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 - Genotoxic Stress

Debug Stats

### Total Build Time: 28 ms 41.913 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 330 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 173 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= 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=6 ms Completed: 6 ms rowSize= 3.718 KB
CONCEPT_GENES gt=14 ms Completed: 14 ms rowSize= 36.483 KB
CONCEPT_XREFS gt=4 ms Completed: 4 ms rowSize= 1.150 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Genotoxic Stress C1257899

Definition (1)

DNA DAMAGE in vivo.

Relationships (5)

Relation Types:

diso_to_anat : 1

diso_to_diso : 1

diso_to_phys : 3

Relationships:

biological_process_results_from_biological_process : 2

is_location_of_biological_process : 1

isa : 1

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_ANAT		is_location_of_biological_process	Chromosome Structures C0729606
DISO_to_DISO		permuted_term_of	Genotoxic Stress C1257899
DISO_to_PHYS		isa	Beta Radiation Effect C1511112
DISO_to_PHYS		biological_process_results_from_biological_process	Cellular Stress Response C1516374
DISO_to_PHYS		biological_process_results_from_biological_process	DNA Damage Repair C0012899

Genes (32)

Species:

human : 32

Page Size

Current 25

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Prior Page

Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	CDK5RAP3	80279	CDK5 regulatory subunit associated protein 3	GENERIF, Score=1000, Pubmed Id: 15790566, UMLKSK CUI: C1257899 results strongly indicate that in response to genotoxic stress, Cdk5 activator-binding protein C53(C53) serves as an important regulatory component of DNA damage checkpoint through modulating cyclin dependent kinase 1-cyclin B1 function
Human	CLSPN	63967	claspin	GENERIF, Score=734, Pubmed Id: 16880517, UMLKSK CUI: C1257899 These results suggest that while TopBP1 is a general regulator of ATR, Claspin operates downstream of TopBP1 to selectively regulate the Chk1-controlled branch of the genotoxic stress response
Human	LRDD	55367	p53-induced death domain protein	GENERIF, Score=1000, Pubmed Id: 17637755, UMLKSK CUI: C1257899 PIDD isoforms are capable of activating nuclear factor-kappaB in response to genotoxic stress, but only isoform 1 interacts with RIP-associated ICH-1/CED-3 homologous protein with a death domain and activates caspase-2 GENERIF, Score=1000, Pubmed Id: 16982033, UMLKSK CUI: C1257899 The functional consequences of the identified PIDD/nucleolin interaction remain to be elucidated, but may be related to a recently discovered new role for PIDD in the activation of NF-kappaB upon genotoxic stress
Human	TIPIN	54962	TIMELESS interacting protein	GENERIF, Score=734, Pubmed Id: 17141802, UMLKSK CUI: C1257899 TIM and Tipin are functional orthologs of their replisome-associated yeast counterparts capable of coordinating replication with genotoxic stress responses, and distinguishes mammalian TIM from the circadian-specific paralogs
Human	APTX	54840	aprataxin	GENERIF, Score=1000, Pubmed Id: 15044383, UMLKSK CUI: C1257899 aprataxin influences the cellular response to genotoxic stress
Human	FZR1	51343	fizzy/cell division cycle 20 related 1 (Drosophila)	GENERIF, Score=1000, Pubmed Id: 18662541, UMLKSK CUI: C1257899 In response to genotoxic stress in G2, the phosphatase Cdc14B translocates from the nucleolus to the nucleoplasm and induces the activation of the ubiquitin ligase APC/C(Cdh1), with the consequent degradation of Plk1, a prominent mitotic kinase
