428, UMLKSK CUI: C1367654 Our data suggest that CD43 could be useful to separate the group of patients with extranodal marginal zone B-cell lymphomas with unfavorable prognosis from those that have a good prognosis. NCI, Score=801, Pubmed Id: 15894925, UMLKSK CUI: C1367654 Expression of CD43 by B cells is often used as a diagnostic criterion in favor of a B-cell lymphoproliferative disorder, including small lymphocytic lymphoma/chronic lymphocytic leukemia, mantle cell lymphoma, Burkitt lymphoma, precursor B-lymphoblastic lymphoma, and a subset of marginal zone B-cell lymphomas. NCI, Score=801, Pubmed Id: 15948117, UMLKSK CUI: C1367654 Summary To clarify the confusion surrounding the diagnosis of cutaneous lymphoid hyperplasia (CLH) that was formerly described as lymphadenosis benigna cutis, lymphocytoma cutis, or lymphocytic infiltration of Jessner and to assess whether newly recognized diagnoses, such as cutaneous marginal zone lymphoma and pseudolymphomatous folliculitis (PLF), may have been overlooked, we reexamined 55 Japanese cases of nonepidermotropic lymphoproliferative disorder that had previously been diagnosed as ;cutaneous pseudolymphoma.; In all these cases, the immunohistochemical expressions of CD1a, CD3, CD4, CD8, CD20, CD21, CD30, CD43, CD56, CD68, CD79a, kappa and lambda chains, S-100 protein, and latent membrane protein were assessed. NCI, Score=801, Pubmed Id: 12452994, UMLKSK CUI: C1367654 Most or all of the lesions did not stain for CD10, CD43, and bcl-2 protein, and immunostaining for kappa and lambda immunoglobulin light chain restriction was much more useful diagnostically in MZL. NCI, Score=801, Pubmed Id: 9888708, UMLKSK CUI: C1367654 No coexpression of CD20 and CD43 was seen in any case of either MZL or CLH. NCI, Score=801, Pubmed Id: 10478136, UMLKSK CUI: C1367654 The immunoperoxidase technique was used with antibodies against B-cell-associated antigens, including CD20, CD79a, CD10, CD23, CD43, cyclin D1, bcl-2, and kappa and lambda immunoglobulin light chains on formalin-fixed and B5-fixed tissue sections of follicular, small lymphocytic, mantle cell, and marginal zone lymphomas. NCI, Score=801, Pubmed Id: 15894925, UMLKSK CUI: C1367654 The presence of CD43 coexpression in B-cell populations of the terminal ileum, including those of Peyer;s patches, should not be used as a diagnostic parameter to differentiate extranodal marginal zone B-cell lymphoma of MALT type from reactive processes.
Human	SDC1	6382	syndecan 1	NCI, Score=801, Pubmed Id: 15772984, UMLKSK CUI: C1367654 PRDM1 and CD138 were expressed simultaneously in human lymphomas with plasma cell differentiation, but not in marginal zone lymphomas or chronic lymphocytic leukaemias.
Human	PTPRJ	5795	protein tyrosine phosphatase, receptor type, J	NCI, Score=801, Pubmed Id: 12685844, UMLKSK CUI: C1367654 All cases of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma, Burkitt;s lymphoma, and the vast majority of cases of marginal zone B cell lymphoma and most cases of plasmacytoma/myeloma expressed CD148 and CD27.
Human	POU2F2	5452	POU class 2 homeobox 2	NCI, Score=801, Pubmed Id: 16778825, UMLKSK CUI: C1367654 Primary cutaneous marginal zone B-cell lymphoma showed expression of Pax-5, PU.1, Oct2 and BOB.1, but not Bcl-6 by the neoplastic B-cells, and Mum1/IRF4 and Blimp-1 by the neoplastic plasma cells.
