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 - Prematurity of fetus

Debug Stats

### Total Build Time: 29 ms 44.246 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 338 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
Skipping details on: CONCEPT_DEFINITION gt=NONE 0 Completed: 0 ms rowSize= 0 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= 14 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=0 Completed: 0 ms rowSize= 7 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 15 bytes
CONCEPT_RELATIONSHIPS gt=14 ms Completed: 14 ms rowSize= 6.239 KB
CONCEPT_GENES gt=13 ms Completed: 13 ms rowSize= 36.452 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.154 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Prematurity of fetus C0728731

Relationships (14)

Relation Types:

diso_to_diso : 14

Relationships:

associated_with : 10

isa : 4

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO		isa	Born very premature C0565824
DISO_to_DISO		isa	Extreme immaturity C0270078
DISO_to_DISO		associated_with	Hyperbilirubinaemia of prematurity C0158971
DISO_to_DISO		associated_with	Interstitial pulmonary fibrosis of prematurity C0270169
DISO_to_DISO		associated_with	Intraventricular haemorrhage of prematurity C0475735
DISO_to_DISO		isa	Premature - weight 1000g-2499g or gestation of 28-37weeks C0411096
DISO_to_DISO		associated_with	Retinopathy of Prematurity C0035344
DISO_to_DISO		associated_with	Retinopathy of Prematurity Stage 1 Demarcation Line C1443381
DISO_to_DISO		associated_with	Retinopathy of Prematurity Stage 2 Intraretinal Ridge C1443382
DISO_to_DISO		associated_with	Retinopathy of Prematurity Stage 4 Subtotal Retinal Detachment C1443384
DISO_to_DISO		associated_with	Retinopathy of Prematurity Stage 5 Total Retinal Detachment C1443385
DISO_to_DISO		associated_with	Retinopathy of prematurity stage 3 - ridge with extraretinal fibrovascular proliferation C1443383
DISO_to_DISO		associated_with	Transitory ileus of prematurity C0455996
DISO_to_DISO		isa	Very premature - less than 1000g or less than 28 weeks C0411095

Genes (31)

Species:

human : 31

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Species	Gene	GeneId	Gene Name	Evidence
Human	NAA15	80155	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	GENERIF, Score=1000, Pubmed Id: 16518308, UMLKSK CUI: C0728731 Loss of retinal endothelial Tbdn-1 expression may be a contributing factor in retinal blood vessel proliferation in retinopathy of prematurity
Human	VEGFA	7422	vascular endothelial growth factor A	GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C0728731 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Y\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF.
Human	SCGB1A1	7356	secretoglobin, family 1A, member 1 (uteroglobin)	GENERIF, Score=966, Pubmed Id: 16690962, UMLKSK CUI: C0728731 CC10 is detectable in the blood of newborn infants, and a production surge occurs at birth; surge is more pronounced in term infants and may confer them with superior extrauterine pulmonary protection compared with preterm infants
Human	TNNT2	7139	troponin T type 2 (cardiac)	GENERIF, Score=966, Pubmed Id: 18322550, UMLKSK CUI: C0728731 There was a significant inverse correlation between cTnT (cardiac troponin T) and echocardiographic markers of myocardial function and stroke volume in preterm infants
Human	TNF	7124	tumor necrosis factor	GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C0728731 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Not Found\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF.
Human	TLR4	7099	toll-like receptor 4	GENERIF, Score=1000, Pubmed Id: 17709532, UMLKSK CUI: C0728731 Two TLR4 polymorphisms heterozygosity is highly associated with symptomatic RSV disease in high-risk infants and supports a dual role for TLR4 SNPs in prematurity and increased susceptibility to RSV not revealed by analysis of either alone
Human	THPO	7066	thrombopoietin	GENERIF, Score=966, Pubmed Id: 15647951, UMLKSK CUI: C0728731 expression of TPO receptor on platelets until 1 month after birth cause a decreased TPO clearance and keep a high level of free TPO in blood, resulting in the subsequent thrombocytosis in preterm infants GENERIF, Score=1000, Pubmed Id: 17763151, UMLKSK CUI: C0728731 Increased TPO levels and the percentage of reticulated platelets indicate that thrombocytopoiesis is more active in prematurity
Human	TGFB1	7040	transforming growth factor, beta 1	GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C0728731 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Not Found\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF.
Human	TEAD4	7004	TEA domain family member 4	GENERIF, Score=694, Pubmed Id: 17652751, UMLKSK CUI: C0728731 Novel RTEF-1 transcripts are present within human ocular vascular endothelial cells and mouse neural retina during normal and retinopathy of prematurity development, and alternatively spliced products are produced under hyperoxic and hypoxic conditions
Human	S100B	6285	S100 calcium binding protein B	GENERIF, Score=966, Pubmed Id: 16340181, UMLKSK CUI: C0728731 determination of urinary S-100B concentrations might be helpful in term infants with severe asphyxia, while high urinary S-100B concentrations in preterm infants are to be attributed to immaturity
Human	PRSS2	5645	protease, serine, 2 (trypsin 2)	GENERIF, Score=966, Pubmed Id: 12949286, UMLKSK CUI: C0728731 High levels of pulmonary trypsin-2 may be associated with the development of bronchopulmonary dysplasia in preterm infants
Human	NPPB	4879	natriuretic peptide B	GENERIF, Score=966, Pubmed Id: 18322550, UMLKSK CUI: C0728731 there was significant negative correlation between NTpBNP (natriuretic peptide precursor B) and left ventricular (LV) function in preterm infants
Human	NDP	4693	Norrie disease (pseudoglioma)	GAD, Score=1000, Pubmed Id: 16052165, UMLKSK CUI: C0728731 Title:Norrie disease gene sequence variants in an ethnically diverse population with retinopathy of prematurity.\|Association:Not Found\|Conclusion:Of the six sequence alterations found, five were novel nucleotide changes: One in the 5' UTR region of exon 2, and four in the 3' UTR region of exon 3. The extent of NDP polymorphisms in this large, racially diverse group of infants is moderate. NDP polymorphisms may play a role in the pathogenesis of ROP, but do not appear to be a major causative factor. GAD, Score=1000, Pubmed Id: 12145535, UMLKSK CUI: C0728731 Title:A C597-->A polymorphism in the Norrie disease gene is associated with advanced retinopathy of prematurity in premature Kuwaiti infants.