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Статті в журналах з теми "Analisi microarray"
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Naufal, Shidqi Aqil, Adiwijaya Adiwijaya, and Widi Astuti. "Analisis Perbandingan Klasifikasi Support Vector Machine (SVM) dan K-Nearest Neighbors (KNN) untuk Deteksi Kanker dengan Data Microarray." JURIKOM (Jurnal Riset Komputer) 7, no. 1 (February 15, 2020): 162. http://dx.doi.org/10.30865/jurikom.v7i1.2014.
Повний текст джерелаАнотація:
Cancer is a disease that can cause human death in various countries. According to WHO in 2018, cancer causes 9.6 million human deaths worldwide. Globally, about 1 in 6 deaths is due to cancer. Therefore, we need a technology that can be used for cancer detection with high acuration so that cancer can be detected early. Microarrays technique can predict certain tissues in humans and can be classified as cancer or not. However, microarray data has a problem with very large dimensions. To overcome this problem, in this study use one of the dimension reduction techniques, namely Partial Least Square(PLS) and use Support vector Machine (SVM) and K-Nearest Neighbors as a classification method, which will be used to compare which is better.The system built was able to reach 98.54% in leukemia data with PLS-KNN, 100% in lung data with KNN, 66.52% in breast data with PLS-KNN, and 85.60% in colon data with PLS- SVM. KNN is able to get the best in three data from four valued data.
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MUNZIR, ANDI FUTRI HAFSAH, ,. ADIWIJAYA, and ANNISA ADITSANIA. "ANALISIS REDUKSI DIMENSI PADA KLASIFIKASI MICROARRAY MENGGUNAKAN MBP POWELL BEALE." E-Jurnal Matematika 7, no. 1 (February 3, 2018): 17. http://dx.doi.org/10.24843/mtk.2018.v07.i01.p179.
Повний текст джерелаАнотація:
Cancer is the second leading cause of death in the world based on World Health Organization (WHO) survey in 2015. It took DNA microarray technology to analyze and diagnose cancer. DNA microarray has large dimensions so it influences the process of cancer ‘s classification. GA and PCA are used as reduction method and MBP Powell Beale as classification method. The testing of MBP classification without dimension reduction results 70, 59% ? 100% accuracy. MBP+PCA results 76, 47% ? 100% accuracy. MBP + GA results 76, 47% ? 92, 31% accuracy.
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SHIMOMURA, Takashi, Xiaoming HAN, Akito HATA, Takuro NIIDOME, Takeshi MORI, and Yoshiki KATAYAMA. "Optimization of Peptide Density on Microarray Surface for Quantitative Phosphoproteomics." Analytical Sciences 27, no. 1 (2011): 13–17. http://dx.doi.org/10.2116/analsci.27.13.
Повний текст джерела
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Yang, Liu, and Kristiaan Pelckmans. "Machine Learning Approaches to Survival Analysis: Case Studies in Microarray for Breast Cancer." International Journal of Machine Learning and Computing 4, no. 6 (2014): 483–90. http://dx.doi.org/10.7763/ijmlc.2014.v6.459.
Повний текст джерела
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TODA, Kyoko, Seiichi ISHIDA, Kotoko NAKATA, Rieko MATSUDA, Yukari SHIGEMOTO-MOGAMI, Kayoko FUJISHITA, Shogo OZAWA, et al. "Test of Significant Differences with a priori Probability in Microarray Experiments." Analytical Sciences 19, no. 11 (2003): 1529–35. http://dx.doi.org/10.2116/analsci.19.1529.
Повний текст джерела
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Kegel, Jessica U., Delphine Guillebault, and Linda K. Medlin. "Application of microarrays (phylochips) for analysis of community diversity by species identification." Perspectives in Phycology 3, no. 2 (September 9, 2016): 93–106. http://dx.doi.org/10.1127/pip/2016/0048.
Повний текст джерела
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Nurlaily, Diana, Farida Nur Hayati, and Elly Pusporani. "Membandingkan Seleksi variabel Pada Data Microarray Menggunakan Important Variable Value dan Genetic Algorithm (Studi Kasus Lung Cancer Dataset dan Prostate Cancer Dataset)." J Statistika: Jurnal Ilmiah Teori dan Aplikasi Statistika 14, no. 1 (July 31, 2021): 38–43. http://dx.doi.org/10.36456/jstat.vol14.no1.a3853.
Повний текст джерелаАнотація:
Teknologi DNA microarray menarik minat yang luar biasa baik di kalangan komunitas ilmiah maupun kalangan industri. Meskipun data microarray telah diterapkan dalam berbagai bidang, penanganan volume data besar yang dihasilkan bukanlah perkara yang mudah. Ukuran sampel kecil dengan dimensi tinggi adalah tantangan utama analisis menggunakan data microarray. Oleh karena itu perlu dilakukan analisis lebih lanjut untuk mengatasi hal ini. Banyak penelitian yang telah dirancang berkaitan dengan data microarray misalnya untuk menyelidiki mekanisme genetik kanker, dan untuk mengklasifikasikan berbagai jenis kanker atau membedakan antara jaringan kanker dan non-kanker. Semua penelitian ini bertujuan untuk menghasilkan kesimpulan dan interpretasi yang bermanfaat dari kumpulan data yang kompleks. Dalam penelitian ini, data yang digunakan adalah data kanker paru-paru sebanyak 24257 Variabel dan data kanker prostat sebanyak 12626 Variabel. Data tersebut kemudian akan dianalisis dengan beberapa metode feature selection yaitu important variable value dan genetic algorithm untuk memilih dimensi atau variabel data sehingga dapat meningkatkan akurasi klasifikasi data. Berdasarkan hasil analisis feature selection menggunakan data kanker paru-paru, didapatkan jumlah variabel terpilih sebanyak 112 variabel dengan metode feature selection important. Sedangkan metode genetic algorithm didapatkan jumlah variabel terpilihnya sebanyak 12266 variabel. Pada data kanker prostat, didapatkan jumlah variabel terpilih sebanyak 299 variabel dengan metode feature selection important. Sedangkan metode genetic algorithm didapatkan jumlah variabel terpilihnya sebanyak 6359 variabel.
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Hamim, Mohammed, Ismail El Mouden, Mounir Ouzir, Hicham Moutachaouik, and Mustapha Hain. "A NOVEL DIMENSIONALITY REDUCTION APPROACH TO IMPROVE MICROARRAY DATA CLASSIFICATION." IIUM Engineering Journal 22, no. 1 (January 4, 2021): 1–22. http://dx.doi.org/10.31436/iiumej.v22i1.1447.
Повний текст джерелаАнотація:
Cancer tumor prediction and diagnosis at an early stage has become a necessity in cancer research, as it provides an increase in the treatment success chances. Recently, DNA microarray technology became a powerful tool for cancer identification, that can analyze the expression level of a different and huge number of genes simultaneously. In microarray data, the large genes number versus a few records may affect the prediction performance. In order to handle this "curse of dimensionality” constraint of microarray dataset while improving the cancer identification performance, a dimensional reduction phase is necessary. In this paper, we proposed a framework that combines dimensional reduction methods and machine learning algorithms in order to achieve the best cancer prediction performance using different microarray datasets. In the dimensional reduction phase, a combination of feature selection and feature extraction techniques was proposed. Pearson and Ant Colony Optimization was used to select the most important genes. Principal Component Analysis and Kernel Principal Component Analysis were used to linearly and non-linearly transform the selected genes to a new reduced space. In the cancer identification phase, we proposed four algorithms C5.0, Logistic Regression, Artificial Neural Network, and Support Vector Machine. Experimental results demonstrated that the framework performs effectively and competitively compared to state-of-the-art methods. ABSTRAK: Ramalan tumor kanser dan diagnosis pada peringkat awal telah menjadi keperluan dalam kajian kanser, kerana ia membuka peluang peningkatan kejayaan dalam rawatan. Kebelakangan ini, teknologi mikrotatasusunan DNA menjadi alat berkuasa bagi mengenal pasti kanser, di mana ia mampu menganalisa level ekspresi yang pelbagai dan gen-gen yang banyak secara serentak. Dalam data mikrotatasusunan, gen-gen yang banyak ini bakal menentukan ramalan prestasi berbanding analisa melalui rekod-rekod yang sebilangan. Fasa pengurangan dimensi adalah perlu bagi mengawal kakangan “penentuan kedimensian” dataset mikrotatasusunan, sementara itu ia memantapkan lagi keberkesanan kenal pasti kanser. Kajian ini mencadangkan rangka kombinasi kaedah pengurangan dimensi dan algoritma pembelajaran mesin bagi mencapai prestasi ramalan kanser terbaik dengan menggunakan pelbagai dataset mikrotatasusunan. Dalam fasa pengurangan dimensi, kombinasi pemilihan ciri dan teknik pengekstrakan ciri telah dicadangkan, Pengoptimuman Pearson dan Koloni Semut bagi memilih gen yang paling penting, Analisis Komponen Prinsipal dan Analisis Komponen Prinsipal Kernel, bagi menukar gen terpilih yang linear dan tak linear kepada ruang baru yang dikurangkan. Dalam menentukan fasa mengenal pasti kanser, kajian ini mencadangkan empat algoritma iaitu C5.0, Regresi Logistik, Rangkaian Neural Buatan dan Mesin Vektor Sokongan. Dapatan kajian menunjukkan rangka ini adalah berkesan dan kompetitif berbanding kaedah semasa.
