1. Rudarjenje asociativnih pravil z evolucijskimi algoritmi : magistrsko deloKatja Božič, 2025, master's thesis Abstract: V magistrskem delu smo raziskali uporabo evolucijskih algoritmov za rudarjenje asociativnih pravil pri analizi genetskih podatkov na področju bioinformatike. Evolucijske algoritme smo uporabili za odkrivanje znanja iz podatkov, kjer nam asociacijska pravila prikažejo skrite povezave med atributi v podatkovni množici. S pomočjo evolucijskih algoritmov za rudarjenje asociativnih pravil smo na genetskih podatkih zdravih tkiv in tkiv z miomi maternice naredili analizo, s katero smo odkrili neznane povezave med geni. Ugotovili smo, da lahko evolucijske algoritme za rudarjenje asociativnih pravil uporabimo za odkrivanje genetskih vzorcev. Pridobljene podatke bi lahko uporabili za razumevanje molekularnih mehanizmov bolezni, kar bi prispevalo k napredku v diagnostiki in zdravljenju bolezni.
Keywords: bioinformatika, evolucijski algoritmi, geni, miomi maternice, rudarjenje asociativnih pravil
Published in DKUM: 08.05.2025; Views: 0; Downloads: 18
 Full text (1,74 MB) |
2. Diferencialno izražanje genov in učinek filtriranja nizko izraženih genov pri analizi RNA sekvenciranjaŠpela Fabčič, 2025, master's thesis Abstract: Uvod: Sekvenciranje RNA (analiza RNA-seq) se sooča z izzivi obdelave podatkov in razvojem metod za učinkovito shranjevanje, pridobivanje in obdelavo velikih količin podatkov z namenom, da se zmanjša število napak določevanja nukleotidnega zaporedja med drugim tudi na način z odstranitvijo odčitkov nižje kakovosti.
Metode: S pomočjo programskega orodja R smo iz treh različnih podatkovnih baz za tri različne bolezni (Crohnova bolezen, astma, miomi maternice) izvedli RNA-seq analizo v katero smo vključili filtriranje nizko izraženih z metodo CPM, kjer smo določili prag filtriranja nizko izraženih genov na podlagi statističnega izračuna minimuma, maksimuma in povprečja izražanja genov.
Rezultati: V okviru naloge smo ugotovili, da različni pragi filtriranja ne spremenijo števila nabora genov v končnih rezultatih analize RNA-seq. Pri vplivu postavitve različnih pragov filtriranja na nabor prvih 20 najbolj statistično značilno diferencialno izraženih genov je bila izrazita razlika med različno zastavljenimi pragi filtriranja samo v primeru Crohnove bolezni. Pri testiranju, ali se izločeni geni pri danem pragu filtriranja pojavijo kot statistično značilno diferencialno izraženi geni v analizi brez filtriranja, smo ugotovili, da se velik delež izločenih genov, še posebej pri nižjih pragovih filtriranja, še vedno pojavi kot statistično značilen v analizi brez filtriranja.
Razprava in sklep: Na podlagi rezultatov smo ugotovili, da postavitev različnih pragov filtriranja nima posebnega učinka na rezultate diferencialnega izražanja genov.
Keywords: genska ekspresija, astma, Crohnova bolezen, miomi maternice
Published in DKUM: 06.05.2025; Views: 0; Downloads: 2
Full text (1,39 MB) |
3. Genetic background of cattle temperament : a short reviewJože Smolinger, Mario Gorenjak, Dejan Škorjanc, 2024, review article Abstract: Animal temperament describes behavioural differences between individuals that are consistent over time and across different circumstances. Knowledge of the animal's temperament has a major effect on the safety of handling and caring for the animals as well as on the adaptation of the animals to changing rearing conditions. To understand animal temperament, we need to know not only the genetic basis of temperament, but also the influence of the environment on its expression. Similarly the temperament of dairy cows can be defined as the animal's response to environmental or social stimuli. In this review article, chromosomes with genomic regions containing QTLs, genes and candidate genes responsible for the expression of temperament traits in cattle are presented. Knowledge of the genetic background of temperament expression in cattle and its variability in these traits allows temperament to be included in the selection index.
