2016 International Conference on Bioinformatics and Systems Biology (BSB)最新文献_第3页

Systems biology approach for gene set enrichment and topological analysis of Alzheimer's disease pathway 阿尔茨海默病通路基因集富集和拓扑分析的系统生物学方法

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552132

Ashwani Kumar, T. Singh

{"title":"Systems biology approach for gene set enrichment and topological analysis of Alzheimer's disease pathway","authors":"Ashwani Kumar, T. Singh","doi":"10.1109/BSB.2016.7552132","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552132","url":null,"abstract":"Deciphering the underlying mechanisms of all complex interactions involved in different signaling pathways is a pivotal step in the dissection and study of network-based data. Heuristic statistical solutions are conventionally used across the world to derive a meaningful perspective of the network based data by identifying related biological networks. However, classical pathway analysis gives us elusive results by ignoring important aspects of biology. To overcome the limitations of the classical analysis, we have implemented systems biology approach which includes enrichment analysis of Alzheimer's disease (AD) gene set and topological enrichment analysis. Exploration of pathway ranking and regression analysis on the basis of XD-Score and Fisher-q value is also elucidated. Topology-based enrichment studies gave us insight on important parameters such as shortest path length, node betweenness, degree, clustering coefficient, eigenvector centrality and their association in AD based statistical score which turned out to be significantly high (5.062) at a significant threshold (0.74). A linear fit in regression plot and enrichment in associated gene pathways were observed.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123121086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A new PVC/SPB detection method: Based on analytical spectra technique 一种新的PVC/SPB检测方法:基于分析光谱技术

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552150

V. Antsiperov, A. Bugaev, I. V. Zabrosaev

引用次数: 2

Comprehensive computational analysis of chromosome 11 11号染色体的综合计算分析

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552151

Abhivyakti Srivastava, Mottadi Shiva, P. Kumari, Y. Hasija

{"title":"Comprehensive computational analysis of chromosome 11","authors":"Abhivyakti Srivastava, Mottadi Shiva, P. Kumari, Y. Hasija","doi":"10.1109/BSB.2016.7552151","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552151","url":null,"abstract":"Even before the onset of Human Genome Project in 1990, various research, analysis and experiments was going on human genome. In human genome, approximately 3 billion base pairs are structured in the form of 23 pairs of chromosomes. Chromosome 11 is a chromosome that is rich in disease and has a size of 134 million base pairs. From over 1000 genome web servers, the sequence data for the chromosome 11 has been taken as a (.bam) file. On Chromosome 11, approximately 45 different analyses were performed across various fields and categories, such as determining the sequence quality, over represented sequence, peak model, visualizing BAC end pairs, secondary structure prediction by analyses hydroxyl cleavage sites, GC percentage, studying phenotype and disease associated with respect to chromosome 11. Here, we have analysed the evolutionary relationship by isolating positively selected genes across 6 species; predicted the t-RNA and RNA secondary structures and aligned them discretely with the human genome chromosome 11. All these analyses was done primarily with the help of two tools, 1) Web based program-NEBULA and 2) UCSC genome browser.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134141546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A method of analysis of EEG wave trains in early stages of Parkinson's disease 一种分析帕金森病早期脑电图波列的方法

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552163

O. Sushkova, A. Morozov, A. Gabova

引用次数: 15

Estimating percentage epigenetic modifications in human genome using NGS data 利用NGS数据估计人类基因组表观遗传修饰的百分比

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552141

Aamna Lawrence, R. Shukla, Utkarsh Raj, Pritish Kumar Varadwaj

引用次数: 0

Identification of functional genetic variants in miRNA binding site in genes associated with lung cancer 肺癌相关基因miRNA结合位点功能基因变异的鉴定