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Lykhenko, O. "СONSECUTIVE INTEGRATION OF AVAILABLE MICROARRAY DATA FOR ANALYSIS OF DIFFERENTIAL GENE EXPRESSION IN HUMAN PLACENTA". Biotechnologia Acta 14, № 1 (лютий 2021): 38–45. http://dx.doi.org/10.15407/biotech14.01.38.
Повний текст джерелаАнотація:
The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.
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SHIGAKI, Syuhei, Takayuki YAMAJI, Xiaoming HAN, Go YAMANOUCHI, Tatsuhiko SONODA, Osamu OKITSU, Takeshi MORI, Takuro NIIDOME, and Yoshiki KATAYAMA. "A Peptide Microarray for the Detection of Protein Kinase Activity in Cell Lysate." Analytical Sciences 23, no. 3 (2007): 271–75. http://dx.doi.org/10.2116/analsci.23.271.
Повний текст джерелаДисертації з теми "Analisi microarray"
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Pedotti, P. S. "Analisi dell'espressione genica : determinazione e confronto della potenza per diverse piattaforme microarray." Doctoral thesis, Università degli Studi di Milano, 2009. http://hdl.handle.net/2434/50368.
Повний текст джерела
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BASSI, DANIELA. "Interazioni tra batteri sporigeni e ambiente - Analisi molecolare di clostridi associati agli alimenti." Doctoral thesis, Università Cattolica del Sacro Cuore, 2009. http://hdl.handle.net/10280/402.
Повний текст джерелаАнотація:
Per varie ragioni, tra cui le loro specifiche condizioni di crescita, la diagnosi di infezione e di contaminazione alimentare da clostridi presenta ancora numerose difficoltà sia a livello clinico-batteriologico che a livello molecolare.
In questo lavoro di tesi si è cercato di ampliare lo spettro di conoscenze riguardo i clostridi e la loro diffusione; durante il primo anno di ricerca è stato studiato, applicando nuove tecniche di microscopia, il processo di germinazione di Clostridium tyrobutyricum, uno dei batteri maggiormente responsabili del gonfiore tardivo dei formaggi a pasta dura; l’applicazione di tecniche di Real-Time PCR ha nel contempo reso possibile una determinazione quantitativa dello stesso in latte.
Successivamente, è stata condotta un’analisi di tipizzazione molecolare di clostridi nell’ambito di una filiera agro-zoo-casearia finalizzata alle matrici di processo al fine di individuare le possibili vie di diffusione dei microrganismi.
La parte finale del lavoro è stata dedicata allo studio di espressione genica di un altro Clostridium responsabile di gonfiore ma scelto perché geneticamente indistinguibile da Clostridium botulinum, ovvero il Clostridium sporogenes; l’analisi trascrizionale dei suoi geni durante le fasi vegetativa, di sporulazione, germinazione ed esocrescita ha permesso di assegnare diverse funzioni a geni singoli o a gruppi di geni allo scopo di utilizzare queste informazioni per formulare ipotesi future anche su altre specie di clostridi patogeni.For several reasons, including their specific growth requirements, the diagnosis of infections and food contamination caused by clostridia still presents much difficulty at the clinical, bacteriological and molecular levels. The main purpose of this work is to learn more about clostridia and their interactions with environment. First, new microscopy techniques have been used to study the germination process in Clostridium tyrobutyricum, an anaerobic bacterium responsible for late blowing defects during cheese ripening; meanwhile, the application of real-time PCR methods have been employed to enumerate C. tyrobutyricum cells and spores in milk. Then, a molecular genotyping has been set in order to identify the most common clostridia in a agro-dairy production aimed to detect the possible ways of diffusion of these microbial species. The last part concerns the study of expression patterns of Clostridium sporogenes, an apathogenic gram positive clostridium usually involved in food damage and frequently isolated from late bowled cheese; Clostridium sporogenes is genetically indistinguishable from Clostridium botulinum and is often used as a model for the toxic subtypes. The objective of this study is to use an array-based large-scale transcriptional analysis in order to study gene expression in four different steps of Clostridium sporogenes life cycle: vegetative cells, sporulating cells, dormant spores and germinating ones. Our aims includes being able to relate gene-expression patterns to specific phenotypes and to discover gene expression divergences between the different phases of living, germination and outgrowth of spore-forming bacteria. An important aim is to assign functions to groups of or individual C. sporogenes genes and use this information to formulate specific hypotheses for further testing also on pathogenic clostridia types.
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BASSI, DANIELA. "Interazioni tra batteri sporigeni e ambiente - Analisi molecolare di clostridi associati agli alimenti." Doctoral thesis, Università Cattolica del Sacro Cuore, 2009. http://hdl.handle.net/10280/402.
Повний текст джерелаАнотація:
Per varie ragioni, tra cui le loro specifiche condizioni di crescita, la diagnosi di infezione e di contaminazione alimentare da clostridi presenta ancora numerose difficoltà sia a livello clinico-batteriologico che a livello molecolare.
In questo lavoro di tesi si è cercato di ampliare lo spettro di conoscenze riguardo i clostridi e la loro diffusione; durante il primo anno di ricerca è stato studiato, applicando nuove tecniche di microscopia, il processo di germinazione di Clostridium tyrobutyricum, uno dei batteri maggiormente responsabili del gonfiore tardivo dei formaggi a pasta dura; l’applicazione di tecniche di Real-Time PCR ha nel contempo reso possibile una determinazione quantitativa dello stesso in latte.
Successivamente, è stata condotta un’analisi di tipizzazione molecolare di clostridi nell’ambito di una filiera agro-zoo-casearia finalizzata alle matrici di processo al fine di individuare le possibili vie di diffusione dei microrganismi.
La parte finale del lavoro è stata dedicata allo studio di espressione genica di un altro Clostridium responsabile di gonfiore ma scelto perché geneticamente indistinguibile da Clostridium botulinum, ovvero il Clostridium sporogenes; l’analisi trascrizionale dei suoi geni durante le fasi vegetativa, di sporulazione, germinazione ed esocrescita ha permesso di assegnare diverse funzioni a geni singoli o a gruppi di geni allo scopo di utilizzare queste informazioni per formulare ipotesi future anche su altre specie di clostridi patogeni.For several reasons, including their specific growth requirements, the diagnosis of infections and food contamination caused by clostridia still presents much difficulty at the clinical, bacteriological and molecular levels. The main purpose of this work is to learn more about clostridia and their interactions with environment. First, new microscopy techniques have been used to study the germination process in Clostridium tyrobutyricum, an anaerobic bacterium responsible for late blowing defects during cheese ripening; meanwhile, the application of real-time PCR methods have been employed to enumerate C. tyrobutyricum cells and spores in milk. Then, a molecular genotyping has been set in order to identify the most common clostridia in a agro-dairy production aimed to detect the possible ways of diffusion of these microbial species. The last part concerns the study of expression patterns of Clostridium sporogenes, an apathogenic gram positive clostridium usually involved in food damage and frequently isolated from late bowled cheese; Clostridium sporogenes is genetically indistinguishable from Clostridium botulinum and is often used as a model for the toxic subtypes. The objective of this study is to use an array-based large-scale transcriptional analysis in order to study gene expression in four different steps of Clostridium sporogenes life cycle: vegetative cells, sporulating cells, dormant spores and germinating ones. Our aims includes being able to relate gene-expression patterns to specific phenotypes and to discover gene expression divergences between the different phases of living, germination and outgrowth of spore-forming bacteria. An important aim is to assign functions to groups of or individual C. sporogenes genes and use this information to formulate specific hypotheses for further testing also on pathogenic clostridia types.