Keywords: cattle temperament genetics, QTL, SNP, heritability, serotonin, dopamine
Published in DKUM: 23.04.2025; Views: 0; Downloads: 0
 Link to file |
4. MFUM-BrTNBC-1, a newly established patient-derived triple-negative breast cancer cell line : molecular characterisation, genetic stability, and comprehensive comparison with commercial breast cancer cell linesKristijan Skok, Lidija Gradišnik, Helena Sabina Čelešnik, Marko Milojević, Uroš Potočnik, Gregor Jezernik, Mario Gorenjak, Monika Sobočan, Iztok Takač, Rajko Kavalar, Uroš Maver, 2022, original scientific article Abstract: Triple-negative breast cancer (TNBC) is a breast cancer (BC) subtype that accounts for
approximately 15–20% of all BC cases. Cancer cell lines (CLs) provide an efficient way to model the
disease. We have recently isolated a patient-derived triple-negative BC CL MFUM-BrTNBC-1 and
performed a detailed morphological and molecular characterisation and a comprehensive comparison
with three commercial BC CLs (MCF-7, MDA-MB-231, MDA-MB-453). Light and fluorescence
microscopy were used for morphological studies; immunocytochemical staining for hormone receptor,
p53 and Ki67 status; RNA sequencing, qRT-PCR and STR analysis for molecular characterisation; and
biomedical image analysis for comparative phenotypical analysis. The patient tissue-derived MFUMBrTNBC-1 maintained the primary triple-negative receptor status. STR analysis showed a stable and
unique STR profile up to the 6th passage. MFUM-BrTNBC-1 expressed EMT transition markers and
displayed changes in several cancer-related pathways (MAPK, Wnt and PI3K signalling; nucleotide
excision repair; and SWI/SNF chromatin remodelling). Morphologically, MFUM-BrTNBC-1 differed
from the commercial TNBC CL MDA-MB-231. The advantages of MFUM-BrTNBC-1 are its isolation
from a primary tumour, rather than a metastatic site; good growth characteristics; phenotype identical
to primary tissue; complete records of origin; a unique identifier; complete, unique STR profile;
quantifiable morphological properties; and genetic stability up to (at least) the 6th passage.
Keywords: hormonal receptors, MFUM-BrTNBC-1, MCF-7, MDA-MB-231, MDA-MB-453
Published in DKUM: 10.04.2025; Views: 0; Downloads: 4
Full text (5,33 MB)
This document has many files! More... |
5. Impaired neurodevelopmental genes in Slovenian autistic children elucidate the comorbidity of autism with other developmental disordersDanijela Krgović, Mario Gorenjak, Nika Rihar, Iva Opalič, Špela Stangler Herodež, Hojka Gregorič Kumperščak, Peter Dovč, Nadja Kokalj-Vokač, 2022, original scientific article Abstract: Autism spectrum disorders (ASD) represent a phenotypically heterogeneous group of patients that strongly intertwine with other neurodevelopmental disorders (NDDs), with genetics playing a significant role in their etiology. Whole exome sequencing (WES) has become predominant in molecular diagnostics for ASD by considerably increasing the diagnostic yield. However, the proportion of undiagnosed patients still remains high due to complex clinical presentation, reduced penetrance, and lack of segregation analysis or clinical information. Thus, reverse phenotyping, where we first identified a possible genetic cause and then determine its clinical relevance, has been shown to be a more efficient approach. WES was performed on 147 Slovenian pediatric patients with suspected ASD. Data analysis was focused on identifying ultrarare or “single event” variants in ASD-associated genes and further expanded to NDD-associated genes. Protein function and gene prioritization were performed on detected clinically relevant variants to determine their role in ASD etiology and phenotype. Reverse phenotyping revealed a pathogenic or likely pathogenic variant in ASD-associated genes in 20.4% of patients, with subsequent segregation analysis indicating that 14 were de novo variants and 1 was presumed compound heterozygous. The diagnostic yield was further increased by 2.7% by the analysis of ultrarare or “single event” variants in all NDD-associated genes. Protein function analysis established that genes in which variants of unknown significance (VUS) were detected were predominantly the cause of intellectual disability (ID), and in most cases, features of ASD as well. Using such an approach, variants in rarely described ASD-associated genes, such as SIN3B, NR4A2, and GRIA1, were detected. By expanding the analysis to include functionally similar NDD genes, variants in KCNK9, GNE, and other genes were identified. These would probably have been missed by classic genotype–phenotype analysis. Our study thus demonstrates that in patients with ASD, analysis of ultrarare or “single event” variants obtained using WES with the inclusion of functionally similar genes and reverse phenotyping obtained a higher diagnostic yield despite limited clinical data. The present study also demonstrates that most of the causative genes in our cohort were involved in the syndromic form of ASD and confirms their comorbidity with other developmental disorders.