Human	PAX5	5079	paired box 5	NCI, Score=801, Pubmed Id: 14676435, UMLKSK CUI: C1367654 Pax5 was strongly expressed in most of the B cell lymphomas; 44 of 47 diffuse large B cell lymphomas (93.6%), 15 of 16 marginal zone B cell lymphomas (93.8%), all 3 mantle cell lymphomas, 2 follicular lymphomas, and 2 Burkitt;s lymphomas (100%). NCI, Score=801, Pubmed Id: 9694719, UMLKSK CUI: C1367654 Eight of 12 (67%) marginal zone lymphoma cases showed negative or low BSAP levels, and 17 of 24 (71%) large B-cell lymphomas displayed moderate to strong expression. NCI, Score=801, Pubmed Id: 9808580, UMLKSK CUI: C1367654 Deregulated PAX-5 transcription from a translocated IgH promoter in marginal zone lymphoma.
Human	NME1	4830	NME/NM23 nucleoside diphosphate kinase 1	NCI, Score=801, Pubmed Id: 16891807, UMLKSK CUI: C1367654 The expression of nm23-H1 protein was immunohistochemically examined in 150 cases of non-Hodgkin;s lymphomas; 85 diffuse large B cell lymphomas (DL-BCL), 18 marginal zone B cell lymphomas (MZL), 3 mantle cell lymphomas, 25 peripheral T cell lymphomas, not otherwise specified (TCLNOS), and 19 NK/T cell lymphomas (NK/T). NCI, Score=801, Pubmed Id: 16891807, UMLKSK CUI: C1367654 The gene mutation of nm23-H1 was detected in 10.3% of DLBCL and 30.7% of NK/T; but none in MZL and TCLNOS. NCI, Score=801, Pubmed Id: 16891807, UMLKSK CUI: C1367654 Eighty-one cases (58 DLBCL, 6 MZL, 4 TCLNOS, and 13 NK/T) were studied for nm23-H1 gene mutation in exon 1 to 5.
Human	MLLT4	4301	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	NCI, Score=801, Pubmed Id: 2364363, UMLKSK CUI: C1367654 Immunohistologic analysis of paraffin sections revealed the following characteristic immunophenotype of MZL: L26, LN2, NUB1 and T2/48 positive, and LN5, LN1, AF6 and UCHL1 negative.
Human	LRMP	4033	lymphoid-restricted membrane protein	NCI, Score=801, Pubmed Id: 16739114, UMLKSK CUI: C1367654 Approximately half of the marginal zone lymphomas were Jaw1/LRMP-positive.
Human	ITGB2	3689	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	NCI, Score=801, Pubmed Id: 8334643, UMLKSK CUI: C1367654 A lower intensity of H-CAM along with a stronger expression of LFA-1, LFA-3, ICAM-1, and BL-CAM were also detected by comparing BZSLL with ILL/MZL.
Human	ITGAL	3683	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	NCI, Score=801, Pubmed Id: 8334643, UMLKSK CUI: C1367654 A lower intensity of H-CAM along with a stronger expression of LFA-1, LFA-3, ICAM-1, and BL-CAM were also detected by comparing BZSLL with ILL/MZL.
Human	IL10	3586	interleukin 10	GENERIF, Score=1000, Pubmed Id: 17990180, UMLKSK CUI: C1367654 study did not support an important role of the proximal IL-10-1082, IL-10-819, IL-10-592 polymorphisms in increased risk of developing follicular lymphoma, marginal zone lymphoma and mantle cell lymphoma
Human	HOXC5	3222	homeobox C5	NCI, Score=801, Pubmed Id: 9354682, UMLKSK CUI: C1367654 In contrast, HOXC5 expression was found in only 26 of 87 NHLs and appeared to be preferentially expressed by two specific subsets of lymphomas, ie, primary cutaneous anaplastic T-cell lymphomas (9 of 9) and extranodal marginal zone B-cell lymphomas (maltomas; 7 of 9).

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1367654	Marginal Zone B-Cell Lymphoma	0		self

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