Browsing by Subject "Network analysis"

Now showing 1 - 9 of 9

Open Access
Dynamic integration and network structure of the EMU sovereign bond markets
(Springer, 2019) Şensoy, Ahmet; Nguyen, D. K.; Rostom, A.; Hacıhasanoğlu, E.
In this paper, we propose a novel concept of correlation-based stable networks to empirically investigate the dynamic integration and network structure of the European Monetary Union (EMU) sovereign bond markets. The obtained results uncover a high degree of market integration between sample markets over the period preceding the recent financial crises, while segmentation is found afterwards. The stable network analysis shows, for its part, the existence of two different network structures before and after the onset of the European debt crisis, where the in-crisis network structure is characterized by two groups of countries with respect to their fiscal performance. In particular, Belgium is the unique vertex connecting the two groups, making it the channel for shock transmission in the event of worsening debt crisis in the EMU.
Open Access
Essays on financial connectivity and stability
(2019-11) Demir, Müge
This thesis investigates the structure of cross-border lending market by using network analysis and examines the relationship between financial connectivity and probability of systemic crises, controlling for macroeconomic variables. A country-level panel data set of BIS locational banking statistics for bank-to-bank and bank-to-non-bank cross-border lending markets including 177 countries is used in the analysis for the 1978-2016 period. Systemic crisis periods are retrieved from European Systemic Risk Board ( Lo Duca et al. (2017)) and Laeven and Valencia (2013, 2018). In the literature, there are two conflicting arguments on the relationship between financial connectivity and stability. On the one hand, it is argued that an increase in the level of financial connectivity enhances financial stability by allowing financial institutions to absorb the negative impacts of a shock among many counterparties through risk sharing. On the other hand, depending on the structure of the financial markets, it can also deteriorate financial stability by facilitating the spread of a shock from one institution to another, leading to an increase in systemic risk. We, first, examine cross-border bank-to-bank and bank-to-non-bank lending markets of 13 advanced economies. We find that an increase in financial connectivity reduces the probability of systemic crises. However, this effect is found to be mitigated or completely eliminated in credit boom and capital inflow upsurge periods in both lending markets. Second, we examine European bank-to-bank and bank-to-non-bank cross-border lending markets comprised of 25 countries, during 1978-2016 period, as it allows us to test the effect of the level of financial integration measured by the level of financial connectivity on the probability of crisis. We find that while using the single currency, Euro, helps to improve the resiliency of EU in response to crisis in both networks, legislative-regulatory integration across member states without eliminating currency risk undermines the resiliency of the EU bank-to-bank lending network. During the excessive cross-border lending period, an increase in connectivity is found to raise the probability of crisis for both lending networks, regardless of the membership status. Finally, we extend our data set to 177 countries and examine the relationship between financial connectivity and stability in the global lending network. We find that in bank-to-bank lending network, an increase in global financial connectivity decreases the probability of crises, but this effect is found to be eliminated only in credit boom periods. On the other hand, an increase in local connectivity is found to be associated with an increase in the probability of crisis. This effect seems to be mainly driven by emerging countries, rather than advanced countries. In both lending markets we find that capital inflow periods do not affect the relationship between connectivity and probability of crisis. The findings suggest that policy-makers should design a financial market mechanism that can reduce risks associated with an increase in financial connectivity, while maintaining its benefits.
Open Access
Financial connectivity and excessive liquidity: benefit or risk?
(Elsevier, 2019) Demir, Müge; Önder, Zeynep
This paper explores the structure of cross-border lending market by using network analysis and examines the relationship between financial connectivity and probability of systemic crises during normal, credit boom and capital inflow upsurge periods, controlling for macroeconomic variables. A country-level panel data set for bank-to-bank and bank-to-non-bank cross-border lending markets of 13 advanced economies is used in the analysis for the 1978–2016 period. We find that a rise in financial connectivity reduces the probability of systemic crises. However, this effect is found to be mitigated or completely eliminated in credit boom and capital inflow upsurge periods in both markets. The findings suggest that bank-to-non-bank lending market is more stable in terms of both the number and the amount of lending relationships and recovered faster than bank-to-bank lending market following the recent global financial crisis.