Keywords: reverse phenotyping, single event variants, NDD-associated genes, GRIA1 gene, NR4A2 gene, SIN3B gene, autism, child
Published in DKUM: 12.12.2024; Views: 0; Downloads: 7
Full text (6,36 MB)
This document has many files! More... |
6. Single-cell transcriptomic and targeted genomic profiling adjusted for inflammation and therapy bias reveal CRTAM and PLCB1 as novel hub genes for anti-tumor necrosis factor alpha therapy response in Crohn’s diseaseMario Gorenjak, Boris Gole, Larisa Goričan, Gregor Jezernik, Uršula Prosenc Zmrzljak, Cvetka Pernat Drobež, Pavel Skok, Uroš Potočnik, 2024, original scientific article Abstract: The lack of reliable biomarkers in response to anti-TNFα biologicals hinders
personalized therapy for Crohn’s disease (CD) patients. The motivation behind our study is to shift
the paradigm of anti-TNFα biomarker discovery toward specific immune cell sub-populations using
single-cell RNA sequencing and an innovative approach designed to uncover PBMCs gene expression
signals, which may be masked due to the treatment or ongoing inflammation; Methods: The singlecell
RNA sequencing was performed on PBMC samples from CD patients either naïve to biological
therapy, in remission while on adalimumab, or while on ustekinumab but previously non-responsive
to adalimumab. Sieves for stringent downstream gene selection consisted of gene ontology and
independent cohort genomic profiling. Replication and meta-analyses were performed using publicly
available raw RNA sequencing files of sorted immune cells and an association analysis summary.
Machine learning, Mendelian randomization, and oligogenic risk score methods were deployed to
validate DEGs highly relevant to anti-TNFα therapy response; Results: This study found PLCB1 in
CD4+ T cells and CRTAM in double-negative T cells, which met the stringent statistical thresholds
throughout the analyses. An additional assessment proved causal inference of both genes in response
to anti-TNFα therapy; Conclusions: This study, jointly with an innovative design, uncovered
novel candidate genes in the anti-TNFα response landscape of CD, potentially obscured by therapy
or inflammation.
Keywords: inflammatory bowel diseases, Crohn’s disease, tumor necrosis factor alpha, adalimumab, single-cell gene expression analysis
Published in DKUM: 10.12.2024; Views: 0; Downloads: 8
Full text (7,36 MB)
This document has many files! More... |
7. Discovery of novel biomarkers with extended non-coding RNA interactor networks from genetic and protein biomarkersGregor Jezernik, Damjan Glavač, Pavel Skok, Martina Krušič, Uroš Potočnik, Mario Gorenjak, 2024, original scientific article Abstract: Curated online interaction databases and gene ontology tools have streamlined the analysis of highly complex gene/protein networks. However, understanding of disease pathogenesis has gradually shifted from a protein-based core to complex interactive networks where non-coding RNA (ncRNA) is thought to play an essential role. As current gene ontology is based predominantly on protein-level information, there is a growing need to analyze networks with ncRNA. In this study, we propose a gene ontology workflow integrating ncRNA using the NPInter V5.0 database. To validate the proposed workflow, we analyzed our previously published curated biomarker datasets for hidden disease susceptibility processes and pharmacogenomics. Our results show a novel involvement of melanogenesis in psoriasis response to biological drugs in general. Hyperpigmentation has been previously observed in psoriasis following treatment with currently indicated biological drugs, thus calling attention to melanogenesis research as a response biomarker in psoriasis. Moreover, our proposed workflow highlights the need to critically evaluate computed ncRNA interactions within databases and a demand for gene ontology analysis of large miRNA blocks.
Keywords: gene ontology, non-coding RNA, disease pathogenesis
Published in DKUM: 06.12.2024; Views: 0; Downloads: 8
Full text (9,14 MB)
This document has many files! More... |
8. Meta-analytic comparison of global RNA transcriptomes of acute and chronic myeloid leukemia cells reveals novel gene candidates governing myeloid malignanciesStaša Jurgec, Gregor Jezernik, Mario Gorenjak, Tomaž Büdefeld, Uroš Potočnik, 2022, original scientific article Abstract: Despite advances in the understanding of genetic risk factors and molecular mechanisms underlying acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), clinical outcomes of current therapies in terms of disease relapse and mortality rate pose a great economic and social burden. To overcome this, the identification of new molecular prognostic biomarkers and pharmacological targets is crucial. Recent studies have suggested that AML and CML may share common pathogenic mechanisms and cellular substrates. To this end, in the present study, global transcriptome profiles of AML and CML at the molecular and cellular level were directly compared using a combination of meta-analysis and modern statistics, and novel candidate genes and specific biological processes associated with the pathogenesis of AML and CML were characterized. Our study significantly improves our current understanding of myeloid leukemia and will help develop new therapeutic targets and biomarkers for disease progression, management and treatment response.
