GATACA

Credits

Hide Credits

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 - Frontotemporal Lobar Degeneration

Debug Stats

### Total Build Time: 31 ms 34.511 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 364 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 620 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= 201 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=6 ms Completed: 6 ms rowSize= 984 bytes
CONCEPT_CHILDREN gt=3 ms Completed: 3 ms rowSize= 1,016 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 5.368 KB
CONCEPT_RELATIONSHIPS gt=10 ms Completed: 10 ms rowSize= 5.844 KB
CONCEPT_GENES gt=6 ms Completed: 6 ms rowSize= 18.994 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.167 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Frontotemporal Lobar Degeneration C0751072

Definition (1)

Heterogeneous group of neurodegenerative disorders characterized by frontal and temporal lobe atrophy associated with neuronal loss, gliosis, and dementia. Patients exhibit progressive changes in social, behavioral, and/or language function. Multiple subtypes or forms are recognized based on presence or absence of TAU PROTEIN inclusions. FTLD includes three clinical syndromes: FRONTOTEMPORAL DEMENTIA, semantic dementia, and PRIMARY PROGRESSIVE NONFLUENT APHASIA.

Semantic Types (1)

Mental or Behavioral Dysfunction (T048)

Parents (2)

C2718017

C0497327

Children (2)

C0751706

C0338451

Ancestral Roots

Relationships (12)

Relation Types:

diso_to_anat : 2

diso_to_chem : 4

diso_to_diso : 4

diso_to_phen : 1

diso_to_phys : 1

Relationships:

none : 11

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	121		genetic aspects C0017399
DISO_to_DISO	58		Complication Aspects C1171258
DISO_to_DISO	49		Alzheimer Disease C0002395
DISO_to_CHEM	46		Binding Protein, DNA C0012940
DISO_to_ANAT	37		Brain C0006104
DISO_to_DISO	37		Amyotrophic Lateral Sclerosis C0002736
DISO_to_CHEM	32		INTERCELLULAR SIGNALING PEPTIDES PROTEINS C1136108
DISO_to_CHEM	25		RNA-Binding Protein FUS C0950472
DISO_to_ANAT	21		Temporal Lobe C0039485
DISO_to_CHEM	17		tau Proteins C0085401
DISO_to_PHYS	17		Mutation C0026882
DISO_to_DISO		permuted_term_of	Frontotemporal Lobar Degeneration C0751072

Genes (10)

Species:

human : 10

Species	Gene	GeneId	Gene Name	Evidence
Human	LOC643387	643387	TAR DNA binding protein pseudogene	GENERIF, Score=1000, Pubmed Id: 18097163, UMLKSK CUI: C0751072 Motor neuron disease and frontotemporal lobar degeneration reveal identical inclusions of TDP-43 GENERIF, Score=1000, Pubmed Id: 17923628, UMLKSK CUI: C0751072 distinct TDP-43 profiles may affect clinical phenotypes differentially in patients with frontotemporal lobar degeneration with ubiquitin-positive inclusions
Human	LRRK2	120892	leucine-rich repeat kinase 2	GENERIF, Score=1000, Pubmed Id: 17151837, UMLKSK CUI: C0751072 This study identified a LRRK2 mutation leading to the G2019S amino acid substitution in a 79-year-old woman with frontotemporal lobar degeneration with ubiquitinated neuronal intranuclear inclusions and a possible family history of tremor
Human	CHMP2B	25978	charged multivesicular body protein 2B	GENERIF, Score=1000, Pubmed Id: 17956895, UMLKSK CUI: C0751072 These data suggest that C-truncating mutations in CHMP2B might underlie the pathogenic mechanism in frontotemporal lobar degeneration
Human	TARDBP	23435	TAR DNA binding protein	GENERIF, Score=1000, Pubmed Id: 17023659, UMLKSK CUI: C0751072 findings showed that TDP-43 is the major disease protein in frontotemporal lobar degeneration and amyotrophic lateral sclerosis; it was recovered only from affected central nervous system regions GENERIF, Score=1000, Pubmed Id: 18755042, UMLKSK CUI: C0751072 Neuropathological examination reveals cytoplasmic deposition of the TDP-43 protein in affected pedigree members with frontotemporal lobar degeneration--motor neuron disease GENERIF, Score=1000, Pubmed Id: 18379440, UMLKSK CUI: C0751072 TAR DNA-binding protein 43 immunohistochemistry reveals extensive neuritic pathology in frontotemporal lobar degeneration with ubiquitinated inclusions GENERIF, Score=1000, Pubmed Id: 17492294, UMLKSK CUI: C0751072 TDP-43 proteinopathy is the common pathologic substrate linking frontotemporal lobar degeneration and amyotrophic lateral sclerosis GENERIF, Score=1000, Pubmed Id: 17569066, UMLKSK CUI: C0751072 TDP-43 immunoreactivity was detected in the hypoglossal nucleus in all cases of amyotrophic lateral sclerosis, all cases of frontotemporal lobar degeneration and some of cases of primary lateral sclerosis (PLS) GENERIF, Score=1000, Pubmed Id: 18656473, UMLKSK CUI: C0751072 These results suggest that the phosphorylation of Ser409/410 is an abnormal event in frontotemporal lobar degeneration and amyotrophic lateral sclerosis GENERIF, Score=1000, Pubmed Id: 18088371, UMLKSK CUI: C0751072 TDP-43 is a neuronal activity-responsive factor functioning in the regulation of neuronal plasticity, the impairment of which leads to frontotemporal lobar degeneration
Human	SQSTM1	8878	sequestosome 1	GENERIF, Score=1000, Pubmed Id: 18379439, UMLKSK CUI: C0751072 Frontotemporal lobar degeneration with ubiquitin-positive inclusions visualized with ubiquitin-binding protein p62
Human	VEGFA	7422	vascular endothelial growth factor A	GENERIF, Score=923, Pubmed Id: 18729809, UMLKSK CUI: C0751072 VEGF gene variability represents a susceptibility factor for sporadic frontotemporal lobar degeneration
Human	SLC6A4	6532	solute carrier family 6 (neurotransmitter transporter), member 4	GENERIF, Score=1000, Pubmed Id: 19020798, UMLKSK CUI: C0751072 SLC6A4 single nucleotide polymorphisms are associated with frontotemporal lobar degeneration
Human	MAPT	4137	microtubule-associated protein tau	GENERIF, Score=923, Pubmed Id: 18458217, UMLKSK CUI: C0751072 The ratio of CSF tau/A beta(42) is a sensitive and specific biomarker at discriminating frontotemporal lobar degeneration from Alzheimer disease in patients with known pathology GAD, Score=1000, Pubmed Id: 11939896, UMLKSK CUI: C0751072 Title:Differences in tau and apolipoprotein e polymorphism frequencies in sporadic frontotemporal lobar degeneration syndromes\|Association:Not Found\|Conclusion:Clinical subtypes of FTLD have different tau and APOE genotype frequencies, suggesting these genes may influence the clinical presentation. Further studies should be performed to confirm this finding and to see if the pathologic phenotypes are also associated with different tau and APOE genotype frequencies.
Human	GRN	2896	granulin	GENERIF, Score=1000, Pubmed Id: 17572900, UMLKSK CUI: C0751072 Progranulin mutations cause haploinsufficiency leading to TDP-43 accumulation in frontotemporal lobar degeneration GENERIF, Score=1000, Pubmed Id: 18223198, UMLKSK CUI: C0751072 Findings demonstrate a distinct molecular phenotype for GRN in frontotemporal lobar degeneration with ubiquitinated inclusions, not readily apparent on clinical or histopathological examination GENERIF, Score=923, Pubmed Id: 16983685, UMLKSK CUI: C0751072 familial frontotemporal lobar degeneration with ubiquitin-positive, tau-negative inclusions caused by a missense mutation in the signal peptide of progranulin.(ALA-9 ASP)
Human	APOE	348	apolipoprotein E	GAD, Score=1000, Pubmed Id: 11939896, UMLKSK CUI: C0751072 Title:Differences in tau and apolipoprotein e polymorphism frequencies in sporadic frontotemporal lobar degeneration syndromes\|Association:Not Found\|Conclusion:Clinical subtypes of FTLD have different tau and APOE genotype frequencies, suggesting these genes may influence the clinical presentation. Further studies should be performed to confirm this finding and to see if the pathologic phenotypes are also associated with different tau and APOE genotype frequencies.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0751072	Frontotemporal Lobar Degeneration	0		self

Gataca is supported by...