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552154

Anju Gupta, P. Kumari, Mottadi Shiva, Y. Hasija

{"title":"Identification of functional genetic variants in miRNA binding site in genes associated with lung cancer","authors":"Anju Gupta, P. Kumari, Mottadi Shiva, Y. Hasija","doi":"10.1109/BSB.2016.7552154","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552154","url":null,"abstract":"The miRNAs are 22-46 nucleotidelong, non-protein coding RNAsthat act as oncogenes. Their altered expression can cause diseases, includingcancer. Lung cancer is causing death of million peopleworldwide. Yet only few genetic biomarkers are known for detecting lung cancer. miRNAs are those non-coding RNAs that act as such biomarkers. They act as oncogenes and regulate many biological processesand cellular pathways. The miRNAs regulate gene expression of protein coding genes by generating either translation repression or RNAdegradation. When they bind with 3' UTR of newly formed miRNA transcripts along with other helper proteins, they inhibit their expression and function. This translation inhibition, affects tumor suppressor genes and leads to cancer.miRNAexpression deregulation found in various cancers such as Prostrate, Breast, Colonialand Lung canceretc. In this study insilico approach has been used to find out functional genetic variation in miRNA binding sites of genes responsible for causing lung cancer. As a result of this study we have found 7 SNPs involved in such cancers-rs6772, rs1036672, rs739442, rs1050700, rs3185695, rs12723035, rs3787030. These SNPs can act as candidate biomarkers for lung cancer.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122081530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DrovePred: Server for DNA stem and BIME's prediction using Particle Swarm Optimization DrovePred:基于粒子群优化的DNA茎和BIME预测服务器

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552142

Aman Chandra Kaushik, Avinash Dhar, S. Sahi

引用次数: 2

Noninvasive arterial blood pressure monitoring: By active sensor based on the principle of pulse wave compensation 无创动脉血压监测:基于脉搏波补偿原理的主动传感器

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552149

V. Antsiperov, G. Mansurov, A. Polupanov, Basil Bonch-Bruevich

引用次数: 1

Insilico screening of Prevotella Intermedia 17 identifies Lipopolysaccharide Biosynthesis Pathway genes as potential drug targets 普雷沃特菌中间体17的计算机筛选鉴定了脂多糖生物合成途径基因作为潜在的药物靶点

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552138

N. Mathivanan, G. Kiruthika, R. Subashree

引用次数: 1

ShinyMDE: Shiny tool for microarray meta-analysis for differentially expressed gene detection ShinyMDE:用于差异表达基因检测的微阵列荟萃分析的Shiny工具

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552152

H. Shashirekha, A. Wani

{"title":"ShinyMDE: Shiny tool for microarray meta-analysis for differentially expressed gene detection","authors":"H. Shashirekha, A. Wani","doi":"10.1109/BSB.2016.7552152","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552152","url":null,"abstract":"The advancement in high-throughput microarray experiments has paved a way for several transcriptomic studies across the globe by several researchers in the area of functional genomics, molecular genetics, gene discovery, differentially expressed gene detection, diagnosis and prognosis etc. As a result, the tremendous amount of data that has been produced and accumulated in various public repositories such as Gene Expression Omnibus (GEO) and ArrayExpress, have been frequently used by researchers to readdress various biological goals. Since an independent study often comes with less sample size and limited statistical power, researchers are now relying on a more powerful technique called meta-analysis, an integrated analysis of existing data from different related independent studies. Meta-analysis is an active area in biomedical research which plays a vital role in increasing the statistical power to detect differentially expressed genes and to understand molecular and cellular aspects in a broader way. However, little efforts have been put to design user friendly tool/software to carry out meta-analysis automatically. In this paper, we present ShinyMDE, a user friendly tool to integrate different gene expression data for differentially expressed gene detection in an easy and efficient way. The tool handles processed and raw data generated from most widely used data platforms such as Affymetrix and Illumina. In addition, the tool provides user with an option of choosing the method of their choice from the list for meta-analysis. The tool is very simple to use and is developed with the aim of having an automated meta-analysis of gene expression data facilitating screening and downloading the results.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"84 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133610262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3