Journal of Data Mining in Genomics & Proteomics最新文献

{"title":"Suffix Graph - An Efficient Approach for Network Motif Mining","authors":"R. Nikam, U. Chauhan","doi":"10.4172/2153-0602.1000200","DOIUrl":"https://doi.org/10.4172/2153-0602.1000200","url":null,"abstract":"Network motif is a pattern of inter-connections occurring in complex network in numbers that are significantly higher than those in similar randomized network. The basic premise of finding network motifs lie in the ability to compute the frequency of the subgraphs. In order to discover network motif, one has to compute a subgraph census on the original network that calculates the frequency of all the subgraphs of certain type. Then there is a need to compute the frequency of a set of subgraphs on the randomized similar network. The bottleneck of the entire motif discovery process is therefore to compute the subgraph frequencies and this is the core computational problem. The proposed work is to present the Suffix-Graph, a data structure that store graphs efficiently and to design an algorithm to retrieve subgraph efficiently that detects network motifs and apply them to transcriptional interactions in Escherichia coli.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"41 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2016-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86228097","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}

{"title":"Genome Mining of Rice ( Oryza sativa subsp. indica ) for Detection and Characterization of Long Palindromic Sequences","authors":"Elmira Katanchi Kheiavi, A. Ahmadikhah, A. M. Mosammam","doi":"10.4172/2153-0602.1000199","DOIUrl":"https://doi.org/10.4172/2153-0602.1000199","url":null,"abstract":"Because the rice genome has been sequenced entirely, search to find specific features at genome-wide scale is of high importance for studying genome evolution and subsequent applications. Palindromic sequences are important DNA motifs involved in the regulation of different cellular processes and are a potential source of genetic instability. A genome mining approach was applied to detect and characterize the long palindromic sequences in the rice genome. All palindromes, defined as identical inverted repeats with spacer DNA, could be analyzed and sorted according to their frequency, size, GC content, compact index etc. The results showed that the overall palindrome frequency is high in rice genome (nearly 51000 palindromes), that totally cover 41.4% of nuclear genome of rice, with highest and lowest number of palindromes, respectively belongs to chromosome 1 and 12. Palindrome number could well explain the rice chromosome expansion (R2>92%). Average GC content of the palindromic sequences is 42.1%, indicating AT-richness and hence, the low-complexity of palindromic sequences. The results also showed different compact indices of palindromes in different chromosomes (43.2 per cM in chromosome 8 and 34.5 per cM in chromosome 3, as highest and lowest, respectively). Co-location analysis showed that more than 20% of rice genes overlapped with palindromic regions, mainly concentrating on chromosomal arms. Based on the results of this research it can be concluded that the rice genome is rich in long palindromic sequences that triggered most variation during evolution. Generally, both sections of palindromic sequences including stems and loops are AT-rich, indicating that these regions locate in the low-complexity segments of the rice chromosomes.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"103 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2016-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79524925","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}

{"title":"Visualization of High Throughput Genomic Data Using R and Bioconductor","authors":"R. Yadav, P. Srivastava","doi":"10.4172/2153-0602.1000197","DOIUrl":"https://doi.org/10.4172/2153-0602.1000197","url":null,"abstract":"DNA microarrays, technology aims at the measurement of mRNA levels in particular cells or tissues for many genes simultaneously. Microarray in molecular biology results in huge datasets that need rigorous computational analysis to extract biological information that lead to some conclusion. From printing of microarray chip to hybridization and scanning process it results in variability in quality of data due to which actual information is either lost or it is over represented. Computational analysis plays an important part related to the processing of the biological information embedded in microarray results and for comparing gene expression result obtained from different samples in different condition for biological interpretation. A basic, yet challenging task is quality control and visualization of microarray gene expression data. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project for the analysis and comprehension of genomic data, based on the R programming language. This paper describes specific procedures for conducting quality assessment of Affymetrix Gene chip using data from GEO database GSE53890 and describes quality control packages of bioconductor with reference to visualization plots for detailed analysis. This paper can be helpful for any researcher working on microarray analysis for quality control analysis of affymetrix chip along with scientific interpretations.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"28 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2016-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73553023","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}

