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 - Diabetic Neuropathies

Debug Stats

### Total Build Time: 105 ms 41.044 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 340 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 722 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= 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= 1,010 bytes
CONCEPT_CHILDREN gt=1 ms Completed: 1 ms rowSize= 551 bytes
CONCEPT_ANCESTRAL_ROOTS gt=1 ms Completed: 1 ms rowSize= 4.092 KB
CONCEPT_RELATIONSHIPS gt=77 ms Completed: 77 ms rowSize= 14.433 KB
CONCEPT_GENES gt=16 ms Completed: 16 ms rowSize= 18.592 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.155 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Diabetic Neuropathies C0011882

Definition (1)

Peripheral, autonomic, and cranial nerve disorders that are associated with DIABETES MELLITUS. These conditions usually result from diabetic microvascular injury involving small blood vessels that supply nerves (VASA NERVORUM). Relatively common conditions which may be associated with diabetic neuropathy include third nerve palsy (see OCULOMOTOR NERVE DISEASES); MONONEUROPATHY; mononeuropathy multiplex; diabetic amyotrophy; a painful POLYNEUROPATHY; autonomic neuropathy; and thoracoabdominal neuropathy. (From Adams et al., Principles of Neurology, 6th ed, p1325)

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0342257

C0031117

Children (1)

C0206172

Ancestral Roots

Root	Root Plus One	Depth	Parent
Endocrine System Diseases C0014130	Diabetes Mellitus C0011849	4	Diabetes Complications C0342257
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	6	Diabetes Complications C0342257
Nervous System Diseases C0027765	Neuromuscular Diseases C0027868	4	Peripheral Nervous System Diseases C0031117

Relationships (192)

Relation Types:

diso_to_anat : 28

diso_to_chem : 86

diso_to_diso : 69

diso_to_phen : 2

diso_to_phys : 7

Relationships:

none : 117

classified_as : 4

is_associated_anatomic_site_of : 1

is_primary_anatomic_site_of_disease : 1

isa : 11

mapped_to : 2

may_treat : 55

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	300		Diabetes Mellitus, Non-Insulin-Dependent C0011860
DISO_to_DISO	230		Complication Aspects C1171258
DISO_to_DISO	214		Complication Aspects C1171258
DISO_to_DISO	191		Diabetes Mellitus, Non-Insulin-Dependent C0011860
DISO_to_DISO	168		Diabetes Mellitus, Insulin-Dependent C0011854
DISO_to_DISO	147		Diabetes Mellitus, Insulin-Dependent C0011854
DISO_to_DISO	140		DIABETES MELLITUS EXPER C0011853
DISO_to_ANAT	95		In Blood C0005768
DISO_to_DISO	89		DIABETES MELLITUS EXPER C0011853
DISO_to_DISO	81		Diabetic Foot C0206172
DISO_to_DISO	81		Pain C0030193
DISO_to_DISO	73		Autonomic Nervous System Diseases C1145628
DISO_to_DISO	73		Diabetic Foot C0206172
DISO_to_DISO	73		Pain C0030193
DISO_to_DISO	71		Autonomic Nervous System Diseases C1145628
DISO_to_DISO	70		Angiopathies, Diabetic C0011875
DISO_to_PHYS	60		Nerve conduction function C0027788
DISO_to_CHEM	59		Analgesics C0002771
DISO_to_ANAT	58		In Blood C0005768
DISO_to_DISO	57		Neuralgia C0027796
DISO_to_DISO	55		Diabetes Mellitus C0011849
DISO_to_PHEN	54		genetic aspects C0017399
DISO_to_DISO	52		Angiopathies, Diabetic C0011875
DISO_to_DISO	52		Peripheral Nervous System Diseases C0031117
DISO_to_PHEN	47		genetic aspects C0017399

Genes (16)

Species:

human : 16

Species	Gene	GeneId	Gene Name	Evidence
Human	TNFSF11	8600	tumor necrosis factor (ligand) superfamily, member 11	GENERIF, Score=1000, Pubmed Id: 15322748, UMLKSK CUI: C0011882 (RANK-L)/osteoprotegerin (OPG) signalling pathway is central to the processes regulating bone turnover in a wide variety of medical conditions, including diabetic neuropathy (review)
Human	UCP3	7352	uncoupling protein 3 (mitochondrial, proton carrier)	GENERIF, Score=1000, Pubmed Id: 16373902, UMLKSK CUI: C0011882 C-55T polymorphism in the UCP3 gene is associated with a reduced risk of diabetic neuropathy in type 1 diabetes
Human	UCP2	7351	uncoupling protein 2 (mitochondrial, proton carrier)	GENERIF, Score=1000, Pubmed Id: 16373902, UMLKSK CUI: C0011882 G-866A polymorphism in the UCP2 gene is associated with a reduced risk of diabetic neuropathy in type 1 diabetes
Human	TXN	7295	thioredoxin	GENERIF, Score=1000, Pubmed Id: 17360766, UMLKSK CUI: C0011882 Overexpression in transgenic mice inhibits development of diabetic neuropathy
Human	TLR4	7099	toll-like receptor 4	GENERIF, Score=1000, Pubmed Id: 14693986, UMLKSK CUI: C0011882 Asp299Gly and Thr399Ile genotypes of the TLR4 gene are associated with reduced prevalence of diabetic neuropathy in type 2, but not in type 1, diabetes
Human	THBD	7056	thrombomodulin	GENERIF, Score=1000, Pubmed Id: 12031986, UMLKSK CUI: C0011882 substantial reduction of vascular endothelial thrombomodulin expression throughout human diabetic neuropathy may contribute to microvascular ischemia in the pathogenesis of diabetic neuropathy
Human	RELA	5970	v-rel avian reticuloendotheliosis viral oncogene homolog A	GENERIF, Score=1000, Pubmed Id: 15599399, UMLKSK CUI: C0011882 data demonstrate, for the first time to our knowledge, that the RAGE-NF-kappaB axis operates in diabetic neuropathy, by mediating functional sensory deficits, and that its inhibition may provide new therapeutic approaches
Human	PLAT	5327	plasminogen activator, tissue	GENERIF, Score=1000, Pubmed Id: 17636064, UMLKSK CUI: C0011882 Regionally deficient tissue plasminogen activator expression in microvessel endothelium contributes to impaired endogenous fibrinolysis and microvascular ischemia in diabetic neuropathy
Human	NPY	4852	neuropeptide Y	GENERIF, Score=1000, Pubmed Id: 17984244, UMLKSK CUI: C0011882 The Leu7Pro polymorphism of neuropeptide Y confers susceptibility to development of diabetic neuropathy in Swedish female type I diabetes patients
Human	NOS3	4846	nitric oxide synthase 3 (endothelial cell)	GAD, Score=1000, Pubmed Id: 15856945, UMLKSK CUI: C0011882 Title:[Polymorphic markers of the NO synthase genes and genetic predisposition to diabetic polyneuropathy in patients with type 1 diabetes mellitus]\|Association:Not Found\|Conclusion:Only in the case of (CCTTT)n marker of NOS2 gene we have found a tendency for the association of 14 allele with DPN development. The carriers of this allele have the lower risk of DPN in T1DM.
Human	NOS2	4843	nitric oxide synthase 2, inducible	GAD, Score=1000, Pubmed Id: 15856945, UMLKSK CUI: C0011882 Title:[Polymorphic markers of the NO synthase genes and genetic predisposition to diabetic polyneuropathy in patients with type 1 diabetes mellitus]\|Association:Not Found\|Conclusion:Only in the case of (CCTTT)n marker of NOS2 gene we have found a tendency for the association of 14 allele with DPN development. The carriers of this allele have the lower risk of DPN in T1DM.
Human	DEFB4A	1673	defensin, beta 4A	INFERRED, Score=800, UMLKSK CUI: C0011882
Human	CAT	847	catalase	GAD, Score=1000, Pubmed Id: 15125229, UMLKSK CUI: C0011882 Title:[Search for the association of polymorphic markers for genes coding for antioxidant defense enzymes, with development of diabetic polyneuropathies in patients with type 1 diabetes mellitus]\|Association:Y\|Conclusion:On this evidence, these markers were not associated with DPN in the sample examined.
Human	APOB	338	apolipoprotein B	GAD, Score=1000, Pubmed Id: 15856946, UMLKSK CUI: C0011882 Title:[Association of polymorphic markers of lipid metabolism genes with diabetic polyneuropathy in type 1 diabetes mellitus]\|Association:Y\|Conclusion:Our findings show that APOB gene, encoding one of the main components of lipid metabolism system, is involved into the diabetic polyneuropathy development in type 1 diabetes mellitus.
Human	AGER	177	advanced glycosylation end product-specific receptor	GENERIF, Score=1000, Pubmed Id: 15599399, UMLKSK CUI: C0011882 data demonstrate that the RAGE-NF-kappaB axis operates in diabetic neuropathy, by mediating functional sensory deficits, and that its inhibition may provide new therapeutic approaches GENERIF, Score=1000, Pubmed Id: 18046662, UMLKSK CUI: C0011882 Plasma soluble RAGE and endogenous secretory RAGE are not associated with measures of diabetic neuropathy in type 2 diabetes patients
Human	PARP1	142	poly (ADP-ribose) polymerase 1	GENERIF, Score=1000, Pubmed Id: 18054108, UMLKSK CUI: C0011882 Results suggest that the PARP1 gene is involved in the pathogenesis of diabetic neuropathy in a Russian population

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0011882	Diabetic Neuropathies	0		self

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