Design of a sequence based miRNA clustering method; analysis of fungal miRNAs and host organism target genes

Download

index.pdf

Date

2014

Author

Narcı, Kübra

Metadata

Show full item record

Item Usage Stats

267
views

115
downloads

MicroRNAs are small non-coding RNA molecules which contain 21-25 nucleotides, and function in post transcriptional regulation by inhibiting the translation of mRNA targets. miRNAs typically affect gene regulation by forming composite feed forward circuits (cFFCs) which also comprise a transcription factor (TF) and a target gene. By analyzing these cFFCs, the contribution of miRNAs in altering TF networks can be revealed. These contributions could either be the de-escalation of the target gene repertoire or to increase the redundancy through cFFC formation. To conduct the analysis, the connections between genes, miRNAs, and TFs are obtained using two datasets one of which is obtained from human myeloid leukemia cell line. These two datasets are also different from each other in terms of the numbers of TFs and miRNAs that are included in the networks and the significance of the predicted connections. The first dataset which contains connectivity information of a normal cell involves 83 TFs, 564 miRNAs and 5169 genes which construct 124,740 and 34,298 human-mouse conserved TF and miRNA regulatory connections, respectively. The second dataset which contains 137 miRNAs, 274 TFs and 6749 genes which are compiled from the FANTOM 4 database from which the total number of human-mouse conserved regulatory connections is identified as 6631 for miRNAs and 60969 for TFs. Then, in order to reveal the significance on a statistical level, the randomization tests are applied to the connectivity matrix. Obtaining the significance of miRNA-based cFFCs lead us to conclusions about the effect of miRNAs in fine-tuning gene regulatory networks and the evolutionary role of miRNAs in the cell regulation.

Subject Keywords

RNA., Nucleic acids., Genetic regulation., Nucleotide sequence., Plant-fungus relationships.

URI

http://etd.lib.metu.edu.tr/upload/12617681/index.pdf
https://hdl.handle.net/11511/23859

Collections

Graduate School of Informatics, Thesis

Suggestions

OpenMETU
Core

Analysis of motifs in microRNA-transcription factor gene regulatory networks Sürün, Bilge; Acar, Aybar Can; Purutçuoğlu Gazi, Vilda; Department of Bioinformatics (2014) MicroRNAs are small non-coding RNA molecules which contain 21-25 nucleotides, and function in post transcriptional regulation by inhibiting the translation of mRNA targets. miRNAs typically affect gene regulation by forming composite feed forward circuits (cFFCs) which also comprise a transcription factor (TF) and a target gene. By analyzing these cFFCs, the contribution of miRNAs in altering TF networks can be revealed. These contributions could either be the de-escalation of the target gene repertoire or ...
Design and construction of double promoter systems and their use in pharmaceutical protein production in P. Pastoris Demir, İrem; Çalık, Pınar; Department of Chemical Engineering (2019) Intracellular phenomena such as promoter strength, mRNA secondary structure, translation efficiency and codon preference, 5′-untranslated region processing, and protein turnover, have impacts directly on the expression of heterologous genes. Design of multi-promoter expression systems with constituent strong promoters and engineered promoter variants is a novel metabolic engineering strategy for increasing the promoter strength further, and tuning the expression for recombinant protein (r-protein) productio...
Integration of clavaminate synthase 2 gene into the chromosome of an industrial strain of Streptomyces Clavuligerus for enhanced clavulanic acid production Vanlı, Güliz; Özcengiz, Gülay; Özkan, Melek; Department of Biotechnology (2010) Streptomyces clavuligerus is a gram-positive, filamentous bacterium which has a great ability to produce secondary metabolites including isopenicillin N, cephamycin C and a beta-lactamase inhibitor clavulanic acid. Clavulanic acid (CA) which is a bicyclic beta-lactam, inhibits most of class A beta-lactamases by binding irreversibly to the serine hydroxyl group at the active center of beta-lactamases and resulting in the stable acyl-enzyme complexes. Clavaminate synthase (CAS) is one of the best characterize...
Inference of Gene Regulatory Networks Via Multiple Data Sources and a Recommendation Method Ozsoy, Makbule Gulcin; Polat, Faruk; Alhajj, Reda (2015-11-12) Gene regulatory networks (GRNs) are composed of biological components, including genes, proteins and metabolites, and their interactions. In general, computational methods are used to infer the connections among these components. However, computational methods should take into account the general features of the GRNs, which are sparseness, scale-free topology, modularity and structure of the inferred networks. In this work, observing the common aspects between recommendation systems and GRNs, we decided to ...
Analysis of ligand-receptor cross-linked fragments by mass spectrometry Son, Çağdaş Devrim; Hurst, GB; Naider, F; Becker, JM (Wiley, 2005-03-01) G-protein coupled receptors (GPCRs) are a class of integral membrane receptor proteins that are characterized by a signature seven-transmembrane (7-TM) configuration. The alpha-factor receptor (Ste2p) from Saccharomyces cerevisiae is a GPCR that, upon binding of a peptide ligand, transduces a signal to initiate a cascade of events leading to the mating of haploid yeast cells. This study summarizes the application of affinity purification and of matrix-assisted laser-desorption ionization time-of-flight (MAL...

Citation Formats

K. Narcı, “Design of a sequence based miRNA clustering method; analysis of fungal miRNAs and host organism target genes,” M.S. - Master of Science, Middle East Technical University, 2014.