Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

Inferring Species Diversity and Variability over Climatic Gradient with Spectral Diversity Metrics

Filling in the void between forest ecology and remote sensing through monitoring biodiversity variables is of great interest. In this study, we utilized imaging spectroscopy data from the ISRO–NASA Airborne Visible InfraRed Imaging Spectrometer—Next Generation (AVIRIS-NG) India campaign to investigate how the measurements of biodiversity attributes of forests over wide areas can be augmented by synchronous field- and spectral-metrics. Three sites, Shoolpaneshwar Wildlife Sanctuary (SWS), Vansda National Park (VNP), and Mudumalai Tiger Reserve (MTR), spread over a climatic gradient (rainfall and temperature), were selected for this study. Abundant species maps of three sites were produced using a support vector machine (SVM) classifier with a 76–80% overall accuracy. These maps are a valuable input for forest resource management. Convex hull volume (CHV) is computed from the first three principal components of AVIRIS-NG spectra and used as a spectral diversity metric. It was observed that CHV increased with species numbers showing a positive correlation between species and spectral diversity. Additionally, it was observed that the abundant species show higher spectral diversity over species with lesser spread, provisionally revealing their functional diversity. This could be one of the many reasons for their expansive reach through adaptation to local conditions. Higher rainfall at MTR was shown to have a positive impact on species and spectral diversity as compared to SWS and VNP. Redundancy analysis explained 13–24% of the variance in abundant species distribution because of climatic gradient. Trends in spectral CHVs observed across the three sites of this study indicate that species assemblages may have strong local controls, and the patterns of co-occurrence are largely aligned along climatic gradient. Observed changes in species distribution and diversity metrics over climatic gradient can help in assessing these forests’ responses to the projected dynamics of rainfall and temperature in the future