Asociacijska analiza nekaterih genov vključenih v regulacijo aktivacije T celic pri bolnikih s kronično vnetno črevesno boleznijo

Sovec, Andrej

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Title:	Asociacijska analiza nekaterih genov vključenih v regulacijo aktivacije T celic pri bolnikih s kronično vnetno črevesno boleznijo
Authors:	ID Sovec, Andrej (Author) ID Potočnik, Uroš (Mentor) More about this mentor... ID Ferkolj, Ivan (Comentor)
Files:	MAG_Sovec_Andrej_2011.pdf (1,77 MB) MD5: 6A51C662B062EE7DB5116E19A055CF9A PID: 20.500.12556/dkum/62420e24-0c39-4bed-abe9-e9d61e44b4ee
Language:	Slovenian
Work type:	Master's thesis/paper
Organization:	FZV - Faculty of Health Sciences
Abstract:	Kronično vnetna črevesna bolezen (KVČB) je kompleksna genetska bolezen. Dva glavna tipa KVČB sta Crohnova bolezen (CB) in ulcerozni kolitis (UC). Za Crohnovo bolezen je značilno, da je vnetje razširjeno po celotni prebavni cevi, pri ulceroznem kolitisu pa je omejeno na debelo črevo in danko. Namen magistrskega dela je bil s podatkovnimi zbirkami genske ontologije in ustreznimi bioinformatskimi orodji ugotoviti najpomembnejše biološke procese in poti, v katerih sodelujejo geni, ki so jih v asociacijskih študijah statistično značilno povezali s KVČB; ugotoviti, v katerih molekularnih funkcijah sodelujejo ti geni in katere celične komponente sestavljajo proteini, ki jih kodirajo ti geni; s podatkovnimi zbirkami genske ontologije poiskati gene, ki so vključeni v biološki proces Regulacija aktivacije T celic in jih analizirati kot kandidatne gene za asociacijsko študijo pri slovenskih bolnikih s KVČB. S pomočjo podatkovne zbirke HuGE Navigator smo izdelali seznam 180 genov, ki so jih v asociacijskih študijah na podlagi polimorfizmov posameznega nukleotida (SNP) statistično značilno povezali s KVČB, in ga uporabili za identifikacijo najpomembnejših bioloških procesov, molekularnih funkcij, celičnih komponent in bioloških poti v patogenezi KVČB. S pomočjo podatkovnih zbirk genske ontologije (DAVID 6.7, Gene Ontology, KEGG in BioCarta) in ustreznih bioinformatskih orodij ter seznama KVČB genov smo najprej identificirali 380 bioloških procesov, 18 molekularnih funkcij, 10 celičnih komponent in 15 bioloških poti v KEGG in 12 bioloških poti v BioCarti. Med njimi smo v nadaljnji raziskavi z uporabo istih podatkovnih zbirk in bioinformatskih orodij kot najpomembnejše v patogenezi KVČB identificirali 12 bioloških procesov, 2 molekularni funkciji, 2 celični komponenti in 10 bioloških poti. Z uporabo podatkovnih zbirk Gene Ontology in HuGE Navigator smo v biološkem procesu Regulacija aktivacije T celic izbrali 5 kandidatnih genov in 2 izmed njih, IL10 in IL12A, na podlagi SNP-jev (rs3024505 in rs17810546), statistično značilno povezali, P<0,05, s fenotipskimi podtipi slovenskih bolnikov s KVČB.
Keywords:	Kronično vnetna črevesna bolezen (KVČB), Gene Ontology (GO), DAVID 6.7, biološki proces, biološka pot, molekularna funkcija, celična komponenta, asociacijska študija, BioCarta, KEGG, HuGE Navigator, ulcerozni kolitis (UC), Crohnova bolezen (CB)
Place of publishing:	Maribor
Publisher:	[A. Sovec]
Year of publishing:	2011
PID:	20.500.12556/DKUM-21641
UDC:	616.3
COBISS.SI-ID:	1756580
NUK URN:	URN:SI:UM:DK:EPKKEOAR
Publication date in DKUM:	06.01.2012
Views:	3813
Downloads:	366
Metadata:
Categories:	FZV
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Secondary language

Language:	English
Title:	The association analysis of some genes involved in the regulation of T cells activation in patients with inflammatory bowel disease
Abstract:	Inflammatory bowel disease (IBD) is a complex genetic disorder. The two main types of IBD are Crohn disease and ulcerative colitis. In Crohn disease inflammation is extended through whole digestive tract, in UC is restricted to colon and rectum.The purpose of this Master thesis was the determination of the most important biological processes and pathways, in which participate genes, that were in association studies significant related to IBD; to determinate, in which molecular functions these genes participate and which cell components are consisted of proteins, that are encoded with these genes; with gene ontology databases finding genes, that participate in the biological process regulation of T cell activation, and their analysis as candidate genes for association study at Slovene patients with IBD. With the database HuGE Navigator we have made a list of 180 genes that were in association studies on the basis of single nucleotide polymorphism (SNP) significant related to IBD, and have used it for the identification of the most important biological processes, molecular functions, cell components and biological pathways in the pathogenesis of IBD. With the databases (DAVID 6.7, Gene Ontology, KEGG and BioCarta), appropriate bioinformatics tools and the list of IBD genes we have first identificated 380 biological processes, 18 molecular functions, 10 cell components and 15 biological pathways in KEGG and 12 biological pathways in BioCarta. In the following research with the same databases and bioinformatics tools we have identificated between them as the most significant in the pathogenesis of IBD 12 biological processes, 2 molecular functions, 2 cell components and 10 biological pathways. With the use of the databases Gene Ontology and HuGE Navigator we have chosen 5 candidate genes in the biological process Regulation of T cell activation and have related 2 among them, IL10 and IL12A, on the basis of SNP (rs3024505 in rs17810546), significant, P<0,05, with phenotype subtypes of Slovene patients with IBD.
Keywords:	Inflammatory bowel disease (IBD), Gene Ontology, DAVID 6.7, biological process, biological pathway, molecular function, cell component, association study, BioCarta, KEGG, HuGE Navigator, ulcerative colitis (UC), Crohn's disease (CD)

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