{"title":"Computational Approach to Identify the Major Histocompatibility Complex Binding Antigenic Peptides from ‘Ascariasis’","authors":"S. Mishra, G. Vs","doi":"10.4172/2153-0602.1000198","DOIUrl":"https://doi.org/10.4172/2153-0602.1000198","url":null,"abstract":"The Ascaris lumbricoides cause ‘ascariasis’ in human and its elimination is the major public concern. In this current investigation, we predicted the MHC (Major Histocompatibility Complex) class I & II binding peptides with computational approach like PSSM (Position Specific Scoring Matrices) and SVM (Support Vector Machine) algorithms. We predict the peptide binders of Cytochrome b (mitochondrion) protein from Ascaris lumbricoide sequence to MHC-I molecules are as 11mer_H2_Db, 10mer_H2_Db, 9mer_H2_Db, 8mer_H2_Db. Also study integrates prediction of peptide MHC class I binding; proteasomal C terminal cleavage and TAP transport efficiency by using sequence and properties of the amino acids. We also found the binding of peptides to different alleles by using Position Specific Scoring Matrix. Cytochrome B from Ascaris lumbricoides (365 residues long) with 357 nonamers having antigenic MHC binding peptides. PSSM based server will predict the peptide binders from sequence to MHCII molecules are as I_Ab.p, I_Ad.p, I_Ag7, which are found antigenic epitopes region in Cytochrome B from Ascaris lumbricoides. This investigation can be useful in rational vaccine design and simultaneously increase the understanding the role of the immune system against antigenic.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"52 1 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2016-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83533934","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}

{"title":"Infectomic Insights into the Roles of Exosymbiosis-Endosymbiosis Imbalance (EESI) in HIV-1 and SIV Infections","authors":"Sheng-He Huang, Yanhong Zhou","doi":"10.4172/2153-0602.1000196","DOIUrl":"https://doi.org/10.4172/2153-0602.1000196","url":null,"abstract":"The vast majority of microbes form a healthy symbiotic ‘superorganism’ with the hosts. There are two types of symbiosis (Sym), exosymbiosis (e.g. microbiota) and endosymbiosis (e.g. mitochondria). It has been suggested that the exo-endo Sym balance (EESB) highly contribute to maintain the host homeostasis. However, alterations to the EESB caused by microbial (e.g. bacterial and viral pathogens) and non-microbial factors (e.g. substance abuse, diet and/or lifestyle) can disturb this symbiotic relationship and promote disease, such as inflammatory bowel diseases and acquired immune deficiency syndrome (AIDS). Progressive AIDS caused by human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is characterized by systemic inflammation, opportunistic infection and malignant disorders resulting from generalized immune activation-mediated destruction of the healthy symbiotic super organism. Two extreme phenotypes are present in both HIV and SIV infections, including slow or rapid progression to AIDS (Pat: pathogenesis) in a majority of the infected human subjects and the non-natural primate host (i.e. rhesus macaques, RMs), and nonprogression to AIDS (Sym) in a minority of the infected people and the natural primate hosts (i.e. sooty mangabeys, SMs). Recently, it has been demonstrated that both exosymbiotic and endosymbiotic disorders contribute to the development of AIDS through infectomic studies of the extreme phenotypes of HIV/SIV infections. The involvement of the EESB in the pathogenesis and therapeutics of HIV infections is becoming increasingly clear. Indeed, many changes in the microbial diversity, abundance and composition of the gut microbiota and mitochondrial functions have been reported in HIV/AIDS, suggesting that there exist EESB problems in this disease. HIV virotoxins have been implicated in exploiting mitochondria to promote the targeted progressive and inexorable depletion of key immune cells (e.g. CD4 T cells), a hallmark of HIV/SIV infections. These findings support the notion that the exo-endo Sym imbalance (EESI) may play a central role in epidemiology, pathogenesis and management of infectious diseases, including AIDS caused by HIV-1 and SIV. Correction of the EESI problems in HIV/SIV infections may lead to a rational control of AIDS.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"5 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2016-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79784937","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}

