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Home > Genome Wide Mapping of Chromatin States Based on Histone Combinatorics for Determination of Epigenetic Expression

Genome Wide Mapping of Chromatin States Based on Histone Combinatorics for Determination of Epigenetic Expression

Thesis Info

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Author

Noureen, Nighat

Program

PhD

Institute

Capital University of Science & Technology

City

Islamabad

Province

Islamabad.

Country

Pakistan

Thesis Completing Year

2015

Thesis Completion Status

Completed

Subject

Bioinformatics

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/9652/1/Nighat_Noureen_Bioinfromatics_2016_CUST_Islamabad_10.05.2016.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726328768

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Histone proteins wrap DNA around in small globular entities commonly known as nucleosomes. The post translational modifications to the histone tails are referred as histone modifications (HMs). The regulation of DNA in order to access the transcription machinery is epigenetically programmed by specific DNA and chromatin covalent modifications. HMs could either be present or absent at particular genomic loci and the combinatorial patterns of the specific modifications being addressed as ‘histone codes’, are believed to co-regulate significant biological processes. Regions defined by combinatorial patterns of marks can be referred to as chromatin states. Chromatin states associated with genomic locations correlate with specific functional elements as enhancers, transcription start sites, which can be exclusively inferred from successive combinations of chromatin marks in their contiguous locations. Biologically significant combinatorics of epigenetic modifications and their subsequent functional interplay are still mostly unrevealed. We aimed to use ChIP-Seq data of Histone modifications at different genomic loci to highlight the unbiased genomic grouping and to decode the complex biological network of HMs in association with other chromatin players in defining various chromatin states. We used different tools and techniques to accomplish our task. Complex biological networks underlying the hidden chromatin states were revealed via merging machine learning and graph theory existing approaches. Histone modification efficient and simple combinatorics was studied at a global and local scale by developing and implementing a clustering and biclustering tool. Results have been compared with the existing approaches. Meanwhile a simple and efficient computational methodology for efficient chromatin states identification for ChromHMM (HMM based chromatin segmentation) has also been developed by utilizing Hidden Markov Models components. As a result of above study we revealed the role of various factors in maintaining the chromatin state connectivity via focusing chromatin state networks. Our studies highlighted the minimum dominating nodes set and various hubs in chromatin state networks focusing their interaction patterns. Along with we developed and tested a clustering tool ChromClust and a biclustering tool ChromBiSim to highlight histone combinatorics in binarized signal data in an efficient and interactive way. ChromClust operates at global level while ChromBiSim mines local patterns of histone modifications associations. We conclude that epigenomic landscape is portrayed as interplay of various factors including histone combinations, transcription factors, chromatin modifiers and most importantly the underlying DNA motifs. Each chromatin state has a specific set of these factors which interact with each other to mark that state hence creating the whole chromatin states network.
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دو بہادر دوست

دو بہادر دوست

اک واری دی گل اے کہ کسے پنڈ وچ دو دوست رہندے سن۔ اوہ رج کے نکمے سن۔ کوئی کم نہیں کر دے تے ہر ویلے روٹیاں کھاندے سن۔ اوہناں دے گھر والے اوہناں توں بہت تنگ سن۔ جدوں اوہ اوہناں نوں کم کرن دا آکھدے تاں اوہ کوئی نہ کوئی بہانہ بنا کے اوہناں دا حکم ٹال دیندے۔ تنگ آ کے گھر والیاں اوہناں نوں گھروں کڈھ دتا تے زہر والیاں روٹیاں پکا کے اوہناں نوں نال دے دتیاں۔ اوہ گھروں ٹر پیندے نیں۔ کافی دور جا کے اوہناں نوں بھکھ لگدی اے۔ اوہ روٹی کھاون لئی اک درخت تھلے بہہ جاندے نیں۔ جدوں اوہناں روٹی رومال وچوں کھول کے سامنے رکھی تاں ویکھدے نیں کہ اک شیر اوہناں ول آ رہیا اے۔ تے اوہدے پچھے بادشاہ دی فوج لگی ہوئی اے۔ شیر سدھا اوہناں ول آیا تے اوہ ڈر کے درخت اتے چڑھ گئے۔ شیر نوں بھکھ لگی ہوئی سی۔ اوس ساریاں روٹیاں کھالئیاں تے تھوڑی دیر بعد زہر دے اثر پاروں مر گیاں۔ جدوں اوہناں ویکھیا کہ شیر مر گیا اے تاں اوہ درخت توں تھلے اترے تے شیر دی گردن اتے بہہ گئے۔ اینے چر وچ فوجی اوتھے آوندے نیں۔ اوہناں ویکھیا کہ دو بندیاں نے شیر نوں مار دتا اے۔ اوہ فوجی اوہناں دو نواں نوں لے کے بادشاہ کول آندے نیں۔ بادشاہ اوہناں دی بہادری اتے بہت خوش ہوندا اے تے اوہناں نوں اپنی فوج وچ ملازم رکھ لیندا اے۔ بادشاہ علاقے وچ اعلان کروا دیندا اے کہ ایہہ دونویں بندے شہر وچوں جو کجھ وی کھاون ایہناں نوں روکیا نہ جاوے۔ اوہ دونویں بہت خوش ہوندے نیں تے ون سونّے کھانے کھا کے موٹے ہو جاندے نیں۔

اک دن اچانک بادشاہ دی دوجے ملک دے بادشاہ نال لڑائی شروع ہو جاندی...

Indian Muslim Freedom Fighters Based in Afghanistan and Soviet Russia

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Financial Liberalization and its Impact on Economic Growth of Pakistan

This dissertation is an attempt to contribute theoretically and empirically in the area of research regarding financial liberalization and economic growth for Pakistan. On account of growing importance of financial liberalization in the promotion of growth in the developed and emerging economies and dearth of significant literature on this topic in the case of Pakistan, the present study examines the impact of financial liberalization on economic growth. The thesis investigates both the domestic and external components of the financial liberalization process and their impact on economic growth of Pakistan. The dissertation in particular develops an index of domestic financial liberalization using the technique of principal component analysis. The index captures the important dimension of reform process and quantifies the impact of domestic financial liberalization on growth. The external financial liberalization is examined through the de jure and de facto measures of external financial liberalization. The dissertation develops a quantitative measure of external financial openness through de jure approach on the basis of information under the capital account liberalization. The de facto measure of external financial liberalization is based on the work of Lane and Ferretti (2006) while the data for remaining years are updated utilizing their methodology. A joint impact of both the domestic and external components of financial liberalization (showing an overall impact of financial liberalization on growth) is also examined through the measure of domestic financial liberalization index and de facto measure of external financial liberalization. The results of the study indicate a positive impact of composite index of domestic financial liberalization on economic growth. External financial liberalization when measured through de jure approach positively impacts economic growth. However, the de facto measure shows a negative association between external financial openness and economic growth. The empirical results finally report an overall positive impact of financial liberalization on economic growth examined by including both the domestic and external components of financial liberalization. The positive impact of financial liberalization on economic growth is on account of financial intermediation, financial deepening and easy access to capital brought through domestic and external liberalization. However, to get more pronounced benefits out of liberalization process, financial sector needs more strengthening both at the domestic and external fronts.