Human	C16orf5	29965		GENERIF, Score=1000, Pubmed Id: 17599062, UMLKSK CUI: C1257899 These findings support a novel p53 --> CDIP --> TNF-alpha apoptotic pathway that directs apoptosis after exposure of cells to genotoxic stress
Human	HIPK2	28996	homeodomain interacting protein kinase 2	GENERIF, Score=1000, Pubmed Id: 18093972, UMLKSK CUI: C1257899 the regulatory mechanisms by which HIPK2 is maintained at a low level, by WSB-1 in cells under normal conditions, and stabilized by genotoxic stresses
Human	SMG1	23049	SMG1 phosphatidylinositol 3-kinase-related kinase	GENERIF, Score=1000, Pubmed Id: 15175154, UMLKSK CUI: C1257899 Expression of hSMG-1 is required for optimal p53 activation after cellular exposure to genotoxic stress, and depletion of hSMG-1 leads to spontaneous DNA damage and increased sensitivity to ionizing radiation
Human	PDZD2	23037	PDZ domain containing 2	GENERIF, Score=1000, Pubmed Id: 18639375, UMLKSK CUI: C1257899 sPDZD2 sensitized mutant p53-positive DU145 cells and wild-type p53-positive MCF-7 cells to apoptosis induction through genotoxic stress imposed by sub-lethal concentration of hydrogen peroxide
Human	TOPBP1	11073	topoisomerase (DNA) II binding protein 1	GENERIF, Score=1000, Pubmed Id: 16314514, UMLKSK CUI: C1257899 TopBP1 plays a critical role in the maintenance of genomic stability during normal S phase as well as following genotoxic stress
Human	GNA13	10672	guanine nucleotide binding protein (G protein), alpha 13	GENERIF, Score=1000, Pubmed Id: 17510313, UMLKSK CUI: C1257899 G alpha(12/13) regulate basal p53 levels via mdm4, which constitutes a cell signaling pathway distinct from p53 phosphorylations elicited by genotoxic stress
Human	RNF8	9025	ring finger protein 8, E3 ubiquitin protein ligase	GENERIF, Score=1000, Pubmed Id: 18001825, UMLKSK CUI: C1257899 RNF8 is a novel DNA-damage-responsive protein that integrates protein phosphorylation and ubiquitylation signaling and plays a critical role in the cellular response to genotoxic stress
Human	SPHK1	8877	sphingosine kinase 1	GENERIF, Score=1000, Pubmed Id: 14988393, UMLKSK CUI: C1257899 SK1 is down-regulated by genotoxic stress, and basal SK1 function may be necessary for the maintenance of tumor cell growth
Human	RIPK1	8737	receptor (TNFRSF)-interacting serine-threonine kinase 1	GENERIF, Score=1000, Pubmed Id: 17301840, UMLKSK CUI: C1257899 We describe how RIP1 acts as a key integrator of signalling pathways initiated by stimulation of death receptors, bacterial or viral infection, genotoxic stress and T-cell homeostasis
Human	IKBKG	8517	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma	GENERIF, Score=1000, Pubmed Id: 14651848, UMLKSK CUI: C1257899 Genotoxic stress induces SUMO-1 modification and ATM activation, which work in concert to cause nuclear targeting and ubiquitylation of free NEMO to permit the NF-kappaB survival pathway GENERIF, Score=1000, Pubmed Id: 16497931, UMLKSK CUI: C1257899 results show that ATM phosphorylates Ser85 of NEMO in response to genotoxic stress & that this is required for ubiquitination of NEMO; this modification is essential for nuclear export of NEMO & ATM & their interaction with IKK in the cytoplasm GENERIF, Score=1000, Pubmed Id: 18201555, UMLKSK CUI: C1257899 The NEMO shuttle may link genotoxic stress to the activation of the innate immunity system and cause premature aging via inflamm-aging process
Human	BAT3	7917		GENERIF, Score=1000, Pubmed Id: 17403783, UMLKSK CUI: C1257899 Bat3 is a novel and essential regulator of p53-mediated responses to genotoxic stress, and that Bat3 controls DNA damage-induced acetylation of p53
