Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Criminal justice system in pondicherry - a comparative critical study of the past and the presen

The Union Territory of Pondicherry prior to its merger with the Indian Union was a French Colony. The erstwhile territory of Pondicherry along with its hamlets, namely, KARAIKKAL, MAHE and YANAM was administered by the French Regime. Before it was established by French in 1 6 74 A.D. it was part of Vijayanagara Empire. Prior to this, Pondicherry was a part of the Kingdom of Chola and Pallava Kings. During French Regime, the laws which were in force in France in relation to administration of civil and criminal justice were extended to the erstwhile Territory of Pondicherry. Thus while Pondicherry stood influenced by the Inquisitorial system since the beginning of the 18th century, the neighboring states forming part of the Indian Union since Independence came under the Influence of the British system, viz. accusatorial system. The territory of Pondicherry, for administrative reasons, came to be merged with the Indian Union in the early 60's. Following the merger, the Indian administration sought to extent its own laws from time to time replacing erstwhile French Laws, however, subject to certain savings. Thus the transitional period witnessed consequential changes in the administration of the territory, including the sphere of judicial system. Since I 963, the Union Territory of Pondicherry was brought under the spell of the Indian Legal System The people in Pondicherry ' thus have had the benefit of experiencing both the svstems. Their experiences will be of much help to those who undertake comparative studies in law. The plus and minus points of the respective systems help one to develop a detachment that helps independent evaluation of the svstents. The result of these studies could be relevant in revitalising our criminal systems.The present system is evaluated in the light of the past system. New dimensions are added by way' of an empirical study also.

Evaluation of cyanobacteria for biomass production and effluent treatment

The microalgae gained importance as food and feed as well as source of fine chemicals since the l960’s. Spirulina became the trend setter due to its easily culturable properties as well as nutritional composition. A rapid expansion of microalgal industry occurred in the Asia-Pacific region as microalgae came to stay as a health food supplement. Microalgae have been an integral component of oxidation ponds usually incorporated with wastewater treatment. Over the last few decades, efforts have been made to apply intensive microalgal cultures to perform biological tertiary treatment of secondary effluents. Given the limited number of species still available for commercial exploitation, it is imperative to isolate and cultivate those photosynthetic organisms with high growth rate and biomass accumulation, which could play the dual role of cleaning the wastewater and also providing useful biomass. This has been the objective of this study ie. 0 To develop pure cultures of local isolates of Cyanobacteria for extraction of biochemicals of commercial value 0 To couple biomass production with effluent treatment

Water Quality Variation, its Influence on Drinking Water Treatment and Remedial Measures - A Case Study of Peechi reservoir, Thrissur, Kerala

The Kerala Water Authority requested the School of Environmental Studies to carry out investigations on the mechanism of sporadic mobilization of iron and odour in the raw water drawn to the drinking water treatment plant. The currently used treatment process failed to remove iron completely. This led to problems in the filter and complaints of taste and colour due to iron in the finished water. The sporadic nature of the problem itself made the trouble shooting difficult. The problem was looked in from three points of view. 1. Influence of environmental (climatic) conditions on the dynamics of the relevant basin of the reservoir. 2. Influence of the physical dynamics on the physico — chemical quality of water. 3. Identification of cost-effective treatment processes to suit the existing plant. Since the problem emerged only during the post- monsoon to pre-monsoon months, a related problem was investigated, namely, influence of anions on the oxidation of Fe(II) in natural waters by air. This is presented in Part II of the dissertation.

Distribution and bioactive potential of soil actinomycetes from different ecological habitats

Emergence of drug resistance among pathogenic bacteria to currently available antibiotics has intensified the search for novel bioactive compounds from unexplored habitats. In the present study actinomycetes were isolated from two relatively unexplored and widely differing habitats such as mountain and wetlands and their ability to produce antibacterial substances were analyzed. Pure cultures of actinomycetes were identified by morphological and biochemical tests. Various genera of actinomycetes encountered included Nocardia, Pseudonocardia, Streptomyces, Nocardiopsis, Streptosporangium, Micromonospora, Rhodococcus, Actinosynnema, Nocardiodes, Kitasatosporia, Gordona, Intrasporangium and Streptoalloteichus. The frequency of occurrence of each genus was found to vary with sample. About 47% of wetland isolates and 33% of mountain isolates were identified as various species of Nocardia. The isolated strains differed among themselves in their ability to decompose proteins and amino acids and also in enzyme production potential. Antibiotic activities of these actinomycetes were evaluated against 12 test pathogenic bacteria by well diffusion method using agar wells in glycerol-yeast extract agar. About 95% of actinomycete isolates from wetland ecosystem and 75% of highland isolates suppressed in different degrees the growth of test pathogens. Relatively high antibacterial activity among these isolates underlined their potential as a source of novel antibiotics.

Quantile based reliability aspects of partial moments

Partial moments are extensively used in literature for modeling and analysis of lifetime data. In this paper, we study properties of partial moments using quantile functions. The quantile based measure determines the underlying distribution uniquely. We then characterize certain lifetime quantile function models. The proposed measure provides alternate definitions for ageing criteria. Finally, we explore the utility of the measure to compare the characteristics of two lifetime distributions