Open Access
Identification of protein-protein interaction bridges for multiple sclerosis
(2022-12) Yazıcı, Gözde
Identifying and prioritizing disease-related proteins is an important scientific problem to understand disease etiology. Network science has become an important discipline to prioritize such proteins. Multiple sclerosis (MS), an autoimmune disease which still cannot be cured, is characterized by a damaging process called demyelination. Demyelination is the destruction of the crucial nerve sheath, myelin, and oligodendrocytes, the cells producing myelin, by immune cells. Identifying the proteins having special features on the network formed by the proteins of oligodendrocyte and immune cells can reveal useful information about the disease. To this end, we investigated the most significant protein pairs for the intraand intercellular protein networks that we define as bridges among the proteins providing the interaction between the two cells in demyelination. We analyzed two protein networks including the oligodendrocyte and each type of two immune cells, macrophage and T-cell. We developed a model called BriFin that prioritizes contact protein pairs using network analysis techniques and integer programming. We showed several proteins it prioritized have already been associated with MS in the relevant literature. For the oligodendrocyte-macrophage network, we showed that 77% to 100% of the proteins BriFin detected, depending on the parametrization, are MS-associated. We further experimentally investigated 4 proteins prioritized by BriFin, and observed that the mRNA expression levels of 2 out of these 4 proteins significantly decreased in a group of MS patients. We therefore here present a model, BriFin, which can be used to analyze processes where interactions of two cell types play an important role.
Open Access
Lower connectivity of tumor coexpression networks is not specific to cancer
(IOP, 2019-05) Dalgıç, E.; Konu, Özlen; Safi Öz, Z.; Chan, C.
Global level network analysis of molecular links is necessary for systems level view of complex diseases like cancer. Using genome-wide expression datasets, we constructed and compared gene co-expression based specific networks of pre-cancerous tumors (adenoma) and cancerous tumors (carcinoma) with paired normal networks to assess for any possible changes in network connectivity. Previously, loss of connectivity was reported as a characteristic of cancer samples. Here, we observed that pre-cancerous conditions also had significantly less connections than paired normal samples. We observed a loss of connectivity trend for colorectal adenoma, aldosterone producing adenoma and uterine leiomyoma. We also showed that the loss of connectivity trend is not specific to positive or negative correlation based networks. Differential hub genes, which were the most highly differentially less connected genes in tumor, were mostly different between different datasets. No common gene list could be defined which underlies the lower connectivity of tumor specific networks. Connectivity of colorectal cancer methylation targets was different from other genes. Extracellular space related terms were enriched in negative correlation based differential hubs and common methylation targets of colorectal carcinoma. Our results indicate a systems level change of lower connectivity as cells transform to not only cancer but also pre-cancerous conditions. This systems level behavior could not be attributed to a group of genes.
Open Access
Multiomics approaches to overcome drug resistance in cancer
(2021-09) Küçükkaraduman, Barış
Chemotherapy resistance remains one of the major challenges in cancer treatment. Most of the studies on drug resistance have focused on genetic evolution of cancer cells; however, this focus has shifted to non-genetic and epigenetic mechanisms. There is accumulating evidence that mechanisms of drug resistance are not mutually exclusive but instead coexist within a given cancer to develop resistance and therapy failure. Hence, overcoming resistance requires the comprehension of these complex biological processes. Here, we aimed to characterize drug resistance mechanisms by performing both single omics interrogations and multi-omics integrative analysis. For this purpose, we conducted Gene Set Enrichment Analysis (GSEA), functional enrichment analysis on protein-protein interaction (PPI) networks and miRNA-target networks for interpreting gene and miRNA expression data. To gain further biological insights on resistance mechanisms, we focused on identifying a multi-omics molecular signature that discriminates cancer cells based on their drug response profiles. Collectively, these in silico analyses suggested the epithelial-to mesenchymal transition (EMT) as a mediator of 5-FU/irinotecan resistance in colon cancer and irinotecan/gemcitabine resistance in pancreatic cancer. Drug sensitive cancer cells exhibited a more epithelial phenotype with increased cell proliferation. Multi-omics integration analysis revealed some EMT-related genes such as TGM2 and FOSL1, to contribute differential drug response in cancer cells. On the other hand, response of breast cancer cells to doxorubicin exhibited an opposite profile in which mesenchymal phenotype is sensitive while resistant cells have epithelial phenotype. Secondly, we aimed to induce mesenchymal-to-epithelial transition to overcome EMT-mediated drug resistance. We selected eight natural compounds and two re-purposed agents that have been shown to reverse EMT in various studies. We noted transcriptional changes suggesting a shift towards a more epithelial phenotype in 4 out of the 6 cell lines upon treatment with at least one compound tested. None of the natural compounds or re-purposed agents triggered MET in all cancer cells screened. In addition, compounds with clear or slight MET induction did cause these effects in a specific cell line or only in specific cancer type. We investigated next whether the treatment with natural compounds would result in chemosensitization. MET induction by natural compounds is not uniformly related to increased sensitivity to chemotherapeutics but can result in occasional synergistic or additive effects. Lastly, based on cytotoxic activity of a novel c-Src inhibitor 10a in 15 melanoma cells, we report the identification of a new gene signature that can predict chemosensitivity to 10a. Two distinct phenotypes of cells, defined as sensitive and resistant, were further analyzed to reveal an underlying mechanism for this differential response to 10a. We found that proliferative or mesenchymal features of the cells are associated with distinct sensitivity of 10a. Through a protein−chemical interaction network analysis, we identified that three histone deacetylase inhibitors, valproic acid, entinostat, and trichostatin A, were predicted to synergize with 10a. The synergizing effect of valproic acid was validated in vitro. We also aimed to define a minimal number of genes that could be used as biomarkers of 10a sensitivity. We show that the expression level of four genes can be used to predict drug sensitivity against 10a.