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BATTISTA, SERENA. "Nuovi marcatori prognostici nel carcinoma epatocellulare: analisi immunoistochimica in Eastern and Western microarray tissutali." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2009. http://hdl.handle.net/2108/1005.
Повний текст джерелаАнотація:
Il carcinoma epatocellulare (HCC) è la più frequente patologia neoplastica primitiva del fegato, il quinto tumore maligno in ordine di frequenza nel mondo e la terza causa di morte correlata a neoplasia maligna. La sua incidenza annuale è in costante crescita. Tra i fattori patologici che influenzano la sopravvivenza dei pazienti con HCC, la dimensione tumorale, il grado e l’invasione vascolare sono alcuni dei più significativi. Pazienti con tumori di piccole dimensioni (< cm. 3) e senza invasione vascolare hanno una sopravvivenza di circa il 50% in 5 anni. Dato che l’invasione vascolare ed il grado sono criteri difficili da valutare su biopsie, la ricerca si è concentrata sullo studio della biologia dell’HCC nella speranza di individuare marcatori molecolari predittivi del comportamento della malattia.
In questo studio sono stati selezionati alcuni biomarcatori (alfa-tubulina, beta-tubulina, LAMA3, osteopontina, Ep-CAM, PAK1), associati a una prognosi sfavorevole ed alcuni marcatori recentemente usati come marcatori diagnostici (glipican3, glutamina sintetasi, heat shock protein 70) al fine di verificare se la loro iperespressione ha un potere predittivo sul comportamento dell’HCC. -
Materiali e metodi.
Per testare la sensibilità e specificità di questi marcatori, abbiamo usato 1) un microarray tissutale “occidentale” costituito da 98 casi di HCC, HCV-correlati e 2) un microarray tissutale “orientale” costituito da 136 casi di HCC, HBV-correlati. -
Risultati.
Abbiamo rilevato che le tubuline sono gli unici marcatori che si sono rivelati capaci di fornire informazioni prognostiche e consistenti sulle due popolazioni. OPN, Pak1 e Hsp70, singolarmente o combinati, possono predire una prognosi sfavorevole se applicati alla popolazione orientale. Gli altri marcatori devono essere ancora validati con ulteriori studi prima che si possano definire come marcatori prognostici dell’HCC. -
Conclusioni.
Infine, 1) abbiamo osservato un’espressione differente dei vari marcatori nelle due casistiche; 2) queste differenze sull’espressione dei marcatori può essere un riflesso delle differenze genetiche, eziologiche e epidemiologiche delle 2 popolazioni; 3) i parametri che emergono all’analisi multivariata sono tuttora criteri patologici: grado e angioinvasione macrovascolare, pertanto i nuovi anticorpi che saranno sviluppati dovranno essere confrontati a questi parametri.Introduction - HCC ranks among the most lethal cancer in the world with rising incidence. Attempts have been made to predict prognosis in patients with HCC using histopathological features. Tumour grade, size, number of lesions, micro and macrovascular invasion have been correlated with tumor relapse and patient’s survival. However, despite the several therapeutic options today available (tumor ablation, resection, transplantation, chemotherapy and the recent medical therapy with biological drugs) , HCC treatment is largely dictated by gross macroscopic features such as the tumor size and the number of lesions. Thus there is a consistent need to identify tissue biomarkers as individual fingerprints to predict individual. In recent years the interest in molecular biomarkers of HCC genesis and progression has grown, both in terms of prognostic significance and of potential therapeutic targets. We have therefore selected a number of proteins involved in critical cell functions such as staminality, differentiation, adhesion, motility and vascular invasion with the purpose of identify a phenotypic profile able to predict HCC outcome. - Methods. Two tissue microarrays ( a western set composed of 98 HCV-correlated HCC cases and an eastern set composed of 136 HBV-correlated HCC cases) with clinicopathological information (aetiology, age, sex, grade, stage, micro and macro-vascular invasion, and patient’s follow up) was used to test the immunocytochemical expression of the following antigens: Ep-CAM, LAMA3, Osteopontin, PAK1, alpha- and beta-tubulin, CK19, GS, HSP70 e GPC3. - Results. Our data showed that tubulins are the only markers able to reveal prognostic information in both western and eastern population. Osteopontina, Pak1 and HSP70, singularly or associated with each other, are able to predict an unfavorable outcome in the eastern patients; the other markers should be validated with other studies. - Conclusions. Finally, 1) we observe different markers expression profile in the two different populations; 2) it may be a reflection of genetic, aetiology and epidemiology differences between the two populations; 3) grade and macroscopic vascular invasion are still the strongest pathological criteria on the multivariate analysis, so the new antibodies to be developed should be compared to these parameters.
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Padoan, Elisa. "Analisi dell'immuno-trascrittoma di cavallo nelle patologie IAD e RAO." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3425261.
Повний текст джерелаАнотація:
The research project has been developed on the equine inflammatory respiratory diseases, which can be divided in Recurrent Airway Obstruction (RAO) and Inflammatory Airway Disease (IAD). The aim of this study was to investigate immune-related genes expression in the respiratory tract of IAD and RAO-affected horses. Clinical examination and endoscopy were performed. On the Broncho-Alveolar Lavage (BAL) fluid, obtained during endoscopy, cytological and microbiological analysis were performed to evaluate correlations between the gene expressions values and the clinical parameters.
A first analysis was developed by real time RT-PCR comparing the gene expression profile of 10 immune-related target genes (IL-1ß, IL-6, IL-8, IL-13, IL-17, TNFa, INF?, TGF-ß1, NF?-ß and TRL 4) in the BAL of healthy horses and RAO-affected ones, on which sampling was performed twice within 15 days. The aim was to deepen the effects of the respiratory disease on the equine immune system and to assess a potential temporal evolution of the gene expression values and of the other parameters considered. In addition, biopsies of the bronchial tissue were obtained and subsequent, histological evaluation and gene expression analyses were performed. Six of the target genes showed a significant expression values increase in the RAO group compared to the control one. A positive statistical correlation between the amount of mucus in the airways and the expression of some genes investigated was found. Regarding inflammatory mediators expression in the biopsy tissue, neither of target genes was significantly differentially expressed between the RAO horses and the control group.
The second part of the research project included also the study of IAD. On all horses, clinical investigations and assessments of gene expression profiles were carried out twice within 15 days, at the diagnosis moment and at the end of the pharmacological treatment. Considering the results of the first study, no biopsies of the respiratory tissue were performed. The development of a microarray platform specific for equine immune-related genes, provide a global view of the pathways involved in the IAD and RAO inflammatory response. The statistical analyses showed that 379 transcripts (55 up-regulated and 324 down-regulated) were significantly differentially expressed between the IAD group and control horses and 1763 genes (903 up-regulated and 860 down-regulated) between the RAO-affected horses and the healthy animals. Between IAD-affected horses and RAO animals, were showed significant differences of the respiratory rate at rest and of the amount of mucus in the airways. Some transcripts involved in the genesis, length and motility of the respiratory epithelium cilia, were down-regulated both in IAD and in RAO horses. In the IAD population, has been demonstrated the over-expression of genes coding for inflammatory mediators. Some of the transcripts up-regulated in the RAO group, are involved in the inflammatory response, bronchoconstriction, apoptosis and hypoxia pathway. In the same disease, some genes involved in the genesis of the protective muco-protein film of the respiratory epithelium were under-expressed. The analyses carried out by the software Gene Sets Enrichment Analysis (GSEA) showed that the pathway activated during human asthma, is also enriched in equine RAO, albeit marginally significant (False Discovery Rate <25%, p value 0.08 ). The low quality of the RNA extracted from the BAL of some samples, did not allow to reach a significant number of horses, considered before and after the pharmacological treatment, to assess the effect of the therapy on gene expression profiles.