{"title":"Impaired Immune Phenotype of Endothelial Cell-derived Micro Particles: The Missing Link between Diabetes-related States and Risk of Cardiovascular Complications?","authors":"Alex, er E. Berezin","doi":"10.4172/2153-0602.1000195","DOIUrl":"https://doi.org/10.4172/2153-0602.1000195","url":null,"abstract":"Type two diabetes mellitus (T2DM) remains a leading contributor to cardiovascular (CV) mortality worldwide. Although obese and metabolic syndrome are discussed key factors contributing a higher risk of T2DM, the exact molecular mechanisms underlying to the progression of dysmetabolic states are still not completely clear. There is large body of evidence regarding endothelial dysfunction as a key player in increasing CV risk and that vascular damage in the dysmetabolic patients might mediate through an imbalance between various populations of micro particle (MP). The short commentary is discussed a role of impaired ratio between apoptotic MPs and activated MPs derived from endothelial cells that was recognized as “impaired phenotype” of endothelial cell-derived MPs. It has considered the causality epigenetic reprogramming, metabolic disorders, inflammation, and oxidative stress in forming of “impaired phenotype” of MPs. The incorporation of measurement of the endothelial cell-derived MP number into a conventional CV risk factor model aimed improving of risk stratification of the dysmetabolic patients with high probability of CV disease is discussed.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"22 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2016-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81190330","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}

{"title":"The Importance of Next-generation Sequencing for Marine Larvae Research: Insight into Larvae Settlement and Anti-fouling","authors":"Kondethimmanahalli Ch, ramouli","doi":"10.4172/2153-0602.1000E123","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E123","url":null,"abstract":"Larvae of marine invertebrates are important constituents of intertidal and sediment marine ecosystems around the world. They are ecologically and economically important species. For example, the barnacles are most dominant group of fouling organisms and are extensively used in larval settlement and anti-fouling research [1]. The bryozons and polychaetes are also cosmopolitan fouling organisms distributed in intertidal to shallow subtidal water [2,3]. These species form large colonies on ship hulls, piers and underwater structures causing a serious economic loss to shipping industries. It has been reported that biofouling of such species cost billions of dollars in shipping industry [4]. The academic and industrial marine research is mainly focused on biofouling species with the goal of understanding their larval settlement process and hoping for prevention of settlement and accumulation of such species on underwater structures. The life cycle of most marine invertebrates has two distinct stages: the pelagic larvae and the adults attached to marine substratum [5]. Understanding the larval settlement and attachment processes is important for prevention of biofouling. Most of the anti-fouling studies target larvae settlement process. However, process of settlement at molecular level is largely unknown due to limited genome information available for these species. In recent years, rapid technological advances in next-generation sequencers (NGS) have opened up possibilities to sequence larval transcriptome of marine invertebrates. Since NGS rapidly generates huge amount of sequence data in a very cost-effective way, larval biologists are now starting to integrate such sequencing methods into their research methods.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"67 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87626379","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}

