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 - Acidosis, Renal Tubular

Debug Stats

### Total Build Time: 41 ms 44.199 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 344 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 504 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= 1,000 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 6.771 KB
CONCEPT_RELATIONSHIPS gt=25 ms Completed: 25 ms rowSize= 13.073 KB
CONCEPT_GENES gt=8 ms Completed: 8 ms rowSize= 21.174 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.157 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Acidosis, Renal Tubular C0001126

Definition (1)

rare sometimes familial disorder of the renal tubule characterized by the inability to excrete urine of normal acidity; this leads to a hyperchloremic acidosis which is often associated with one or more secondary complications such as hypercalcinuria with nephrolithiasis and nephrocalcinosis, rickets, or osteomalacia and severe potassium depletion.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0035091

C0001122

Ancestral Roots

Relationships (57)

Relation Types:

diso_to_anat : 3

diso_to_chem : 22

diso_to_diso : 28

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 24

clinically_similar : 2

isa : 7

mapped_to : 6

may_treat : 18

Page Size

Current 25

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Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	67		Complication Aspects C1171258
DISO_to_DISO	58		Complication Aspects C1171258
DISO_to_PHEN	54		genetic aspects C0017399
DISO_to_PHEN	53		genetic aspects C0017399
DISO_to_CHEM	25		AE1 Anion Exchanger C0242194
DISO_to_DISO	23		chemically induced C0007994
DISO_to_DISO	18		Sjogren's Syndrome C1527336
DISO_to_DISO	17		Sjogren's Syndrome C1527336
DISO_to_CHEM	16		AE1 Anion Exchanger C0242194
DISO_to_DISO	15		chemically induced C0007994
DISO_to_PHYS	15		Mutation C0026882
DISO_to_DISO	13		Hypokalemia C0020621
DISO_to_PHYS	12		Mutation C0026882
DISO_to_ANAT	11		Distal convoluted renal tubule structure C0022676
DISO_to_ANAT	11		In Blood C0005768
DISO_to_ANAT	11		Kidney C0022646
DISO_to_DISO	10		CALCINOSIS RENAL C0027709
DISO_to_DISO	10		Hearing Loss, Sensorineural C0018784
DISO_to_DISO	10		Hypokalemia C0020621
DISO_to_CHEM	8		Vacuolar Proton-Translocating ATPases C0379099
DISO_to_CHEM	7		Vacuolar Proton-Translocating ATPases C0379099
DISO_to_DISO	7		Albers-Schonberg disease C0029454
DISO_to_DISO	7		CALCINOSIS RENAL C0027709
DISO_to_DISO	7		Osteomalacia C0029442
DISO_to_CHEM		may_treat	2-Hydroxy-1,2,3-propanetricarboxylic Acid, Anhydrous C0725616

Genes (15)

Species:

human : 15

Species	Gene	GeneId	Gene Name	Evidence
Human	NEWENTRY	192343	Record to support submission of GeneRIFs for a gene not in Gene (human; man).	GENERIF, Score=1000, Pubmed Id: 18216089, UMLKSK CUI: C0001126 It was found that herpesvirus 8 RTA can induce K-RBP degradation through the ubiquitin-proteasome pathway and that two regions in RTA are responsible.[K-RBP]
Human	MED12	9968	mediator complex subunit 12	GENERIF, Score=1000, Pubmed Id: 12612078, UMLKSK CUI: C0001126 The TRAP230 subunit of TRAP/Mediator was shown to interact directly with RTA
Human	PIAS2	9063	protein inhibitor of activated STAT, 2	GENERIF, Score=812, Pubmed Id: 16460827, UMLKSK CUI: C0001126 findings show that Epstein-Barr virus Rta interacts and colocalizes with PIASxalpha and PIASxbeta in the nucleus; these interactions seem to enhance Rta sumoylation
Human	SUMO1	7341	small ubiquitin-like modifier 1	GENERIF, Score=812, Pubmed Id: 16460827, UMLKSK CUI: C0001126 findings show that Epstein-Barr virus Rta interacts and colocalizes with PIASxalpha and PIASxbeta in the nucleus; these interactions seem to enhance Rta sumoylation GENERIF, Score=861, Pubmed Id: 15229220, UMLKSK CUI: C0001126 SUMO-1 conjugation at the Lys-19 residue is crucial for enhancing the transactivation activity of EBV Rta
Human	SMARCA4	6597	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	GENERIF, Score=1000, Pubmed Id: 12612078, UMLKSK CUI: C0001126 The Brg1 subunit of SWI/SNF was shown to interact directly with RTA
Human	SLC4A1	6521	solute carrier family 4 (anion exchanger), member 1	GENERIF, Score=1000, Pubmed Id: 12938018, UMLKSK CUI: C0001126 Anion exchanger 1 mutations are associated with distal renal tubular acidosis GAD, Score=926, Pubmed Id: 9312167, UMLKSK CUI: C0001126 Title:Familial distal renal tubular acidosis is associated with mutations in the red cell anion exchanger (Band 3 AE1) gene.\|Association:Y\|Conclusion:We conclude that dominantly inherited dRTA is associated with mutations in band 3; but both the disease and its autosomal dominant inheritance are not related simply to the anion transport activity of the mutant proteins. GENERIF, Score=1000, Pubmed Id: 17533027, UMLKSK CUI: C0001126 most of the patients with distal renal tubular acidosis studied carried autosomal recessive AE1 mutations GENERIF, Score=1000, Pubmed Id: 17941824, UMLKSK CUI: C0001126 Mutations in AE1 can cause Southeast Asian ovalocytosis or distal renal tubular acidosis OMIM, Score=1000, UMLKSK CUI: C0001126 Renal tubular acidosis GENERIF, Score=937, Pubmed Id: 11934690, UMLKSK CUI: C0001126 R589H distal renal tubular acidosis(dRTA)mutation creates a severe trafficking defect in kAE1 but not in erythroid AE1 [kAE1]
Human	PC	5091	pyruvate carboxylase	OMIM, Score=1000, UMLKSK CUI: C0001126 Renal tubular acidosis, proximal
Human	IL6	3569	interleukin 6 (interferon, beta 2)	GENERIF, Score=1000, Pubmed Id: 12359431, UMLKSK CUI: C0001126 Rta expression during lytic reactivation of HHV-8 would lead to expression of some cellular genes, including IL-6, whereas activation of NF-kappa B could inhibit some responses to transcription activator, Rta
Human	RBPJ	3516	recombination signal binding protein for immunoglobulin kappa J region	GENERIF, Score=1000, Pubmed Id: 17055026, UMLKSK CUI: C0001126 RTA activates the Kaposi's sarcoma-associated herpesvirus K8 promoter through an indirect binding mechanism, i.e. being recruited to the K8 promoter through interaction with RBP-Jkappa bound to an RBP-Jkappa motif in the promoter GENERIF, Score=660, Pubmed Id: 12832621, UMLKSK CUI: C0001126 RBP-J kappa-mediated repression is therefore not essential for establishment of latent KHSV infection, but the RTA-mediated redirection of RBP-J kappa activity from repression to activation is critical for lytic viral replication
Human	HMGB1	3146	high mobility group box 1	GENERIF, Score=694, Pubmed Id: 18692049, UMLKSK CUI: C0001126 These results suggest Rta autostimulation may be mediated by a transient complex involving Oct1 and HMGB1
Human	ESR1	2099	estrogen receptor 1	GENERIF, Score=1000, Pubmed Id: 11875103, UMLKSK CUI: C0001126 RTA, a negative coregulator for ERalpha was isolated
Human	CPT1A	1374	carnitine palmitoyltransferase 1A (liver)	OMIM, Score=1000, UMLKSK CUI: C0001126 Renal tubular acidosis
Human	CA2	760	carbonic anhydrase II	OMIM, Score=1000, UMLKSK CUI: C0001126 Renal tubular acidosis, type I
Human	ATP6V1B1	525	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	GENERIF, Score=1000, Pubmed Id: 17216496, UMLKSK CUI: C0001126 This report describes a new mutation in the ATP6V1B1 gene responsible for distal renal tubular acidosis OMIM, Score=1000, UMLKSK CUI: C0001126 Renal tubular acidosis
Human	PARP1	142	poly (ADP-ribose) polymerase 1	GENERIF, Score=1000, Pubmed Id: 14585985, UMLKSK CUI: C0001126 cellular poly(ADP-ribose) polymerase 1 (PARP-1) and Ste20-like kinase hKFC interact with the serine/threonine-rich region of gamma-2 herpesvirus replication and transcription activator (RTA)

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0001126	Acidosis, Renal Tubular	0		self

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