In conclusion, the present studies provided information about the immunological mechanisms activated during the most important equine respiratory diseases.
In the future, the information obtained could lead to the development of new therapies for IAD and RAO, by the inhibition of molecules involved in the pathogenesis of these diseases, as is already done in human medicine.
The involvement of the same pathway in human asthma and equine RAO, could suggest a possible role of horses as animal model for the study of human chronic respiratory diseases.Il lavoro di ricerca svolto nell’arco dei tre anni di dottorato, è stato articolato in due progetti sviluppati nell’ambito delle malattie respiratorie su base infiammatoria che colpiscono gli equini. Tali patologie possono essere distinte in due grandi gruppi: Recurrent Airway Obstruction (RAO) ed Inflammatory Airway Disease (IAD). Lo scopo dei progetti di ricerca si è basato sull’indagine dei profili di espressione di geni immuno-correlati nell’albero respiratorio di cavalli affetti da IAD e RAO, in relazione ad un gruppo di controllo. Su tutti i soggetti, sono stati eseguiti gli esami clinici mirati alla valutazione dell’apparato respiratorio, l’esame endoscopico e l’esame citologico e microbiologico da Broncho-Alveolar Lavage (BAL), per valutare le potenziali correlazioni esistenti tra i profili di espressione genica ed i parametri clinici. Il primo progetto è stato sviluppato comparando cavalli sani con soggetti affetti da RAO, su cui i campionamenti sono stati ripetuti due volte nell’arco di 15 giorni, al fine valutare una potenziale evoluzione temporale dell’espressione genica e degli altri parametri considerati nella ricerca. Inoltre, sono state eseguite biopsie del tessuto bronchiale, sottoposto sia a valutazione istologica che ad analisi di espressione genica. Mediante real time RT-PCR, sono stati indagati i profili di espressione di 10 geni target immuno-correlati (IL-1ß, IL-6, IL-8, IL-13, IL-17, TNFa, INF?, TGF-ß1, NF?-ß e TRL 4), sei dei quali hanno dimostrato una aumento statisticamente significativo dei livelli di espressione nel gruppo RAO rispetto al gruppo di controllo. Le analisi statistiche condotte, hanno riscontrato una correlazione positiva tra la quantità di muco nelle vie aeree e l’ espressione di alcuni dei geni indagati. Non sono state evidenziate differenze di espressione, dei geni inclusi nello studio, tra i tessuti bioptici prelevati dai soggetti affetti da RAO e quelli ottenuti dal gruppo di controllo. Il secondo progetto di ricerca, è stato sviluppato ampliando la casistica dei cavalli affetti da RAO ed introducendo lo studio della IAD. Su tutti i soggetti, le indagini cliniche e le valutazioni dei profili di espressione genica sono state condotte sia al momento della diagnosi che al termine del trattamento farmacologico della durata di 15 giorni. Valutati i risultati del primo lavoro, non sono state eseguite biopsie del tessuto respiratorio. Lo sviluppo di una piattaforma microarray specifica per i geni immuno-correlati di cavallo ha permesso di ottenere una visione globale dei pathway coinvolti nella risposta infiammatoria delle due patologie. Le analisi statistiche effettuate hanno evidenziato una differenza di espressione significativa per 379 trascritti (di cui 55 sovra-espressi e 324 sotto-espressi) tra il gruppo IAD ed il gruppo di controllo e per 1763 geni (di cui 903 sovra-espressi e 860 sotto-espressi) tra i pazienti affetti da RAO ed i soggetti sani. Da un punto di vista clinico, sono state riscontrate differenze statisticamente significative sia della frequenza respiratoria a riposo che della quantità di muco presente nelle vie aeree dei cavalli affetti da IAD rispetto ai soggetti RAO. Tra i geni sotto-espressi nei due gruppi di cavalli affetti da malattia respiratoria, hanno acquistato importanza alcuni trascritti coinvolti nella genesi, lunghezza e motilità dell’apparato ciliare dell’epitelio respiratorio. Nella popolazione IAD, è stata dimostrata la sovra-espressione di geni codificanti per mediatori coinvolti nella risposta infiammatoria. I geni sovra-espressi nel gruppo RAO, caratterizzati da maggior rilievo, sono coinvolti nella risposta infiammatoria, nella broncocostrizione, nella via apoptotica e nel pathway dell’ipossia. Nella medesima patologia, si sono mostrati sotto-espressi anche alcuni geni coinvolti nella genesi del film muco-proteico di protezione dell’epitelio respiratorio. Lo studio condotto mediante Gene Set Enrichment Analysis (GSEA), ha evidenziato che il pathway attivato in corso di asma umano, viene arricchito anche nella patologia RAO equina, sebbene la significatività statistica sia marginale (False Discovery Rate < 25%, p value 0,08). Non è stato possibile valutare l’effetto della terapia farmacologica sui profili di espressione genica, poiché la bassa qualità dell’RNA estratto dal BAL di alcuni campioni non ha permesso di raggiungere un numero significativo di soggetti valutati prima e dopo il trattamento terapeutico. Gli studi effettuati hanno quindi permesso di far luce su alcuni dei meccanismi immunologici che stanno alla base delle patologie respiratorie equine di maggiore importanza veterinaria ed economica. In futuro, le informazioni ottenute, potrebbero condurre allo sviluppo di nuovi mezzi terapeutici per l’inibizione delle molecole coinvolte nello sviluppo di IAD e RAO, come già avviene in medicina umana. Infine, il coinvolgimento di un medesimo pathway nell’asma umano e nella RAO equina, potrebbe condurre all’utilizzo di tale specie come modello animale per lo studio delle patologie respiratorie croniche umane.
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Lauriola, Mattia <1980>. "Studio di marcatori epiteliali del cancro del colon-retto mediante analisi dell'RNA con la tecnica del microarray." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1595/1/lauriola_mattia_tesi.pdf.
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Lauriola, Mattia <1980>. "Studio di marcatori epiteliali del cancro del colon-retto mediante analisi dell'RNA con la tecnica del microarray." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1595/.
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Mininni, Alba Nicoletta. "Risposta allo stress da freddo nei pesci: analisi del trascrittoma di Sparus Aurata (L.) esposta alle basse temperature." Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3421681.
Повний текст джерелаАнотація:
From the second half of past century to nowadays aquaculture keeps on being the fastest-growing animal-food-producing sector, so that it has provided the 46% of total food fish supply in 2010. However, we are faced with a few problems closely connected to some aspects that are still unknown in the biology of certain relevant species such as the gilthead seabream (Sparus aurata). Functional genomics can offer very well-grounded tools to get information about the molecular mechanisms which are involved in physiological processes whose consequences may be very high also from an economic point of view. The issue concerning how the marine organisms and populations react to climatic changes is a question of paramount importance which is still rather unsettled. The gilthead bream is very sensitive to low temperatures, so that it does not survive when temperature falls under 5°C. In fact, in winter time the breeding cause often huge economic losses to their owners since the mortality rate rises because of metabolic syndrome known as winter disease. In this study we considered the gene expression profiles of Sparus aurata individuals which have been exposed to low temperatures, in experimental conditions that could represent as realistic as possible the winter season. The gene expression profile can be used as a tool to link up the genotype to the physiology and to the phenotype. Moreover, the study looked into populations coming from regions with different climatic conditions (Veneto and Sicily), by assuming a different tolerance to cold exposition. Four groups of wild sea bream (120±16 g), coming in pairs from the two regions, were exposed for 21 days to two temperature treatments: 16 ± 0.3 °C (control groups) and 6.8 ± 0.3 °C (cold groups). Liver and gill samples were collected during acute (0, 6 and 24 hours) and chronic exposure (21 days). The gene expression profiles were analyzed using an oligo-nucleotide microarray technology, with about 19,715 ESTs. Results revealed a complex transcriptomic response to cold with many molecular pathways involved among which: lipid and carbohydrate metabolism, regulation of heat shock proteins (HSPs) and other protein chaperones, protein degradation and repair, regulation of cell death, RNA and DNA metabolism, immune response. The earliest transcriptional response is linked to oxidative stress and anti-oxidant/survival cell response, suggesting an immediate disturbance of systemic oxygen balance. The largest transcriptional difference between cold and control groups occurred during long-term exposure, involving primarily several genes of lipid metabolism with a role in the re-allocation of energy sources and immune-related genes indicating an immunosuppressive effect of cold exposure.