{"title":"Identification of Novel Cdc37 Interacting Proteins and Pathways in Human Alzheimers Disease Brain Tissue Using Mass Spectrometry","authors":"M. Narayan, Lisa Kirouac, Dale Chaput, S. Stevens, J. Padmanabhan, U. Jinwal","doi":"10.4172/2153-0602.1000193","DOIUrl":"https://doi.org/10.4172/2153-0602.1000193","url":null,"abstract":"Alzheimer’s disease (AD) is the most common form of dementia and the 6th leading cause of death in the United States. The major pathological hallmarks observed in AD include the formation of intracellular neurofibrillary tangles comprised of phosphorylated forms of the microtubule associated protein tau, and the deposition of extracellular plaques composed of amyloid beta. Cdc37 is a co-chaperone of Hsp90, which recruits client kinases to the Hsp90 complex for folding and stabilization. It has been previously shown that Cdc37 can not only bind and preserve tau, but also stabilize kinases that can phosphorylate tau. The goal of the current study was to identify novel Cdc37- interacting proteins in human AD tissue compared to normal tissue using an immunoprecipitation-based approach combined with mass spectrometry. We identified 39 unique proteins that interacted with Cdc37 in AD samples only and 7 proteins that interacted with Cdc37 in normal samples only. 39 proteins were found to bind Cdc37 in both AD and normal tissue. Of these, 18 showed increased interaction in AD tissue, 10 showed increased interaction in normal tissue and 11 showed equal nteraction in both samples. Ingenuity Pathway Analysis of the data indicates that these Cdc37-interacting proteins could signal through the p70S6K, PI3K / Akt, TGFs, ErbB, NF- kB, calmodulin, p38 MAPK and JNK pathways. Identification of these novel proteins and pathways linked to Cdc37 may indicate its role both as a non-kinase co-chaperone and in other pathways in the AD brain.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"EC-2 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2016-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84585818","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}

{"title":"Marine Proteomics: Challenges and Opportunities","authors":"Kondethimmanahalli Ch, ramouli","doi":"10.4172/2153-0602.1000E122","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E122","url":null,"abstract":"Marine invertebrates such as crustaceans, oysters, polychaetes and bryozones are widely distributed in intertidal and sediment ecosystems and have significant economic and ecological importance. These species serve as model organisms for settlement biology, biofouling, marine pollution, toxicology, climate change and ocean acidification research. Traditionally, marine biologists have studied them in the context of morphology and behavior. Ever since the technological advancement in proteomics and genome sequencing tools, researchers began to adopt such tools in marine larvae biology research [1]. However, the challenge is that none of these tools were applied to marine research before so there is a great deal of optimization of such methods has to be done. In addition, lack of genome information discouraged marine scientists to conduct proteomics studies. Cell culture methods have not been established and species specific antibodies are not yet developed. The direct use of larvae or adults increases the complexity of proteome. Shells and calcareous tubes of crustaceans and oysters and self-secreted mucilage or slime of polychaetes poses greater challenge for proteins extraction and purification protocols. Natural habitat conditions differ substantially thereby variation in data obtained is high.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"44 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85627864","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}

{"title":"Genome-wide Analysis of Acute Inflammatory and Anti-Inflammatory Responses in RAW264 Cells Suggests cis-Elements Associated with Translational Regulation","authors":"H. Sako, Katsuhiko Suzuki","doi":"10.4172/2153-0602.1000191","DOIUrl":"https://doi.org/10.4172/2153-0602.1000191","url":null,"abstract":"Translational regulation plays pivotal roles in mediating inflammatory responses. Glucocorticoids, represented in this study by dexamethasone (DEX), are widely recognized anti-inflammatory agents that exert significant inhibitory effects on the translation of diverse gene groups, including inflammatory genes. However, their regulation is highly complex and diverse, involving transcriptional and translational regulation. Although transcriptional regulation has been investigated by genome-wide transcriptome analyses, translational regulation has been studied by only a few specific gene targets (e.g., Tumor necrosis factor) and the global impact of glucocorticoids on translation levels has scarcely been studied, mainly due to its technical difficulty. Here, using ribosome profiling coupled with high-throughput mRNA sequencing (mRNA-Seq) in which footprints of translating ribosomes can be captured, we conducted a genomewide transcriptional and translational analysis of the acute inflammatory or anti-inflammatory responses of RAW264 cells stimulated by lipopolysaccharide (LPS) or LPS coupled with DEX (LPS + DEX). We showed that the majority of the differential regulation between LPS alone and LPS + DEX were predominated by translation levels rather than transcription levels. Further analysis on the up- and down-regulated gene clusters revealed putative cis regulatory elements exclusively enriched in the 3'-UTR of either up- or down-regulated genes induced by LPS + DEX. The results imply an alternative to the currently recognized mechanisms of glucocorticoid-induced translational regulation in the acute inflammatory response of RAW264 cells.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"1 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2016-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78734464","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}