Open Access
Network structure of Turkish interbank market
(Elsevier B.V., 2022-12-01) Sümer, Tuba Pelin; Özyıldırım, Süheyla
Global financial crisis has shown the importance of understanding the structure of interbank relations. In this study, we investigate the network relations based on interbank exposures in Türkiye. We estimate several network statistics and document how the network relations have changed over the time period of 2002–2021. We find that the network structures vary substantially by financial instruments such as repo, deposit, loan, security issuances, derivatives and other off-balance sheet items showing the significance of covering all type of exposures in network analysis. Using network statistics, we show that Turkish interbank network structure shows a core-periphery structure which is found to be more resilient during stress times in the literature. Finally, we find that larger banks are characterized as having higher network centrality measures as degree, clustering coefficient and closeness centrality showing the importance of these banks in terms of intermediation and substitutability.
Open Access
Quantitative approaches to Hittite historical geography: a network analysis of Hittite toponyms
(2023-08) Akman, M. Ali
There are many references to place names in the Hittite texts, and the understanding of their locations is crucial to the study of Hittite history and society. In the past, the examination of these place names, which occur more than 20,000 times, was limited to methods that were qualitative in nature. Nonetheless, due to the Hittite Toponyms project led by Adam Kryszeń, there is now an exciting opportunity to conduct a comprehensive quantitative study of Hittite toponyms. This research presents an original statistical methodology based on network analysis to gain a deeper understanding of the relative positions of toponyms in Hittite texts. Toponyms are represented as nodes in a network, and the strength of their connections is determined by the frequency of their occurrence in the same text fragment. This thesis demonstrates the proposed methodology's ability to explain geography through examples at different scales, including a modern case study and a case study on Durmitta's location. The results highlight that when combined with qualitative methods, the suggested statistical approach can offer new insights into Hittite historical geography, improving our comprehension of this ancient civilization.
Open Access
Systemic risk and financial networks
(2019-12) Sümer, Tuba Pelin
This thesis investigates the interbank relations of Turkish banks with each other and foreign banks abroad. In the ﬁrst chapter, we focus on the interbank relations between domestic banks and study the eﬀects of bank ownership structure on the in terbank network structure. During the sample period of 2003-2017, we observe that foreign and state-owned banks play dominant role in shaping the network structure. Foreign banks, in particular, have a higher coreness vector in derivative exposures through their comparative advantage in oﬀsetting derivative transactions. More over, our ﬁndings indicate that when a foreign investor acquires a domestic bank, the network structure of the acquired bank changes considerably. We also present evidence that local and Basel III regulations play a signiﬁcant role in the formation of the network structure through liquidity channel. In the second chapter, we focus on the interbank relations between banks in Turkey and foreign banks abroad for 2014-2018 period. Funding from foreign banks in repo, deposit and loan type is an important ﬁnancing channel for domestic banks. For hedging currency risk, domestic banks are also making derivative transactions with foreign counterparties. We docu ment several network statistics and analyze the similarities of bank rankings in these statistics. Moreover, we examine the similarities between diﬀerent instrument-level networks as repo, loan, deposit and derivatives. By diﬀerentiating foreign banks as the banks having shares in domestic banks and others and the banks that work ac cording to islamic principles and others, we investigate the evolvement of interbank relations between these groups.