The data on the liver and gill transcriptome of the gilthead sea bream exposed to cold provide a starting point to investigate physiological mechanisms underlying long term cold adaptation in fish and to address future research for the identification of cold tolerant S. aurata strain for aquaculture.Dalla seconda metà del secolo scorso ad oggi l‟acquacoltura continua ad essere il settore delle produzioni animali in più rapida crescita, con il 46% di pesce fornito sul totale consumato nel 2010. Rimangono, tuttavia, problematiche strettamente legate ad aspetti ancora sconosciuti nell‟ambito della biologia di alcune specie d‟interesse come l‟orata comune (Sparus aurata). La genomica funzionale può fornire validi strumenti per ottenere informazioni sui meccanismi molecolari coinvolti nei processi fisiologici importanti anche da un punto di vista economico. Come le popolazioni e le specie marine reagiscono ai cambiamenti climatici è una questione di importanza centrale ancora non del tutto risolta. L‟orata comune risente fortemente del freddo, non sopravvivendo a temperature inferiori ai 5°C e spesso, durante l‟inverno, gli allevamenti subiscono ingenti danni economici per l‟elevata mortalità data dalla sindrome metabolica winter disease. In questo studio sono stati valutati i profili di espressione genica di individui di S. aurata esposti alle basse temperature, in condizioni sperimentali che fossero il più realistiche possibile con la stagione invernale. Il profilo di espressione genica può servire come strumento per legare il genotipo alla fisiologia e al fenotipo. Sono state, inoltre, esaminate popolazioni provenienti da regioni con condizioni climatiche diverse, Veneto e Sicilia, ipotizzando una differente tolleranza al freddo. Quattro gruppi di orate (120±16 g), provenienti a coppie dalle due regioni, sono state esposte per 21 giorni a due trattamenti di temperatura: 16 ± 0,3 °C (gruppi di controllo) e 6,8 ± 0,3 °C (gruppi dei trattati). Campioni di fegato e branchia sono stati raccolti durante esposizione acuta (0, 6 e 24 ore) e cronica (21 giorni). I profili di espressione sono stati analizzati usando un microarray a oligo-nucleotidi con circa 19.715 geni. I risultati hanno rivelato una risposta trascrizionale complessa per la risposta al freddo, con numerosi pathway coinvolti: metabolismo di lipidi e carboidrati, heat shock protein (HSP) e chaperoni, degradazione proteica, apoptosi, metabolismo di RNA e DNA, risposta immunitaria. La prima risposta è legata allo stress ossidativo, suggerendo un disturbo immediato del bilancio dell‟ossigeno a livello sistemico, mentre le più grandi differenze trascrizionali tra trattati e controlli si rilevano durante l‟esposizione a lungo termine, e coinvolgono principalmente geni del metabolismo lipidico per la ridistribuzione delle riserve energetiche e geni dell‟immunità per l‟importante effetto immuno-soppressivo del freddo. I dati del trascrittoma di branchia e fegato di orate esposte alle basse temperature forniscono un punto di partenza per indagare i meccanismi fisiologici sottostanti l‟adattamento al freddo a lungo termine nei pesci e per indirizzare ricerche future volte all‟identificazione di ceppi di S. aurata resistenti al freddo in acquacoltura.
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Pizzini, Silvia/P S. "A bioinformatic approach to the study of gene, microRNA expression and alternative splicing regulation in colorectal cancer progression and liver metastasis." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422457.
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Expression profiles are increasingly used in cancer research, and a growing number of microarray data is available in public databases such as Gene Expression Omnibus (GEO) and ArrayExpress. Therefore, it is possible to compare studies with similar research aims through a meta-analysis approach. Colorectal cancer (CRC) is a very common disease and represents a fundamental biological model of tumorigenesis. Many experiments comparing the expression profiles of normal colonic mucosa and colorectal cancer (CRC) samples have been conducted and results are available. Using A-MADMAN, a web application that allows the retrieval, annotation, organization and analysis of public available gene expression datasets, we downloaded from the GEO and collected the largest-collected normal colon, adenoma and primary colorectal tumor, with and without metastasis, gene expression dataset which includes 1,795 experiments pertaining to 27 distinct series, obtained from two different generations of Affymetrix, HG-U133A and HG-U133 plus2.0. After we performed the quality control of the downloaded data and have designed three different workflows for signal reconstruction, we conducted preliminary analysis of differential expression. In this first project we focused on right and left colon differences. In particularly, we analyzed normal, adenoma and tumor expression profiles focusing on changes among topologically different samples, under the hypothesis that the use of site-specific normal tissue as reference for the study of right and left tumor samples may facilitate to shed light on specific cell functions, pathways and regulatory circuits altered in each tumor type, and help deepening our understanding of this complex disease. From preliminary data, we concluded that the workflow based on the virtual chips production and on a chip-specific background correction is the most robust. Higher numbers of differentially expressed genes were identified when comparing, respectively, tumor and adenoma versus normal tissue (647 and 683 genes). These tissue samples were then pairwise compared by topology to identify those genes that are differentially expressed, when the matched by topology set of normal samples is considered. We found 72 genes colon left-specific and 1183 colon-right specific in the comparison from adenoma with normal tissues, and 46 genes and 69 genes, respectively, in colon left- and colon right- specific in the comparison from CRC and adenoma tissues. We focused also to the functional information associated to gene expression differences between tumor and normal tissue samples, compared considering only right or left samples, to identify specific functions and pathways involved with cancer present, such as DNA repair, adhesion and cell interaction.
In the second project we reconstructed regulatory networks of colon cancer by integrating gene expression, alternative splicing and microRNA (miRNAs) expression data. We carried out a genome-wide integrative analysis of miRNA and genes and exon expression profiles in tissues of 55 colon cancer patients, comprehensive of normal colon mucosa, primary tumor and liver metastasis. GeneChip Human Exon 1.0 ST (Affymetrix) and Affymetrix GeneChip miRNA arrays have been used to obtain high quality gene, exon and miRNA expression quantification respectively. We analyzed both differential gene expression and alternative splicing applying AltAnalyze software to exon-level analysis, identifying 33,740 genes involved in alternative splicing events. We considered a custom set of expression signals of 449,810 probesets, using MIDAS and FIRMA statistics, and we combined the results with MMBGX software output, to identify a more restricted, but perhaps more robust set of candidate alternative splicing events, possibly relevant for colon cancer biology. When comparing liver metastasis with normal colon tissue whereas 182 genes were identified; comparable numbers of genes were identified when comparing metastasis versus colorectal tumor and colorectal tumor versus normal tissue (51 and 10 respectively). We validated two genes with alternative splicing events, VCL and CALD1.
