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 - Colonic Polyps

Debug Stats

### Total Build Time: 47 ms 48.313 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 326 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 311 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= 191 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=4 ms Completed: 4 ms rowSize= 553 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=8 ms Completed: 8 ms rowSize= 1.542 KB
CONCEPT_RELATIONSHIPS gt=16 ms Completed: 16 ms rowSize= 14.720 KB
CONCEPT_GENES gt=15 ms Completed: 15 ms rowSize= 29.520 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.148 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Colonic Polyps C0009376

Definition (1)

A polypoid lesion that arises from the colon and protrudes into the lumen. This group includes adenomatous polyps, serrated polyps, and hamartomatous polyps.

Semantic Types (1)

Anatomical Abnormality (T190)

Parents (1)

C0021846

Ancestral Roots

Root	Root Plus One	Depth	Parent
Pathological Conditions, Signs and Symptoms C0039058	Pathological Conditions, Anatomical C0752135	5	Intestinal Polyps C0021846

Relationships (90)

Relation Types:

diso_to_anat : 19

diso_to_chem : 3

diso_to_diso : 63

diso_to_gene : 1

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 52

associated_with : 1

is_associated_anatomic_site_of : 2

is_finding_of_disease : 2

is_primary_anatomic_site_of_disease : 2

isa : 10

location_of : 12

manifestation_of : 4

may_be_finding_of_disease : 1

permuted_term_of : 1

related_to : 3

Page Size

Current 25

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250

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	391		COLORECTAL NEOPL C0009404
DISO_to_DISO	300		Adenoma C0001430
DISO_to_DISO	231		COLON NEOPL C0009375
DISO_to_DISO	191		COLORECTAL NEOPL C0009404
DISO_to_DISO	140		COLON NEOPL C0009375
DISO_to_DISO	114		Adenoma C0001430
DISO_to_PHEN	104		genetic aspects C0017399
DISO_to_DISO	73		Complication Aspects C1171258
DISO_to_DISO	72		Adenocarcinoma C0001418
DISO_to_DISO	72		Adenomatous Polyps C0206677
DISO_to_DISO	68		Precancerous Conditions C0032927
DISO_to_ANAT	64		Colon C0009368
DISO_to_PHEN	63		genetic aspects C0017399
DISO_to_ANAT	56		Intestinal Mucosa C0021839
DISO_to_DISO	51		Adenocarcinoma C0001418
DISO_to_ANAT	48		Colon C0009368
DISO_to_DISO	47		Adenomatous Polyps C0206677
DISO_to_DISO	46		Complication Aspects C1171258
DISO_to_DISO	35		Rectal Diseases C0034882
DISO_to_DISO	34		BLEEDING GASTROINTESTINAL C0017181
DISO_to_DISO	32		Precancerous Conditions C0032927
DISO_to_PHYS	32		Automated Pattern Recognition C1448473
DISO_to_DISO	26		Intestinal Polyp C0021846
DISO_to_DISO	23		BLEEDING GASTROINTESTINAL C0017181
DISO_to_DISO	23		Postoperative Hemorrhage C0032788

Genes (19)

Species:

human : 18

mouse : 1

Species	Gene	GeneId	Gene Name	Evidence
Mouse	PPARD	5467	peroxisome proliferator-activated receptor delta	NCI, Score=801, Pubmed Id: 16618765, UMLKSK CUI: C0009376 Whereas administration of a PPARbeta ligand causes increased small intestinal tumorigenesis in Apc(min/+) mice, PPARbeta-null (Pparb-/-) mice exhibit increased colon polyp multiplicity in colon cancer bioassays, suggesting that ligand activation of this receptor will inhibit colon carcinogenesis. NCI, Score=801, Pubmed Id: 16618765, UMLKSK CUI: C0009376 Whereas administration of a PPARbeta ligand causes increased small intestinal tumorigenesis in Apc(min/+) mice, PPARbeta-null (Pparb(-/-)) mice exhibit increased colon polyp multiplicity in colon cancer bioassays, suggesting that ligand activation of this receptor will inhibit colon carcinogenesis. NCI, Score=801, Pubmed Id: 16618765, UMLKSK CUI: C0009376 Consistent with increased colonocyte differentiation and apoptosis, inhibition of colon polyp multiplicity was also found in ligand-treated Pparb+/+ mice, and all of these effects were not found in Pparb-/- mice.
Human	FLCN	201163	folliculin	OMIM, Score=1000, UMLKSK CUI: C0009376 Colonic polyps
Human	HTATIP2	10553	HIV-1 Tat interactive protein 2, 30kDa	NCI, Score=801, Pubmed Id: 14743395, UMLKSK CUI: C0009376 Using two-dimensional (2-D) gel analysis 20 colon polyps (one juvenile polyp, six tubular adenoma (TA), seven tubulovillous adenoma (TVA), six TVA with focal high-grade dysplasia (HGD), were analyzed for the presence of four (CC2, CC3, CC4, CC5) specific NMPs.
Human	PTTG1	9232	pituitary tumor-transforming 1	NCI, Score=801, Pubmed Id: 10703804, UMLKSK CUI: C0009376 FINDINGS: PTTG1 was overexpressed in all of 48 colon carcinomas (median fold-increase 2.2 [IQR 1.8-3.3]) and in 19 of 20 colonic polyps (2.2 [1.6-3.1]) compared with normal colonic tissue.
Human	STK11	6794	serine/threonine kinase 11	NCI, Score=801, Pubmed Id: 14518068, UMLKSK CUI: C0009376 Topics discussed here include PTEN mutations and colonic polyps; WNT signaling, APC, beta-catenin, and gastrointestinal neoplasms; mismatch-repair genes (MLH1, MSH2, PMS1, MSH6) and hereditary nonpolyposis colorectal cancer; MYH mutations and autosomal recessive colorectal tumors; STK11 mutations and Peutz-Jeghers syndrome; TGFbeta and gastrointestinal cancer; BMPR1A mutations and juvenile polyposis; FGF/FGFR alterations in gastrointestinal neoplasms; PTCH mutations and gastrointestinal neoplasms; RUNX3 expression and gastric cancer; role of mucins in gastric carcinogenesis; KIT, PDGFRalpha, and gastrointestinal stromal tumors; intestinal neurofibromatosis; and gastrointestinal tumors in other disorders.
Human	PMS2	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	GENERIF, Score=1000, Pubmed Id: 18273873, UMLKSK CUI: C0009376 new cancer syndrome caused by biallelic mutations in the mismatch repair genes, including PMS2, is now emerging and is characterized by cafe-au-lait macules, colonic polyps and a distinctive tumor spectrum
Human	PMS1	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	NCI, Score=801, Pubmed Id: 14518068, UMLKSK CUI: C0009376 Topics discussed here include PTEN mutations and colonic polyps; WNT signaling, APC, beta-catenin, and gastrointestinal neoplasms; mismatch-repair genes (MLH1, MSH2, PMS1, MSH6) and hereditary nonpolyposis colorectal cancer; MYH mutations and autosomal recessive colorectal tumors; STK11 mutations and Peutz-Jeghers syndrome; TGFbeta and gastrointestinal cancer; BMPR1A mutations and juvenile polyposis; FGF/FGFR alterations in gastrointestinal neoplasms; PTCH mutations and gastrointestinal neoplasms; RUNX3 expression and gastric cancer; role of mucins in gastric carcinogenesis; KIT, PDGFRalpha, and gastrointestinal stromal tumors; intestinal neurofibromatosis; and gastrointestinal tumors in other disorders.
Human	MYH1	4619	myosin, heavy chain 1, skeletal muscle, adult	GAD, Score=1000, Pubmed Id: 15932553, UMLKSK CUI: C0009376 Title:Is prophylactic colectomy indicated in patients with MYH-associated polyposis?\|Association:Y\|Conclusion:A large frequency of biallelic MYH mutations (69%) was found in APC mutation negative patients belonging to families with attenuated polyposis; the highest percentage was observed in families presenting evidence for horizontal transmission of the disease. The high percentage of degeneration found in these patients suggests that colonoscopy with polypectomies is not sufficient and prophylactic colectomy is recommended. The identification of MYH associated polyposis is important to evaluate the level of risk, particularly for the siblings.
Human	MUTYH	4595	mutY homolog (E. coli)	GAD, Score=1000, Pubmed Id: 15761860, UMLKSK CUI: C0009376 Title:Mutation analysis of the MYH gene in an Australian series of colorectal polyposis patients with or without germline APC mutations.\|Association:Not Found\|Conclusion:The results reveal that MYH accounts for 16 percent of polyposis patients without germline mutations in the APC gene and that it does not appear to be a modifier gene in FAP patients diagnosed with APC germline mutations.
Human	JUP	3728	junction plakoglobin	NCI, Score=801, Pubmed Id: 9176391, UMLKSK CUI: C0009376 In this study, we have used immunohistochemistry to localize E-cadherin, alpha-, beta-, and gamma-catenin, and p120 in paraffin-embedded tissues from 60 patients with colonic polyps.
