MARC details
| 000 -LEADER |
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| fixed length control field |
07634nam a22002537a 4500 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION |
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| fixed length control field |
201210b2022 a|||f bm|| 00| 0 eng d |
| 040 ## - CATALOGING SOURCE |
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| Original cataloging agency |
EG-CaNU |
| Transcribing agency |
EG-CaNU |
| 041 0# - Language Code |
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| Language code of text |
eng |
| Language code of abstract |
eng |
| 082 ## - DEWEY DECIMAL CLASSIFICATION NUMBER |
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| Classification number |
610 |
| 100 0# - MAIN ENTRY--PERSONAL NAME |
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| Personal name |
Nourelislam Mohamed Awad Ahmed |
| 245 1# - TITLE STATEMENT |
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| Title |
A framework for Alternative Splicing Isoforms Detection in Lung Cancer/ |
| Statement of responsibility, etc. |
Nourelislam Mohamed Awad Ahmed |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. |
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| Date of publication, distribution, etc. |
2022 |
| 300 ## - PHYSICAL DESCRIPTION |
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| Extent |
124 p. |
| Other physical details |
ill. |
| Dimensions |
21 cm. |
| 500 ## - GENERAL NOTE |
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| Materials specified |
Supervisor: <br/>Walid Ibrahim Ali Al-Atabany<br/>Mohamed El Hadidi<br/> |
| Linkage |
<br/> |
| General note |
Publication:<br/>1-Immunoinformatics approach of epitope prediction for SARS-CoV-2<br/>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9019534/ <br/><br/>2-A feature selection-based framework to identify biomarkers for cancer diagnosis: A focus on lung adenocarcinoma<br/>https://pubmed.ncbi.nlm.nih.gov/36067196/ |
| 502 ## - Dissertation Note |
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| Dissertation type |
Thesis (M.A.)—Nile University, Egypt, 2022 . |
| 504 ## - Bibliography |
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| Bibliography |
"Includes bibliographical references" |
| 505 0# - Contents |
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| Formatted contents note |
Contents:<br/>Certificate of approval…………………………………………………………………………………...II<br/>Abstract …………………………………………………………………………………………………III<br/>List of figures ………………………………………………………………………………………...…VI<br/>List of tables ………………………………………………………………………………………….... VII<br/>List of abbreviations …………………………………………………………………………………...VIII<br/>Chapter 1: Introduction …………………………………………………………………………….….… 1<br/>1.1 Lung cancer…………………………………………………………………………….….……....1<br/>1.2 Alternative splicing…………………………………………………………………….….……... 1<br/>1.3 RNA-seq technology in defining alternative splicing ……………………………….….…….....2<br/>1.4 Detection of alternative splicing ………………………………………………………..……….. 2<br/>1.5 Alternative splicing and cancer ………………………………………………………..………....2<br/>1.6 Thesis objective ………………………………………………………………………….….…….. 3<br/>Chapter 2: Literature review ………………………………………………………………………..……..4<br/>2.1 RNA complexity ……………………………………………………………………………..…… 4<br/>2.2 Alternative splicing and cancer …………………………………………………………….…… 5<br/>2.3 Cancer biomarker and alternative splicing ……………………………………………….……. 7<br/>2.4 Alternative splicing and cancer immunotherapy ………………………………………….…… 8<br/>Chapter 3: Material and methods ……………………………………………………………………….. 10<br/>3.1 Data collection and cleaning ……………………………………………………………………... 10<br/>3.2 Mapping approach ……………………………………………………………...…………………10<br/>3.3 Ttranscriptome assembly ……………………………………………………………………….....12<br/>3.4 Ttranscriptome assembly assessment …………………………………………………………… 13<br/>VIII<br/>3.5 Differential expression analysis …………………………………………………………………...14<br/>3.6 Statistical enrichment analysis …………………………………………………………………... 15<br/>Chapter 4: Results ……………………………………………………………………………………….. 16<br/>4.1 Quality control assessment ………………………………………………………………………. 16<br/>4.2 Sequence mapping ………………………………………………………………………………....17<br/>4.3 Transcriptome assembly ………………………………………………………………………….. 17<br/>4.4 Transcriptome assembly assessment ……………………………………………………………... 18<br/>4.5 Differential expression analysis …………………………………………………………...……… 18<br/>4.6 Visualization of significant features of expression profile ……………………………………….20<br/>4.7 Visualization of splicing events …………………………………………………………………….21<br/>4.8 Enrichment analysis ……………………………………………………………………………… 27<br/>Chapter 5: Discussion ……………………………………………………………………………….……. 39<br/>5.1 Lung cancer and alternative splicing detection …………………………………………………. 39<br/>5.2 Importance of alternative spliced isoform ………………………………………………….…..... 39<br/>5.3 Correlation of alternative spliced isoforms with lung cancer …………………………….……...40<br/>Chapter 6: Conclusion …………………………………………………………………………….………41<br/>6.1 Conclusion ………………………………………………………………………………………….41<br/>6.2 future directions …………………………………………………………………………………....41<br/>Appendix ………………………………………………………………………………………………… 42<br/>Bibliography …………………………………………………………………………………………….. 64 |
| 520 3# - Abstract |
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| Abstract |
Abstract:<br/>Among all malignancies, Lung cancer (LC) is the leading cause of death which occupying the most common tumor worldwide. Accumulated mutations in individual genes leading to the initiation and propagation of lung cancer. One of these mutations results from post-transcription modification of messenger RNA (mRNA) which is played a pivotal role in mRNA maturity. Alternative splicing (AS) is one of the main approaches in detecting this post-processing of mRNA, where is proposed to be the main determinant for the generation of various transcriptional variants within a single gene. Typically, there are different methods for the detection and quantifications of AS from RNA-seq data; isoform-based (IS), exon-based (EX), and event-based (EV), each of these methods relies on a different strategy for AS detection. Here, IS<br/>IV<br/>approach has been used for our analysis in AS detection, for the fact that it provides more biological interpretation, as it reflects the natural process of transcripts synthesis inside the cells, it relies on reconstructing the whole transcript structure within a single gene, instead of defining certain splicing events or junctions. Interestingly, our analysis is not only detecting the genes correlated with lung cancer but also their associated transcripts. Moreover, many potential LC biomarkers have been identified by our analysis, were strongly correlated with LC initiation, propagation, and metastasis. |
| 546 ## - Language Note |
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| Language Note |
Text in English, abstracts in English. |
| 650 #4 - Subject |
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| Subject |
Informatics-IFM |
| 655 #7 - Index Term-Genre/Form |
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| Source of term |
NULIB |
| focus term |
Dissertation, Academic |
| 690 ## - Subject |
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| School |
Informatics-IFM |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) |
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| Source of classification or shelving scheme |
Dewey Decimal Classification |
| Koha item type |
Thesis |
| 650 #4 - Subject |
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| -- |
266 |
| 655 #7 - Index Term-Genre/Form |
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| -- |
187 |
| 690 ## - Subject |
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| -- |
266 |