We then identified respectively 62, 63 and 11 differentially expressed miRNAs in tumors and metastases compared to normal tissue, and comparing metastasis with primary tumors. To assess the reproducibility and robustness of the miRNA signature identified, we measured by qRT-PCR the expression of 5 miRNA in all samples (hsa miR-150, hsa miR-10b, has miR-146a, miR-210 and has miR-122). For each considered contrast, KEGG pathways enriched in genes resulting supported target of differentially expressed miRNAs were identified. The integrated analysis of miRNA and genes expression profiles with target predictions was performed with the purpose of reconstruct post-transcriptional regulatory networks governing tumor and metastases development. Considering expression profiles in the same set of samples of 305 miRNAs and 12,748 genes with variable expression profile, we reconstructed post-transcriptional regulatory networks involving modulated miRNAs. In particular, considering the network associated to the tumor versus normal contrast, we experimentally validated miR-145 – c-Myc and miR-182 – ENTPD5 relationships. This latter is new and may have a relevant pathogenetic role. Looking at our results, we can say that the regulatory signatures that affect tumor progression are complex and difficult to interpret. They involve interactions involving different modulated miRNAs that control the expression of multiple genes belonging to the same pathway in different ways, and alternative transcripts of genes that are differentially expressed in normal tissues, tumors and metastases.Nella ricerca oncologica sono sempre più utilizzati i profili di espressione genica e un numero crescente di dati di microarray è disponibile in database pubblici come NCBI GEO e ArrayExpress. Diventa quindi possibile il confronto di studi con obiettivi di ricerca simili attraverso approcci di “meta-analisi”. Il cancro colorettale (CRC) rappresenta un fondamentale modello biologico di tumorigenesi, oltre ad essere una patologia molto diffusa. Sono a disposizione nei database pubblici molti esperimenti sul CRC, che confrontano mucosa normale con mucosa tumorale del colon attraverso metodologia microarray. Noi abbiamo utilizzato A-MADMAN, un’applicazione web open source di supporto per la meta-analisi di dati grezzi d’espressione genica ottenuti con microarray, per scaricare dal database dell’NCBI Gene Expression Omnibus (GEO), 27 collezioni di esperimenti per un totale di 1045 campioni ottenuti da mucosa normale, adenoma e CRC con e senza metastasi di colon-retto su cui erano state eseguite analisi di espressione genica con tecnologia gene chip Affymetrix. Dopo aver effettuato un controllo di qualità dei dati scaricati e aver disegnato 3 diversi flussi di lavoro per la ricostruzione del segnale d’espressione, sono state condotte delle analisi preliminari di espressione differenziale. In questo primo progetto ci siamo focalizzati sulle differenze molecolari sito–specifiche. Abbiamo quindi analizzato campioni di mucosa sana, di adenoma e di CRC suddivisi per localizzazione in colon destro e colon sinistro. Prendendo come riferimento il tessuto normale destro e sinistro, abbiamo ipotizzato che è possibile discriminare pattern di espressione genica tumorale sede specifica. Dal disegno dei tre flussi di lavoro abbiamo dedotto che il flusso di lavoro basato sulla generazione di chip virtuali e su una correzione del background chip-specifica è il più affidabile. Abbiamo identificato 647 geni differenzialmente espressi confrontando tessuto tumorale con tessuto normale e 683 geni nel confronto adenoma con tessuto normale, poi abbiamo individuato 72 geni nel confronto adenoma-tessuto normale specifici del colon sinistro e 1183 geni nello stesso confronto, colon destro specifici, mentre per quanto riguarda il confronto CRC e adenoma, 46 geni sono colon sinistro specifici e 69 sono colon destro specifici. Abbiamo inoltre trovato termini funzionali e pathway diversi sovra-rappresentati in colon destro rispetto a colon sinistro e rispetto ai corrispondenti normali. Nel secondo progetto, abbiamo ricostruito una rete regolatoria riguardante il CRC e la metastasi epatica da CRC integrando dati di originali di espressione genica, di splicing alternativo e di espressione di microRNA (miRNA). Lo studio si basa sulla raccolta di biopsie di tumore primario al colon, mucosa adiacente normale e metastasi al fegato di 55 pazienti, che sono state analizzate utilizzando piattaforme Affymetrix per l'analisi di espressione genica/esonica (GeneChip Human Exon 1,0 ST), e di microRNA (GeneChip® miRNA Array ). Analizzando l’ espressione differenziale a livello genico ed esonico mediante il software AltAnalyze identificando 33.740 geni coinvolti in probabili eventi di splicing alternativo. Integrando i dati risultati dalle statistiche di questo programma con i risultati ottenuti con un software basato su un approccio Bayesiano, MMBGX, abbiamo identificato una lista più ristretta ma anche più robusta di candidati eventi di splicing possibilmente rilevanti per la formazione e la progressione del CRC. Confrontando metastasi epatiche con tessuto normale del colon sono stati identificati 182 geni, mentre un numero inferiore di geni sono stati identificati nel confronto contro le metastasi del tumore colorettale e del tumore del colon-retto rispetto al tessuto normale (51 e 10 rispettivamente). A partire da questi risultati, abbiamo scoperto il coinvolgimento di trascritti alternativi di due geni, VCL e CALD1, nella progressione tumorale. In parallelo, sono stati identificati microRNA modulati in seguito allo sviluppo del tumore e della metastasi, trovandone rispettivamente 62, 63 e 11 differenzialmente espressi nel tumore rispetto al normale, nella metastasi rispetto al normale e nella metastasi rispetto al tumore. Abbiamo quindi confermato la robustezza dei risultati validando cinque miRNA presenti nella lista dei differenzialmente espressi (hsa miR-150, hsa miR-10b, has miR-146a, miR-210 and has miR-122) mediante RT-PCR. Per ogni contrasto considerato, sono stati identificati i KEGG pathway modulate e quindi sotto putativamente controllate dai miRNA. Grazie all’analisi integrata di profili di espressione di miRNA e dei loro geni target anti-correlati, sono state definite le principali reti di regolazione post-trascrizionale coinvolte nella cancerogenesi. Particolarmente rilevante è la rete che coinvolge il sottoinsieme dei miRNA differenzialmente espressi nel tumore rispetto al normale. Tra le interazioni inferite, abbiamo convalidato sperimentalmente le relazioni miR-145 - c-Myc e miR-182 - ENTPD5. Quest’ultima rappresenta una relazione nuova, il cui ruolo patogenetico può essere rilevante. Dai nostri risultati possiamo concludere che le vie di regolazione che interessano la progressione tumorale sono complesse e difficili da interpretare, che implicano interazioni che coinvolgono miRNA diversamente modulati che agiscono in diversi modi sull’espressione di più geni appartenenti ad una stessa pathway e da trascritti alternativi di geni che vengono espressi in modo differenziale nei tessuti sani, nei tumori e nelle metastasi.
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COSTA, MARTA. "Disturbo bipolare e cefalea a grappolo: identificazione di geni e pathway molecolari e loro potenziale coinvolgimento nella risposta alla terapia con sali di litio tramite analisi dei profili di espressione genome‑wide." Doctoral thesis, Università degli Studi di Cagliari, 2014. http://hdl.handle.net/11584/266468.
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Cluster headache (CH) and bipolar disorder (BD) are pathological conditions affecting 1% and 1.5% of the general population, respectively. Albeit the pathogenesis has not yet been completely elucidated, family and twin studies have suggested a genetic basis for both disorders, with an estimated heritability of 80% for BD and up to 60% for CH. Though BD and CH are very different diseases, they show important clinical similarities, such as a temporal pattern of disturbances, dysregulation of the wake-‐sleep cycle, neuroendocrine derangements, and more important positive clinical response to lithium and valproate treatments in a significant proportion of treated patients. In the present study, we sought to explore whether BD and CH patients responders to lithium share common molecular pathways potentially involved in predisposing to positively respond to prophylactic lithium treatment. To this aim, we carried out a transcriptome study in lymphoblastoid cell lines from 10 BD type I patients, responders to lithium, 8 CH patients responders to lithium treatment and 10 healthy subjects (CO). Expression profiles were measured by Affymetrix GeneChip Human Gene ST 1.0 covering 36,079 transcripts. Expression levels of BD and CH patients were compared with CO using a t-‐test, in order to identify commonly dysregulated genes. Pathway analysis was performed based on the hypergeometric test for over representation of specific Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 544 and 1172 genes were differentially expressed in BD versus CO and CH versus CO respectively. Filtering criteria were based on corrected p value < 0.05 and a Fold Change (FC) ≥ |1.3|. Among these genes, 314 were commonly altered both in CH and BD compared to CO. The most significant dysregulated gene in BD and CH was RNA binding motif (RNP1, RRM) protein 3 (RBM3), a gene implicated in sleep regulation and in the temperature entrained circadian gene expression (corrected p value of 6,30x 10-‐09 in BD vs CO and 1,88x 10-‐09 in CH vs CO). Pathway analysis showed that Protein processing in endoplasmic reticulum pathway was one of the most significantly enriched in BD and CH when compared to CO. In conclusion, data from this pilot microarray study may provide useful and relevant information for a better understanding of the molecular underpinnings of lithium response and on the neurobiology of BD and CH.
Книги з теми "Analisi microarray"
1
Microarray analysis. Hoboken, NJ: Wiley-Liss, 2003.
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2
Khademhosseini, Ali, Kahp-Yang Suh, and Mohammed Zourob. Biological microarrays: Methods and protocols. New York: Humana Press, 2011.
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3
Muller, Hans-Joachim. Microarrays. Burlington, MA: Elsevier Academic Press, 2005.
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4
Thomas, Roeder, ed. Microarrays. Burlington, MA: Elsevier Academic Press, 2006.