Human	XPO1	7514	exportin 1 (CRM1 homolog, yeast)	GENERIF, Score=1000, Pubmed Id: 14617633, UMLKSK CUI: C1257899 CRM1 has a role in mediating a nuclear export signal to govern nuclear accumulation of glyceraldehyde-3-phosphate dehydrogenase following genotoxic stress
Human	TP53	7157	tumor protein p53	GENERIF, Score=1000, Pubmed Id: 10794522, UMLKSK CUI: C1257899 There was a differential upregulation of p53-responsive genes by genotoxic stress in hematopoietic cells containing wild-type p53 (MOLT-4) or a mutant p53 with a codon 161 mutation (U266) GENERIF, Score=1000, Pubmed Id: 19074876, UMLKSK CUI: C1257899 Genotoxic stress promotes the p53-dependent up-regulation of the homologous miRNAs miR-192 and miR-215 GENERIF, Score=901, Pubmed Id: 16897187, UMLKSK CUI: C1257899 These results suggest that DFNA5 plays a role in the p53-regulated cellular response to genotoxic stress probably by cooperating with p53 GENERIF, Score=1000, Pubmed Id: 18639375, UMLKSK CUI: C1257899 sPDZD2 sensitized mutant p53-positive DU145 cells and wild-type p53-positive MCF-7 cells to apoptosis induction through genotoxic stress imposed by sub-lethal concentration of hydrogen peroxide GENERIF, Score=1000, Pubmed Id: 17353266, UMLKSK CUI: C1257899 Data demonstrate a novel link between p53 and Notch1 in keratinocyte differentiation upon genotoxic stress and suggest a novel tumor suppressor mechanism of p53 in the development of HPV-induced tumors GENERIF, Score=734, Pubmed Id: 15710329, UMLKSK CUI: C1257899 MUC1 regulates p53-responsive genes and thereby cell fate in the genotoxic stress response GENERIF, Score=1000, Pubmed Id: 11756653, UMLKSK CUI: C1257899 To determine whether genotoxic stress regulates DNA binding by p53 in vivo, we have performed quantitative chromatin immunoprecipitation (ChIP) assays on tumor and normal cell lines containing wild-type p53
Human	TOP2A	7153	topoisomerase (DNA) II alpha 170kDa	GENERIF, Score=734, Pubmed Id: 16611985, UMLKSK CUI: C1257899 PKCdelta regulates topoisomerase IIalpha and thereby cell fate in the genotoxic stress response
Human	MUC1	4582	mucin 1, cell surface associated	GENERIF, Score=734, Pubmed Id: 15710329, UMLKSK CUI: C1257899 MUC1 regulates p53-responsive genes and thereby cell fate in the genotoxic stress response
Human	MDM2	4193	MDM2 oncogene, E3 ubiquitin protein ligase	GENERIF, Score=1000, Pubmed Id: 18711402, UMLKSK CUI: C1257899 hdmX mRNA levels are kept low following genotoxic stress
Human	JUN	3725	jun proto-oncogene	GENERIF, Score=1000, Pubmed Id: 17920329, UMLKSK CUI: C1257899 c-Jun may sense the strength of genotoxic stress through DNA-damage dependent phosphorylation of T95, which in turn augments c-Jun transactivation by JNKs
Human	HIF1A	3091	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	GENERIF, Score=901, Pubmed Id: 18784753, UMLKSK CUI: C1257899 Data show that CSB mutant cells are unable to react to hypoxic stimuli by properly activating the hypoxia-inducible factor-1 (HIF-1) pathway, a defect that is further enhanced in the event of a concomitant genotoxic stress
Human	DUSP4	1846	dual specificity phosphatase 4	GENERIF, Score=694, Pubmed Id: 16038800, UMLKSK CUI: C1257899 Results demonstrate the in vivo specificity of MKP-2 for JNK and not ERK and show that nuclear-targeted JNK is involved in genotoxic stress-induced apoptosis

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1257899	Genotoxic Stress	0		self

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