Browsing by Author "Nabi, Afshan"

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    Correction to: NoRCE: non‑coding RNA sets cis enrichment tool
    (BioMed Central Ltd., 2021-08-04) Olgun, Gülden; Nabi, Afshan; Tastan, Oznur
    While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results: We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions: NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.
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    Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease
    (Canadian Science Publishing, 2022-02-02) Keşkuş, Ayşe Gökçe; Tombaz, Melike; Arıcı, Burçin İrem; Dinçaslan, Fatma Betül; Nabi, Afshan; Shehwana, Huma; Konu, Özlen
    Human Angiotensin I Converting Enzyme 2 (ACE2) plays an essential role in blood pressure regulation and SARS-CoV-2 entry. ACE2 has a highly conserved, one-to-one ortholog (ace2) in zebrafish, which is an important model for human diseases. However, the zebrafish ace2 expression profile has not yet been studied during early development, between genders, across different genotypes, or in disease. Moreover, a network-based meta-analysis for the extraction of functionally enriched pathways associated with differential ace2 expression is lacking in the literature. Herein, we first identified significant development-, tissue-, genotype-, and gender-specific modulations in ace2 expression via meta-analysis of zebrafish Affymetrix transcriptomics datasets (ndatasets = 107); and the correlation analysis of ace2 meta-differential expression profile revealed distinct positively and negatively correlated local functionally enriched gene networks. Moreover, we demonstrated that ace2 expression was significantly modulated under different physiological and pathological conditions related to development, tissue, gender, diet, infection, and inflammation using additional RNA-seq datasets. Our findings implicate a novel translational role for zebrafish ace2 in organ differentiation and pathologies observed in the intestines and liver.
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    Through divisive lenses: George E. White on the Turkish-Armenian conflict
    (Bilkent University, 2018) Ali, Wissam Al; Ahmed, Usama; Younis, Rola; Nabi, Afshan; İsmayılova, Ayan; Heydarova, Seyid Nargiz
    Türkiye'de 43 yıldır çalışan bir ABCFM misyoneri olan George E. White, deneyimleri hakkında kapsamlı yazılar yazdı. Yazılarının ve diğer ikincil literatürün ışığında, bu çalışma Osmanlı İmparatorluğu'nda misyoner faaliyetin Osmanlı toplumunda bölücü bir rol oynadığını tespit etmeyi amaçlamaktadır. Misyoner odak Osmanlı'da yaşayan Hristiyan halkların yükselişine yardım etti ve dolayısıyla Türk ve Ermeni halkı arasındaki gerginliği artırdı. Dahası, Batı medyasında yaygın olarak dolaşan önyargılı misyonerlik yazıları, dar görüşlü din ve uygarlık alanlarında Batı'da (Ermeniler lehine ve Türklere karşı) önyargılı bir kamuoyunun şekillenmesine yardımcı oldu.