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5
Phillip, Stafford, ed. Methods in microarray normalization. Boca Raton: CRC Press, 2008.
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Dev, Kambhampati, ed. Protein microarray technology. Weinheim: Wiley-VCH, 2004.
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R, Kimmel Alan, and Oliver B, eds. DNA microarrays. Amsterdam: Elsevier/Academic Press, 2006.
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Andreas, Bosio, and Gerstmayer Bernhard, eds. Microarrays in inflammation. Basel: Birkhäuser, 2008.
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Peptide microarrays: Methods and protocols. [New York, NY]: Humana Press, 2009.
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Ulrike, Nuber, ed. DNA microarrays. New York, NY: Chapman&Hall/CRC, 2005.
Знайти повний текст джерелаЧастини книг з теми "Analisi microarray"
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Matson, Robert S., and Jang B. Rampal. "Hybridization Analysis Using Oligonucleotide Probe Arrays." In Microarrays, 279–98. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-303-5_14.
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Page, Grier P., Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, Lang Chen, and Kui Zhang. "Microarray Analysis." In Topics in Biostatistics, 409–30. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-530-5_20.
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Patel, Nisha R., Michael L. Wong, Anthony E. Dragun, Stephan Mose, Bernadine R. Donahue, Jay S. Cooper, Filip T. Troicki, et al. "Microarray Analysis." In Encyclopedia of Radiation Oncology, 501. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-540-85516-3_257.
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Weeraratna, Ashani T., and Dennis D. Taub. "Microarray Data Analysis." In Microarray Data Analysis, 1–16. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_1.
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Samanta, Manoj Pratim, Waraporn Tongprasit, and Viktor Stolc. "In-Depth Query of Large Genomes Using Tiling Arrays." In Microarray Data Analysis, 163–73. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_10.
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Bilke, Sven, and Javed Khan. "Analysis of Comparative Genomic Hybridization Data on cDNA Microarrays." In Microarray Data Analysis, 175–86. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_11.
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Juric, Dejan, Claudia Bredel, Branimir I. Sikic, and Markus Bredel. "Integrated High-Resolution Genome-Wide Analysis of Gene Dosage and Gene Expression in Human Brain Tumors." In Microarray Data Analysis, 187–202. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_12.
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MacDonald, Tobey J., Ian F. Pollack, Hideho Okada, Soumyaroop Bhattacharya, and James Lyons-Weiler. "Progression-Associated Genes in Astrocytoma Identified by Novel Microarray Gene Expression Data Reanalysis." In Microarray Data Analysis, 203–21. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_13.
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Osborne, John D., Lihua (Julie) Zhu, Simon M. Lin, and Warren A. Kibbe. "Interpreting Microarray Results With Gene Ontology and MeSH." In Microarray Data Analysis, 223–41. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_14.
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Ochs, Michael F., Aidan J. Peterson, Andrew Kossenkov, and Ghislain Bidaut. "Incorporation of Gene Ontology Annotations to Enhance Microarray Data Analysis." In Microarray Data Analysis, 243–54. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_15.
Повний текст джерелаТези доповідей конференцій з теми "Analisi microarray"
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Liao, Uland, Armando Tovar, Philip Felgner, and Abraham P. Lee. "A Microfluidic Approach and Enhancement Towards a Colorimetric Enzyme-Linked-Immunosorbant-Assay for Diagnostic Detection of Infectious Diseases." In ASME 2007 2nd Frontiers in Biomedical Devices Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/biomed2007-38105.
Повний текст джерелаАнотація:
Accounting for more than 13 million deaths a year, infectious diseases have become the world’s biggest killer of children and young adults worldwide [1]. Diagnostic tools and technologies are vital towards identifying the presence and treatment of these diseases. Detection methods have commonly relied on DNA using polymerase-chain-reaction (PCR), however antibody methods have become popular due to growing trends in technology and detection sensitivity. ImmPORT Therapeutics, a leading group in generating infectious disease proteome microarrays, has developed multiplex systems for comprehensive analysis of immune responses to multiple infectious diseases [2]. Current microarray handling however requires conventional lab-bench methods that require whole-day processes and large amounts of user-handling confined to laboratory settings. Miniaturization of laboratory processes would provide numerous advantages in terms of cost, time, portability and multistage automation in addition to what is already offered. The proposed microfluidic device is a colorimetric enzyme-linked-immunosorbant assay (ELISA) for antibody detection of infectious agents that draws on ImmPORT Therapeutics technology with a purpose of decreasing reagent volumes and times potentially unattainable through conventional methods.
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LIATSIS, P., and M. A. NAZARBOLAND. "MICROARRAY IMAGE ANALYSIS." In Proceedings of the 9th International Workshop on Systems, Signals and Image Processing. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776266_0078.
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Yang, Youngik, Jong Youl Choi, Kwangmin Choi, Marlon Pierce, Dennis Gannon, and Sun Kim. "BioVLAB-Microarray: Microarray Data Analysis in Virtual Environment." In 2008 IEEE Fourth International Conference on eScience (eScience). IEEE, 2008. http://dx.doi.org/10.1109/escience.2008.57.
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Tozduman, Ersin, and Songul Albayrak. "cDNA microarray image analysis." In 2009 14th National Biomedical Engineering Meeting. IEEE, 2009. http://dx.doi.org/10.1109/biyomut.2009.5130308.
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Cyganov, M. M., M. K. Ibragimova, and A. A. Hozyainova. "PREDICTIVE AND PROGNOSTIC SIGNIFICANCE OF PALB2 GENE MUTATIONS IN BREAST TUMORS." In I International Congress “The Latest Achievements of Medicine, Healthcare, and Health-Saving Technologies”. Kemerovo State University, 2023. http://dx.doi.org/10.21603/-i-ic-146.
Повний текст джерелаАнотація:
It has been shown that the loss of PALB2 function, due to mutations or chromosomal
aberrations, may have an impact on the effectiveness of chemotherapy treatment and disease
prognosis in patients with various oncological diseases. Thus, the aim of this work was to
evaluate the predictive and prognostic potential of DNA copy number aberrations and PALB2
gene mutations in breast tumors.
Materials and methods. The study included 66 patients with breast cancer (BC). To
evaluate the presence of DNA copy number aberrations (CNA), microarray analysis was
used with the CytoScanTMHD Array high density microarrays. Gene mutations were
assessed by sequencing on the MiSeq™ Sequencing System using the Accel-Amplicon
BRCA1, BRCA2, and PALB2 Panel. Results. The presence of the PALB2 CNA gene is not
associated with the effectiveness of neoadjuvant chemotherapy (NAC), p=0.07. The
presence of a deletion is determined by 100% metastatic-free survival, versus 68% in the
group with normal copy number (log-rank test p=0.04). It has been established that
elimination of the frameshift deletion c.2552delA mutation during NAC leads to an
objective response to treatment. Identified missense mutations (c.2993G>A; c.2014G>C;
c.1010T>C) were observed in patients with tumor progression. But only c.1010T>C has
pathogenic significance. The presence of mutations in the PALB2 gene is not associated
with metastatic survival (log-rank test p=0.15). Conclusion. Currently, there is little data on
the impact of disorders in the PALB2 gene on the effectiveness of treatment and prognosis
of the disease, but the study of this gene has great potential for testing focused on diagnosis,
prevention, and a personalized approach to the treatment of cancer patients
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Liu, Yen-Cheng, Saeid Ansaryan, Xiaokang Li, Eduardo R. Arvelo, and Hatice Altug. "High-throughput optofluidic nanoplasmonic biosensor array for monitoring single-cell secretion in real-time." In CLEO: Applications and Technology. Washington, D.C.: Optica Publishing Group, 2022. http://dx.doi.org/10.1364/cleo_at.2022.am2i.6.
Повний текст джерелаАнотація:
We report a high-throughput biosensing microarray platform integrating ultrasensitive nanoplasmonic substrate and microwell compartments for label-free and real-time secretome monitoring. Interleukin-2 from hundreds of single EL4 cells were measured and a statistical analysis was done.
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Han-Yu Chuang, Hongfang Liu, Fang-An Chen, Cheng-Yan Kao, and D. F. Hsu. "Combination methods in microarray analysis." In 7th International Symposium on Parallel Architectures, Algorithms and Networks, 2004. Proceedings. IEEE, 2004. http://dx.doi.org/10.1109/ispan.2004.1300548.