\|Association:Y\|Conclusion:The incidence of the AA genotype of the C597A polymorphism was considerably higher in advanced-stage ROP cases (83.3%) compared to spontaneously regressing ROP cases (0%) and the normal controls (10.4%) (p < 0.0001). For the other genotypes, no significant difference was detected between the controls and ROP cases. In the case of the C110G mutation in the ND gene, no significant differences were detected between the controls and ROP cases, and the majority of subjects had a CC genotype in all three groups. GENERIF, Score=1000, Pubmed Id: 11748312, UMLKSK CUI: C0728731 de novo mutations in the 5' regulatory region in retinopathy of prematurity GENERIF, Score=1000, Pubmed Id: 12145535, UMLKSK CUI: C0728731 Data show a strong association between the AA genotype of the C597A Norrie disease gene polymorphism and progression of retinopathy of prematurity GENERIF, Score=1000, Pubmed Id: 16052165, UMLKSK CUI: C0728731 NDP polymorphisms may play a role in the pathogenesis of retinopathy of prematurity, but do not appear to be a major causative factor GAD, Score=1000, Pubmed Id: 11322656, UMLKSK CUI: C0728731 Title:Insertion and deletion mutations in the dinucleotide repeat region of the Norrie disease gene in patients with advanced retinopathy of prematurity.\|Association:Not Found\|Conclusion:Taking into account the above results, as well as those of other studies, it appears that the ND gene mutations can account for 3% of cases of advanced ROP. Although the ND gene is not frequently involved in advanced ROP, the present large-scale study further supports the hypothesis that genetic influences may play an important role in the development of severe ROP in some premature infants.
Human	MTHFR	4524	methylenetetrahydrofolate reductase (NAD(P)H)	GENERIF, Score=1000, Pubmed Id: 18539994, UMLKSK CUI: C0728731 Here, we report a premature baby with prenatal onset diffuse multicystic encephalomalacia and cerebellar atrophy due to homozygous methylenetetrahydrofolate reductase mutation
Human	MMP9	4318	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	GENERIF, Score=1000, Pubmed Id: 16155381, UMLKSK CUI: C0728731 findings indicate differences in early matrix metalloproteinase 9 (MMP-9) bronchoalveolar lavage fluid levels between resolving respiratory distress syndrome and developing chronic lung disease of prematurity
Human	MBL2	4153	mannose-binding lectin (protein C) 2, soluble	GENERIF, Score=966, Pubmed Id: 17898783, UMLKSK CUI: C0728731 Frequent variants of the MBL gene, leading to low MBL concentrations, are associated with the diagnosis of BPD in preterm infants GENERIF, Score=1000, Pubmed Id: 17653692, UMLKSK CUI: C0728731 The four haplotype combination groups may have a potential diagnostic use as opposite risk factors for lung disease of prematurity
Human	CXCL10	3627	chemokine (C-X-C motif) ligand 10	GENERIF, Score=966, Pubmed Id: 17211148, UMLKSK CUI: C0728731 Preterm infants have the ability to induce a robust chemokine and cytokine response during sepsis, and IP-10 is a sensitive early marker of infection
Human	IL10	3586	interleukin 10	GENERIF, Score=966, Pubmed Id: 17314689, UMLKSK CUI: C0728731 the risk of respiratory distress syndrome is significantly lower in preterm infants with an IL-10 -1082 GG/GA genotype than in those with an AA genotype [odds ratio (OR) = 0.48
Human	IL8	3576	interleukin 8	GENERIF, Score=896, Pubmed Id: 17667842, UMLKSK CUI: C0728731 Azithromycin suppressed NF-kappaB activation and reduced synthesis of IL6/IL8 in tracheal cells from preterm ventilated infants
Human	IL1RN	3557	interleukin 1 receptor antagonist	GENERIF, Score=966, Pubmed Id: 16301842, UMLKSK CUI: C0728731 Increased levels of cord IL-1ra levels are associated with neonatal morbidity and adverse outcome in preterm infants
Human	IGFBP2	3485	insulin-like growth factor binding protein 2, 36kDa	GENERIF, Score=966, Pubmed Id: 17341887, UMLKSK CUI: C0728731 The results provide further evidence that IGFBP-2 and IGF-II in breast milk are relevant factors for the early development of preterm infants
Human	IGF1R	3480	insulin-like growth factor 1 receptor	GENERIF, Score=1000, Pubmed Id: 18050122, UMLKSK CUI: C0728731 The results do not support the association of the most prevalent insulin-like growth factor I receptor gene polymorphism and the risk of advanced retinopathy of prematurity
Human	IGF1	3479	insulin-like growth factor 1 (somatomedin C)	GENERIF, Score=1000, Pubmed Id: 15695599, UMLKSK CUI: C0728731 Results indicate that the degree of prematurity, low enteral protein intake, male gender, and slow weight gain are associated with a slower postnatal increase of IGF-I in preterm infants
Human	HSD11B2	3291	hydroxysteroid (11-beta) dehydrogenase 2	GENERIF, Score=867, Pubmed Id: 12519895, UMLKSK CUI: C0728731 In small preterm infants, reduced placental 11 beta-HSD2 function is asociated with low relative birth weight and severe fetal distress
Human	SLC37A4	2542	solute carrier family 37 (glucose-6-phosphate transporter), member 4	GENERIF, Score=896, Pubmed Id: 17354259, UMLKSK CUI: C0728731 A novel G6PT1 promoter polymorphism, 259C --> T was found; the - 259*T allele frequency was greater in term SIDS infants than in term control infants and preterm SIDS infants

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0728731	Prematurity of fetus	0		self

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