Human	GUCA2B	2981	guanylate cyclase activator 2B (uroguanylin)	NCI, Score=801, Pubmed Id: 11016642, UMLKSK CUI: C0009376 Our experiments demonstrate that mRNA transcripts for guanylin and uroguanylin are markedly reduced in colon polyps and adenocarcinomas.
Human	GUCA2A	2980	guanylate cyclase activator 2A (guanylin)	NCI, Score=801, Pubmed Id: 11016642, UMLKSK CUI: C0009376 Our experiments demonstrate that mRNA transcripts for guanylin and uroguanylin are markedly reduced in colon polyps and adenocarcinomas.
Human	FMO3	2328	flavin containing monooxygenase 3	GAD, Score=1000, Pubmed Id: 16214918, UMLKSK CUI: C0009376 Title:Genetic polymorphisms of flavin monooxygenase 3 in sulindac-induced regression of colorectal adenomas in familial adenomatous polyposis.\|Association:Not Found\|Conclusion:
Human	FGF1	2246	fibroblast growth factor 1 (acidic)	NCI, Score=801, Pubmed Id: 14518068, UMLKSK CUI: C0009376 Topics discussed here include PTEN mutations and colonic polyps; WNT signaling, APC, beta-catenin, and gastrointestinal neoplasms; mismatch-repair genes (MLH1, MSH2, PMS1, MSH6) and hereditary nonpolyposis colorectal cancer; MYH mutations and autosomal recessive colorectal tumors; STK11 mutations and Peutz-Jeghers syndrome; TGFbeta and gastrointestinal cancer; BMPR1A mutations and juvenile polyposis; FGF/FGFR alterations in gastrointestinal neoplasms; PTCH mutations and gastrointestinal neoplasms; RUNX3 expression and gastric cancer; role of mucins in gastric carcinogenesis; KIT, PDGFRalpha, and gastrointestinal stromal tumors; intestinal neurofibromatosis; and gastrointestinal tumors in other disorders.
Human	DEFA5	1670	defensin, alpha 5, Paneth cell-specific	NCI, Score=801, Pubmed Id: 15844706, UMLKSK CUI: C0009376 We sought a correlation between site and morphology of colonic polyps by labeling with neoplastic and general Paneth cell markers, monoclonal antibodies Adnab-9 and anti-alpha-defensin 5, respectively. NCI, Score=801, Pubmed Id: 15844706, UMLKSK CUI: C0009376 Differential labeling by monoclonal antibodies Adnab-9 and anti-alpha-defensin 5 based on the distribution and adenomatous tissue content of colonic polyps.
Human	DCN	1634	decorin	GENERIF, Score=1000, Pubmed Id: 18830193, UMLKSK CUI: C0009376 study concludes expression of decorin may be involved in the differentiation of colonic polyps and reduced expression of decorin may abrogate the defensive potential of stromal tissue and promote the development of common types of colon carcinoma
Human	CCKBR	887	cholecystokinin B receptor	NCI, Score=801, Pubmed Id: 11076881, UMLKSK CUI: C0009376 The purpose of this study was to determine if gastrin and CCKBR are expressed in human colonic polyps and to determine at which stage of progression this occurs. NCI, Score=801, Pubmed Id: 11076881, UMLKSK CUI: C0009376 METHODS: A range of human colonic polyps was assessed for gastrin and CCKBR gene and protein expression.
Human	BMPR1A	657	bone morphogenetic protein receptor, type IA	NCI, Score=801, Pubmed Id: 14518068, UMLKSK CUI: C0009376 Topics discussed here include PTEN mutations and colonic polyps; WNT signaling, APC, beta-catenin, and gastrointestinal neoplasms; mismatch-repair genes (MLH1, MSH2, PMS1, MSH6) and hereditary nonpolyposis colorectal cancer; MYH mutations and autosomal recessive colorectal tumors; STK11 mutations and Peutz-Jeghers syndrome; TGFbeta and gastrointestinal cancer; BMPR1A mutations and juvenile polyposis; FGF/FGFR alterations in gastrointestinal neoplasms; PTCH mutations and gastrointestinal neoplasms; RUNX3 expression and gastric cancer; role of mucins in gastric carcinogenesis; KIT, PDGFRalpha, and gastrointestinal stromal tumors; intestinal neurofibromatosis; and gastrointestinal tumors in other disorders.
Human	APC	324	adenomatous polyposis coli	GAD, Score=1000, Pubmed Id: 15951963, UMLKSK CUI: C0009376 Title:A comparison of the phenotype and genotype in adenomatous polyposis patients with and without a family history.\|Association:Not Found\|Conclusion:Adenomatous polyposis patients without a family history are usually diagnosed with symptoms, and at a later age. Phenotypically, they are similar to those with a family history. However, germline APC mutations are detected far less frequently in patients without a family history. A small percentage of these cases may be secondary to biallelic germline MYH mutations. GAD, Score=1000, Pubmed Id: 15108288, UMLKSK CUI: C0009376 Title:First genotype characterization of Argentinean FAP patients: identification of 14 novel APC mutations.\|Association:Not Found\|Conclusion:Our data indicate that the genotype/phenotype correlations in Argentinean patients are similar to those observed in other populations. GAD, Score=1000, Pubmed Id: 15761860, UMLKSK CUI: C0009376 Title:Mutation analysis of the MYH gene in an Australian series of colorectal polyposis patients with or without germline APC mutations.\|Association:Not Found\|Conclusion:The results reveal that MYH accounts for 16 percent of polyposis patients without germline mutations in the APC gene and that it does not appear to be a modifier gene in FAP patients diagnosed with APC germline mutations.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0009376	Colonic Polyps	0		self

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