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Guse, Frank, and Jakob Bleicher. "Sophisticated lenses for microarray analysis." In BiOS 2001 The International Symposium on Biomedical Optics, edited by Michael L. Bittner, Yidong Chen, Andreas N. Dorsel, and Edward R. Dougherty. SPIE, 2001. http://dx.doi.org/10.1117/12.427975.
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Qi, Fei, and Chengying Hua. "Efficient automated microarray image analysis." In Second International Conference on Image and Graphics, edited by Wei Sui. SPIE, 2002. http://dx.doi.org/10.1117/12.477198.
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Muresan, L., B. Heise, E. P. Klement, and J. Kybic. "Quantitative analysis of microarray images." In rnational Conference on Image Processing. IEEE, 2005. http://dx.doi.org/10.1109/icip.2005.1530295.
Повний текст джерелаЗвіти організацій з теми "Analisi microarray"
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Splitter, Gary, and Menachem Banai. Microarray Analysis of Brucella melitensis Pathogenesis. United States Department of Agriculture, 2006. http://dx.doi.org/10.32747/2006.7709884.bard.
Повний текст джерелаАнотація:
Original Objectives 1. To determine the Brucella genes that lead to chronic macrophage infection. 2. To identify Brucella genes that contribute to infection. 3. To confirm the importance of Brucella genes in macrophages and placental cells by mutational analysis. Background Brucella spp. is a Gram-negative facultative intracellular bacterium that infects ruminants causing abortion or birth of severely debilitated animals. Brucellosis continues in Israel, caused by B. melitensis despite an intensive eradication campaign. Problems with the Rev1 vaccine emphasize the need for a greater understanding of Brucella pathogenesis that could improve vaccine designs. Virulent Brucella has developed a successful strategy for survival in its host and transmission to other hosts. To invade the host, virulent Brucella establishes an intracellular niche within macrophages avoiding macrophage killing, ensuring its long-term survival. Then, to exit the host, Brucella uses placenta where it replicates to high numbers resulting in abortion. Also, Brucella traffics to the mammary gland where it is secreted in milk. Missing from our understanding of brucellosis is the surprisingly lillie basic information detailing the mechanisms that permit bacterial persistence in infected macrophages (chronic infection) and dissemination to other animals from infected placental cells and milk (acute infection). Microarray analysis is a powerful approach to determine global gene expression in bacteria. The close genomic similarities of Brucella species and our recent comparative genomic studies of Brucella species using our B. melitensis microarray, suqqests that the data obtained from studying B. melitensis 16M would enable understanding the pathogenicity of other Brucella organisms, particularly the diverse B. melitensis variants that confound Brucella eradication in Israel. Conclusions Results from our BARD studies have identified previously unknown mechanisms of Brucella melitensis pathogenesis- i.e., response to blue light, quorum sensing, second messenger signaling by cyclic di-GMP, the importance of genomic island 2 for lipopolysaccharide in the outer bacterial membrane, and the role of a TIR domain containing protein that mimics a host intracellular signaling molecule. Each one of these pathogenic mechanisms offers major steps in our understanding of Brucella pathogenesis. Strikingly, our molecular results have correlated well to the pathognomonic profile of the disease. We have shown that infected cattle do not elicit antibodies to the organisms at the onset of infection, in correlation to the stealth pathogenesis shown by a molecular approach. Moreover, our field studies have shown that Brucella exploit this time frame to transmit in nature by synchronizing their life cycle to the gestation cycle of their host succumbing to abortion in the last trimester of pregnancy that spreads massive numbers of organisms in the environment. Knowing the bacterial mechanisms that contribute to the virulence of Brucella in its host has initiated the agricultural opportunities for developing new vaccines and diagnostic assays as well as improving control and eradication campaigns based on herd management and linking diagnosis to the pregnancy status of the animals. Scientific and Agricultural Implications Our BARD funded studies have revealed important Brucella virulence mechanisms of pathogenesis. Our publication in Science has identified a highly novel concept where Brucella utilizes blue light to increase its virulence similar to some plant bacterial pathogens. Further, our studies have revealed bacterial second messengers that regulate virulence, quorum sensing mechanisms permitting bacteria to evaluate their environment, and a genomic island that controls synthesis of its lipopolysaccharide surface. Discussions are ongoing with a vaccine company for application of this genomic island knowledge in a Brucella vaccine by the U.S. lab. Also, our new technology of bioengineering bioluminescent Brucella has resulted in a spin-off application for diagnosis of Brucella infected animals by the Israeli lab by prioritizing bacterial diagnosis over serological diagnosis.
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Haghighi, F. Kernel Principle Component Analysis of Microarray Data. Final Report. Office of Scientific and Technical Information (OSTI), November 2003. http://dx.doi.org/10.2172/823317.
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Khatri, Purvesh, Dechang Chen, Jaques Reifman, Craig M. Lilly, and Larry A. Sonna. Software Tool for Analysis of Variance of DNA Microarray Data. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada460048.
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Wang, Jian, Joy D. Van Nostrand, Zhili He, Liyou Wu, Ye Deng, Xu Zhang, Jizhong Zhou, and Guanghe Li. Microarray-based analysis of survival of soil microbial community during ozonation. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/986918.
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Gopalan, Banu, Christian Posse, Antonio P. Sanfilippo, Mary Stenzel-Poore, S. L. Stevens, Jose Castano, Nathaniel Beagley, et al. Aligning ontologies and integrating textual evidence for pathway analysis of microarray data. Office of Scientific and Technical Information (OSTI), October 2006. http://dx.doi.org/10.2172/948766.
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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.
Повний текст джерелаАнотація:
Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.
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Rimm, David L. Spectral Analysis of Breast Cancer on Tissue Microarrays: Seeing Beyond Morphology. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada417663.
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Tooker, B. C., and Timothy S. Stahly. Microarray Analysis of Gene Expression Essential to Energetic Efficiency in a Porcine Model of Obesity. Ames (Iowa): Iowa State University, January 2005. http://dx.doi.org/10.31274/ans_air-180814-1077.
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Katzir, Nurit, James Giovannoni, Marla Binzel, Efraim Lewinsohn, Joseph Burger, and Arthur Schaffer. Genomic Approach to the Improvement of Fruit Quality in Melon (Cucumis melo) and Related Cucurbit Crops II: Functional Genomics. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592123.bard.
Повний текст джерелаАнотація:
Background: Genomics tools for enhancement of melon research, with an emphasis on fruit, were developed through a previous BARD project of the PIs (IS -333-02). These included the first public melon EST collection, a database to relay this information to the research community and a publicly available microarray. The current project (IS-3877- 06) aimed to apply these tools for identification of important genes for improvement of melon (Cucumis melo) fruit quality. Specifically, the research plans included expression analysis using the microarray and functional analyses of selected genes. The original project objectives, as they appeared in the approved project, were: Objective 1: Utilization of a public melon microarray developed under the existing project to characterize melon transcriptome activity during the ripening of normal melon fruit (cv. Galia) in order to provide a basis for both a general view of melon transcriptome activity during ripening and for comparison with existing transcriptome data of developing tomato and pepper fruit. Objective 2: Utilization of the same public melon microarray to characterize melon transcriptome activity in lines available in the collection of the Israeli group, focusing on sugar, organic acids and aroma metabolism, so as to identify potentially useful candidates for functional analysis and possible manipulation, through comparison with the general fruit development profile resulting from (1) above. Objective 3: Expansion of our existing melon EST database to include publicly available gene expression data and query tools, as the US group has done with tomato. Objective 4: Selection of 6-8 candidate genes for functional analysis and development of DNA constructs for repression or over-expression. Objective 5: Creation of transgenic melon lines, or transgenic heterologous systems (e.g. E. coli or tomato), to assess putative functions and potential as tools for molecular enhancement of melon fruit quality, using the candidate gene constructs from (4).
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Szallasi, Zoltan. CDNA Microarray Based Comparative Gene Expression Analysis of Primary Breast Tumors Versus In Vitro Transformed Neoplastic Breast Epithelium. Fort Belvoir, VA: Defense Technical Information Center, December 2001. http://dx.doi.org/10.21236/ada401181.
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