Keywords: AML, CML, meta-analysis, lincRNA, spliceosome
Published in DKUM: 05.12.2024; Views: 0; Downloads: 5
Full text (1,04 MB)
This document has many files! More... |
9. Identification of novel loci involved in adalimumab response in Crohn’s disease patients using integration of genome profiling and isoform-level immune-cell deconvoluted transcriptome profiling of colon tissueMario Gorenjak, Gregor Jezernik, Martina Krušič, Pavel Skok, Uroš Potočnik, 2022, original scientific article Abstract: Crohn’s disease is a consequence of dysregulated inflammatory response to the host’s microbiota. Although anti-TNF treatment improves the quality of the patient’s life, a large proportion of patients lose response to the treatment. The past decade of research has led to a continuum of studies showcasing the heterogeneity of anti-TNF response; thus, the aim of the present study was to dissect transcriptome-wide findings to transcript isoform specific levels and combine the analyses with refined information of immune cell landscapes in colon tissue, and subsequently select promising candidates using gene ontology and genomic integration. We enrolled Slovenian Crohn’s disease patients who were naïve with respect to adalimumab treatment. We performed colon tissue RNA sequencing and peripheral blood mononuclear cell DNA genotyping with a subsequent contemporary integrative approach to combine immune cell deconvoluted isoform transcript specific transcriptome analysis, gene ontology layering and genomic data. We identified nine genes (MACF1, CTSE, HDLBP, HSPA9, HLA-DMB, TAP2, LGMN, ANAPC11, ACP5) with 15 transcripts and 16 variants involved in the adalimumab response. Our study identified loci, some of which were previously shown to contribute to inflammatory bowel disease susceptibility, as novel loci involved in adalimumab response in Crohn’s disease patients.
Keywords: Crohn’s disease, adalimumab, transcriptome, isoforms, deconvolution
Published in DKUM: 05.12.2024; Views: 0; Downloads: 4
Full text (1,65 MB)
This document has many files! More... |
10. Isoform-level transcriptome analysis of peripheral blood mononuclear cells from breast cancer patients identifies a disease-associated RASGEF1A isoformHelena Sabina Čelešnik, Mario Gorenjak, Martina Krušič, Bojana Crnobrnja, Monika Sobočan, Iztok Takač, Darja Arko, Uroš Potočnik, 2024, original scientific article Abstract: Breast cancer (BC) comprises multiple subtypes with distinct molecular features, which differ in their interplay with host immunity, prognosis, and treatment. Non-invasive blood analyses can provide valuable insights into systemic immunity during cancer. The aim of this study was to analyze the expression of transcriptional isoforms in peripheral blood mononuclear cells (PBMCs) from BC patients and healthy women to identify potential BC immune biomarkers. Methods: RNA sequencing and isoform-level bioinformatics were performed on PBMCs from 12 triple-negative and 13 luminal A patients. Isoform expression validation by qRT-PCR and clinicopathological correlations were performed in a larger cohort (156 BC patients and 32 healthy women). Results: Transcriptional analyses showed a significant (p < 0.001) decrease in the ENST00000374459 RASGEF1A isoform in PBMCs of BC compared to healthy subjects, indicating disease-related expression changes. The decrease was associated with higher ctDNA and Ki-67 values. Conclusions: The levels of the RASGEF1A transcriptional isoform ENST00000374459 may have the potential to distinguish between BC and healthy subjects. The downregulation of ENST00000374459 in breast cancer is associated with higher proliferation and ctDNA shedding. Specialized bioinformatics analyses such as isoform analyses hold significant promise in the detection of biomarkers, since standard RNA sequencing analyses may overlook specific transcriptional changes that may be disease-associated and biologically important.
Keywords: breast cancer, peripheral blood, isoform-level RNA-seq, RASGEF1A ENST00000374459, ctDNA, Ki-67
Published in DKUM: 26.11.2024; Views: 0; Downloads: 6
Full text (1,52 MB)
This document has many files! More... |
