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 - Immunoblastic Lymphadenopathy

Debug Stats

### Total Build Time: 46 ms 42.004 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 420 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 390 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= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=2 ms Completed: 2 ms rowSize= 565 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=4 ms Completed: 4 ms rowSize= 2.815 KB
CONCEPT_RELATIONSHIPS gt=23 ms Completed: 23 ms rowSize= 15.766 KB
CONCEPT_GENES gt=12 ms Completed: 12 ms rowSize= 20.698 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 (2)

Immunoblastic Lymphadenopathy C0020981

Angioimmunoblastic Lymphadenopathy

Definition (1)

An aggressive (fast-growing) type of T-cell non-Hodgkin lymphoma marked by enlarged lymph nodes and hypergammaglobulinemia (increased antibodies in the blood). Other symptoms may include a skin rash, fever, weight loss, or night sweats.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0024314

Ancestral Roots

Root	Root Plus One	Depth	Parent
Immune System Diseases C0021053	Immunoproliferative Disorders C0021070	4	Lymphoproliferative Disorders C0024314
Hemic and Lymphatic Diseases C0018981	Lymphatic Diseases C0024228	4	Lymphoproliferative Disorders C0024314

Relationships (63)

Relation Types:

diso_to_anat : 30

diso_to_chem : 3

diso_to_diso : 28

diso_to_phen : 2

Relationships:

none : 15

is_abnormal_cell_of_disease : 6

is_finding_of_disease : 3

is_normal_cell_origin_of_disease : 5

is_normal_tissue_origin_of_disease : 2

is_not_abnormal_cell_of_disease : 2

is_not_normal_cell_origin_of_disease : 4

is_primary_anatomic_site_of_disease : 2

isa : 7

may_be_abnormal_cell_of_disease : 4

may_be_associated_disease_of_disease : 1

may_be_cytogenetic_abnormality_of_disease : 3

may_be_finding_of_disease : 5

may_be_molecular_abnormality_of_disease : 3

permuted_term_of : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	55		Lymphoma, T-Cell C0079772
DISO_to_DISO	34		Lymphoma, T-Cell C0079772
DISO_to_DISO	25		Lymphoma, T-Cell, Peripheral C0079774
DISO_to_DISO	21		Complication Aspects C1171258
DISO_to_DISO	13		Lymphoma, T-Cell, Peripheral C0079774
DISO_to_PHEN	11		genetic aspects C0017399
DISO_to_PHEN	10		genetic aspects C0017399
DISO_to_ANAT	6		Helper-Inducer T-Lymphocyte C0018894
DISO_to_ANAT	6		T-Lymphocyte C0039194
DISO_to_ANAT	5		Lymph Nodes C0024204
DISO_to_CHEM	5		Antigens, CD C0003322
DISO_to_ANAT	4		In Blood C0005768
DISO_to_ANAT	4		Plasma Cells C0032112
DISO_to_CHEM	4		Apoptosis Regulator C1564881
DISO_to_CHEM	4		Neprilysin C0025250
DISO_to_ANAT		is_abnormal_cell_of_disease	Atypical lymphocyte C0221277
DISO_to_ANAT		is_normal_cell_origin_of_disease	CD4 Positive T Lymphocytes C0039215
DISO_to_ANAT		is_not_abnormal_cell_of_disease	Cells, Reed-Sternberg C0085133
DISO_to_ANAT		is_normal_tissue_origin_of_disease	HEMOLYMPHORETICULAR TISSUE C1512398
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Hematopoietic and Lymphatic System C1512394
DISO_to_ANAT		is_normal_cell_origin_of_disease	Hematopoietic and Lymphoid Cell C1512385
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Lymphatic System C0024235
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Lymphatic Tissue C0024296
DISO_to_ANAT		is_normal_cell_origin_of_disease	Lymphocyte C0024264
DISO_to_ANAT		is_not_normal_cell_origin_of_disease	Myeloid Cells C0887899

Genes (15)

Species:

human : 15

Species	Gene	GeneId	Gene Name	Evidence
Human	PDCD1LG2	80380	programmed cell death 1 ligand 2	GENERIF, Score=1000, Pubmed Id: 18479731, UMLKSK CUI: C0020981 Programmed death 1 is a marker of angioimmunoblastic T-cell lymphoma and B-cell small lymphocytic lymphoma/chronic lymphocytic leukemia
Human	LEF1	51176	lymphoid enhancer-binding factor 1	NCI, Score=801, Pubmed Id: 12707037, UMLKSK CUI: C0020981 Of the Th1-like PTCL studied, 33 of 42 (79%) were immunoreactive for LEF-1 and 32 of 42 (76%) were immunoreactive for TCF-1, including most cases of angioimmunoblastic lymphoma and all cases of lymphoepithelioid lymphoma.
Human	CXCL13	10563	chemokine (C-X-C motif) ligand 13	GENERIF, Score=1000, Pubmed Id: 19095563, UMLKSK CUI: C0020981 The similar pattern of expression of CXCL13 and PD-1 in angioimmunoblastic T-cell lymphoma provides further evidence that AITL is a neoplasm derived from germinal-center T-helper cells
Human	CXCR4	7852	chemokine (C-X-C motif) receptor 4	NCI, Score=801, Pubmed Id: 12645345, UMLKSK CUI: C0020981 Tumors previously identified as exhibiting a composite Th1-like immunophenotype, which include angioimmunoblastic lymphoma, lymphoepithelioid lymphoma, and other peripheral T-cell lymphomas now termed unspecified, were positive for CXCR4/CD184 in 7 (17%) of 41 cases.
Human	VEGFA	7422	vascular endothelial growth factor A	GENERIF, Score=1000, Pubmed Id: 18006812, UMLKSK CUI: C0020981 VEGF is expressed not only by reactive cells, but also by neoplastic cells, and NF-kappaB activation is uncommon in angioimmunoblastic lymphoma, as suggested by frequent exclusively cytoplasmic c-REL localization
Human	TNFRSF4	7293	tumor necrosis factor receptor superfamily, member 4	NCI, Score=801, Pubmed Id: 12958063, UMLKSK CUI: C0020981 In AILD, almost all cases were immunoreactive for OX40/CD134 (96%) and for CXCR3 (89%). NCI, Score=801, Pubmed Id: 11426518, UMLKSK CUI: C0020981 CD134/OX40 expression is characteristic of certain entities (angioimmunoblastic lymphoma, angiocentric T-NHL) and a subset of T-NHLs of unspecified type, whereas CD30 expression is characteristic of ALCL and a largely non-overlapping subset of T-NHLs of unspecified type. NCI, Score=801, Pubmed Id: 10233901, UMLKSK CUI: C0020981 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	TCF7	6932	transcription factor 7 (T-cell specific, HMG-box)	NCI, Score=801, Pubmed Id: 12707037, UMLKSK CUI: C0020981 Of the Th1-like PTCL studied, 33 of 42 (79%) were immunoreactive for LEF-1 and 32 of 42 (76%) were immunoreactive for TCF-1, including most cases of angioimmunoblastic lymphoma and all cases of lymphoepithelioid lymphoma.
Human	SYCP1	6847	synaptonemal complex protein 1	NCI, Score=801, Pubmed Id: 12538465, UMLKSK CUI: C0020981 A majority (9 of 15) of T- NHLs (9 peripheral T-cell lymphomas, 2 lymphoblastic T-cell lymphomas, and 4 cases of AILD) expressed HOM-TES-14/SCP-1.
Human	REL	5966	v-rel avian reticuloendotheliosis viral oncogene homolog	GENERIF, Score=1000, Pubmed Id: 18006812, UMLKSK CUI: C0020981 VEGF is expressed not only by reactive cells, but also by neoplastic cells, and NF-kappaB activation is uncommon in angioimmunoblastic lymphoma, as suggested by frequent exclusively cytoplasmic c-REL localization
Human	RAG2	5897	recombination activating gene 2	NCI, Score=801, Pubmed Id: 8518181, UMLKSK CUI: C0020981 Expression of human recombination activating genes (RAG-1 and RAG-2) in angioimmunoblastic lymphadenopathy and anaplastic large cell lymphoma of T-type. NCI, Score=801, Pubmed Id: 8518181, UMLKSK CUI: C0020981 In order to determine the genotypic maturation status of the proliferating lymphoid cells in angioimmunoblastic lymphadenopathy (AILD) and in anaplastic large cell lymphoma of T-type (T-ALC), recombinase activating gene (RAG-1 and RAG-2) expression was assessed in six AILD and five T-ALC cases using a sensitive reverse transcriptase (RT) and competitive (C) polymerase chain reaction (PCR).
Human	RAG1	5896	recombination activating gene 1	NCI, Score=801, Pubmed Id: 8518181, UMLKSK CUI: C0020981 In order to determine the genotypic maturation status of the proliferating lymphoid cells in angioimmunoblastic lymphadenopathy (AILD) and in anaplastic large cell lymphoma of T-type (T-ALC), recombinase activating gene (RAG-1 and RAG-2) expression was assessed in six AILD and five T-ALC cases using a sensitive reverse transcriptase (RT) and competitive (C) polymerase chain reaction (PCR). NCI, Score=801, Pubmed Id: 8518181, UMLKSK CUI: C0020981 Expression of human recombination activating genes (RAG-1 and RAG-2) in angioimmunoblastic lymphadenopathy and anaplastic large cell lymphoma of T-type.
Human	NFKB1	4790	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	GENERIF, Score=1000, Pubmed Id: 18006812, UMLKSK CUI: C0020981 VEGF is expressed not only by reactive cells, but also by neoplastic cells, and NF-kappaB activation is uncommon in angioimmunoblastic lymphoma, as suggested by frequent exclusively cytoplasmic c-REL localization
Human	MAF	4094	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog	GENERIF, Score=1000, Pubmed Id: 18059226, UMLKSK CUI: C0020981 Angioimmunoblastic T-cell lymphoma(AILT) shows c-Maf expression and provide new insight into the pathogenesis of AILT suggesting c-Maf to be a useful diagnostic marker
Human	CCR4	1233	chemokine (C-C motif) receptor 4	NCI, Score=801, Pubmed Id: 15289861, UMLKSK CUI: C0020981 Among PTCL-U, CCR4 type, CXCR3 type and CCR3 type had prognoses equivalent to ATLL, AILD and ALCL, respectively (P<0.0001).
Human	MS4A1	931	membrane-spanning 4-domains, subfamily A, member 1	NCI, Score=801, Pubmed Id: 15480765, UMLKSK CUI: C0020981 By applying triple immunofluorescent staining with antibodies directed against T-cell receptor Vbeta-family-specific epitopes, we investigated T-cell populations in AILD and their localisation in the tissue in relation to B cells (CD20) and follicular dendritic cells (CD21).

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0020981	Immunoblastic Lymphadenopathy	0		self

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