Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds.

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Storing and processing Remote Sensing (RS) images require large amounts of memory space and computing resources. Consequently, RS images are compressed and stored in various compression formats, such as JPEG2000. However, the processing of RS images for machine interpretation and understanding still necessitates the deployment of an image decompression stage in its entirety, followed by a computationally demanding image analysis pipeline. The image analysis stage is commonly composed of machine learning techniques, such as Deep Convolutional Neural Network (DCNN) models. Classification of remote sensing images is among the most common image analysis tasks. In the scope of this paper, we propose a sub-band image based classification method for the Remote Sensing Scene Classification (RSSC) task in the JPEG2000 compressed domain. The proposed approach exploits the already available sub-band image coefficients to classify RS images without needing for full decompression. Our study shows that our method increases the high frequency information in the LL sub-band and allows the image to contain more detail, leading to improved classifier performance while taking advantage of the partial decompression method.

Due to the increase in gene expression data sets in recent years, various data mining techniques have been proposed for mining gene expression profiles. However, most of these methods target single gene expression data sets and cannot handle all the available gene expression data in public databases in reasonable amount of time and space. In this paper, we propose a novel framework, bi-k-bi clustering, for finding association rules of gene pairs that can easily operate on large scale and multiple heterogeneous data sets. We applied our proposed framework on the available NCBI GEO Homo sapiens data sets. Our results show consistency and relatedness with the available literature and also provides novel associations.

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