Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Empirical Analysis of Competition in Procurement Auctions

A vast amount of public services and goods are contracted through procurement auctions. Therefore it is very important to design these auctions in an optimal way. Typically, we are interested in two different objectives. The first objective is efficiency. Efficiency means that the contract is awarded to the bidder that values it the most, which in the procurement setting means the bidder that has the lowest cost of providing a service with a given quality. The second objective is to maximize public revenue. Maximizing public revenue means minimizing the costs of procurement. Both of these goals are important from the welfare point of view. In this thesis, I analyze field data from procurement auctions and show how empirical analysis can be used to help design the auctions to maximize public revenue. In particular, I concentrate on how competition, which means the number of bidders, should be taken into account in the design of auctions. In the first chapter, the main policy question is whether the auctioneer should spend resources to induce more competition. The information paradigm is essential in analyzing the effects of competition. We talk of a private values information paradigm when the bidders know their valuations exactly. In a common value information paradigm, the information about the value of the object is dispersed among the bidders. With private values more competition always increases the public revenue but with common values the effect of competition is uncertain. I study the effects of competition in the City of Helsinki bus transit market by conducting tests for common values. I also extend an existing test by allowing bidder asymmetry. The information paradigm seems to be that of common values. The bus companies that have garages close to the contracted routes are influenced more by the common value elements than those whose garages are further away. Therefore, attracting more bidders does not necessarily lower procurement costs, and thus the City should not implement costly policies to induce more competition. In the second chapter, I ask how the auctioneer can increase its revenue by changing contract characteristics like contract sizes and durations. I find that the City of Helsinki should shorten the contract duration in the bus transit auctions because that would decrease the importance of common value components and cheaply increase entry which now would have a more beneficial impact on the public revenue. Typically, cartels decrease the public revenue in a significant way. In the third chapter, I propose a new statistical method for detecting collusion and compare it with an existing test. I argue that my test is robust to unobserved heterogeneity unlike the existing test. I apply both methods to procurement auctions that contract snow removal in schools of Helsinki. According to these tests, the bidding behavior of two of the bidders seems consistent with a contract allocation scheme.

Towards Multiculturalism in Turkish Public Service Broadcasting

The announcement of Turkey as a European Union (EU) candidate country in the Helsinki Summit (10, 11 December 1999) marked a distinct change of identity policy and attitudes towards its citizens. A result in the shift of mindset has been the launch of the first public service broadcasting TV channel for Kurdish people on the 1st of January 2009. TRT 6 (Şeş) broadcasting in unofficial Kurdish language is run by Turkish Radio and Television Corporation (TRT). The thesis attempts to elaborate on the discussions surrounding the launch of TRT 6, Turkey’s first public service broadcasting TV channel for its Kurdish citizens. The research aims at finding the discourses of multiculturalism and public service broadcasting through the mainstream Turkish newspapers, Cumhuriyet, Hurriyet, Sabah, Taraf and Zaman. The method used for the research is Critical Discourse Analysis (CDA) and the representative newspapers of the Turkish print media are under the question: How has the launch of TRT 6, as the first public service broadcasting channel of Turkey in Kurdish language, been discussed by Turkish daily newspapers in terms of multiculturalism and minority media? The most significant results of the research is that the concerning newspapers have mostly discussed the launch of TRT 6 in the same line with their political affiliation. Thus it is comprehensively concluded that the selected newspapers proved holding a high level of political parallelism, and low professionalism. However, it should be noted that Taraf differs itself from others while challenging the hegemonic discourses embedded in the articles of the other newspapers. Moreover, the study detected three types of discourses: Pro-multiculturalism discourse, Unification discourse, and Assimilation discourse. It can be concluded that in Turkey, media owners and even individual journalists have incentives to form ideological alliances with political parties, and media appears to be an instrument of power struggle. Today, Turkey seems to restore Kurdish identity in its identity policy and aims to proceed with the negotiation for membership of the European Union (EU). The country still strives to transform from the traditional nation-state to a multiethnic democratic state, with multiculturalism as a policy discussed throughout the two terms that the AKP government has been in power. However, this transformation is not an easy process because of the deep-rooted traditions of the nation-state structure that has also polarized the Turkish press.

Chinese immigrants to Finland: A qualitative study of housing, employment, access to health care and child care as sociological dimensions in their settlement process

The Master’s thesis is qualitative research based on interviews of 15 Chinese immigrants to Finland in order to provide a sociological perspective of the migration experience through the eyes of Chinese immigrants in the Finnish social welfare context. This research is mainly focused upon four crucial aspects of life in the settlement process: housing, employment, access to health care and child care. Inspired by Allardt’s theoretical framework ‘Having, Loving and Being’, social relationships and individual satisfaction are examined in the case of Chinese interviewees dealing with the four life aspects. Finland was not perceived as an attractive migration destination for most Chinese interviewees in the beginning. However, with longer residence in Finland, the Finnish social welfare system gradually became a crucial appealing factor in their permanent settlement in Finland. And meanwhile, social responsibility of attending their old parents in China, strong feelings of being isolated in Finland, and insufficient integration into the Finnish society were influential factors for their decision of returning to China. Social relationships with personal friends, migration brokers, schools, employers and family relatives had great influences in the four life aspects of Chinese immigrants in Finland. The social relationship with the Finnish social welfare sector is supportive to Chinese immigrants, but Chinese immigrants do not heavily rely on Finnish social protection. The housing conditions were greatly improved over time while the upward mobility in the Finnish labour market was not significant among Chinese immigrants. All Chinese immigrants were satisfied with their current housing by the time I interviewed them while most of them had subjective feelings of being alienated in the Finnish labour market, which seriously prevented them from integrating into the Finnish society. In general, Chinese immigrants were satisfied with the low cost of accessing the Finnish public health care services and affordable Finnish child day care services and financial subsidies for children from the Finnish social welfare sector. This research also suggests that employment is the central basis in well-being. Support from the Finnish social welfare sector can improve the satisfaction levels among immigrants, especially when it mitigates the effects of low-paid employment. As well, my empirical study of Chinese immigrants in Finland shows that Having (needs for materials), Loving (needs for social relations) and Being (needs for social integration) are all involved in the four concrete aspects (housing, employment, access to health care and child care).