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A tutorial and tool for exploring feature similarity gradients with MRI data.

ABSTRACT: There has been an increasing interest in examining organisational principles of the cerebral cortex (and subcortical regions) using different MRI features such as structural or functional connectivity. Despite the widespread interest, introductory tutorials on the underlying technique targeted for the novice neuroimager are sparse in the literature. Articles that investigate various "neural gradients" (for example based on region studied "cortical gradients," "cerebellar gradients," "hippocampal gradients" etc … or feature of interest "functional gradients," "cytoarchitectural gradients," "myeloarchitectural gradients" etc …) have increased in popularity. Thus, we believe that it is opportune to discuss what is generally meant by "gradient analysis". We introduce basics concepts in graph theory, such as graphs themselves, the degree matrix, and the adjacency matrix. We discuss how one can think about gradients of feature similarity (the similarity between timeseries in fMRI, or streamline in tractography) using graph theory and we extend this to explore such gradients across the whole MRI scale; from the voxel level to the whole brain level. We proceed to introduce a measure for quantifying the level of similarity in regions of interest. We propose the term "the Vogt-Bailey index" for such quantification to pay homage to our history as a brain mapping community. We run through the techniques on sample datasets including a brain MRI as an example of the application of the techniques on real data and we provide several appendices that expand upon details. To maximise intuition, the appendices contain a didactic example describing how one could use these techniques to solve a particularly pernicious problem that one may encounter at a wedding. Accompanying the article is a tool, available in both MATLAB and Python, that enables readers to perform the analysis described in this article on their own data. We refer readers to the graphical abstract as an overview of the analysis pipeline presented in this work.

SUBMITTER: Bajada CJ

PROVIDER: S-EPMC7116330 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:To tackle the challenges in genomic data analysis caused by their tens of thousands of dimensions while having a small number of examples and unbalanced examples between classes, the technique of unsupervised feature selection based on standard deviation and cosine similarity is proposed in this paper. We refer to this idea as SCFS (Standard deviation and Cosine similarity based Feature Selection). It defines the discernibility and independence of a feature to value its distinguishable capability between classes and its redundancy to other features, respectively. A 2-dimensional space is constructed using discernibility as x-axis and independence as y-axis to represent all features where the upper right corner features have both comparatively high discernibility and independence. The importance of a feature is defined as the product of its discernibility and its independence (i.e., the area of the rectangular enclosed by the feature's coordinate lines and axes). The upper right corner features are by far the most important, comprising the optimal feature subset. Based on different definitions of independence using cosine similarity, there are three feature selection algorithms derived from SCFS. These are SCEFS (Standard deviation and Exponent Cosine similarity based Feature Selection), SCRFS (Standard deviation and Reciprocal Cosine similarity based Feature Selection) and SCAFS (Standard deviation and Anti-Cosine similarity based Feature Selection), respectively. The KNN and SVM classifiers are built based on the optimal feature subsets detected by these feature selection algorithms, respectively. The experimental results on 18 genomic datasets of cancers demonstrate that the proposed unsupervised feature selection algorithms SCEFS, SCRFS and SCAFS can detect the stable biomarkers with strong classification capability. This shows that the idea proposed in this paper is powerful. The functional analysis of these biomarkers show that the occurrence of the cancer is closely related to the biomarker gene regulation level. This fact will benefit cancer pathology research, drug development, early diagnosis, treatment and prevention.

Project description:BackgroundBiochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance.ResultsWe present Transformation of Nucleotide Enrichment Ratios (ToNER), a tool for statistical modeling of enrichment from RNA-seq data obtained from enriched and unenriched libraries. The tool calculates nucleotide enrichment scores and determines the global transformation for fitting to the normal distribution using the Box-Cox procedure. From the transformed distribution, sites of significant enrichment are identified. To increase power of detection, meta-analysis across experimental replicates is offered. We tested the tool on Cappable-seq and dRNA-seq data for identifying Escherichia coli transcript 5' ends and compared the results with those from the TSSAR tool, which is designed for analyzing dRNA-seq data. When combining results across Cappable-seq replicates, ToNER detects more known transcript 5' ends than TSSAR. In general, the transcript 5' ends detected by ToNER but not TSSAR occur in regions which cannot be locally modeled by TSSAR.ConclusionToNER uses a simple yet robust statistical modeling approach, which can be used for detecting RNA 5'ends from Cappable-seq data, in particular when combining information from experimental replicates. The ToNER tool could potentially be applied for analyzing other RNA-seq datasets in which enrichment for other structural features of RNA is employed. The program is freely available for download at ToNER webpage (http://www4a.biotec.or.th/GI/tools/toner) and GitHub repository (https://github.com/PavitaKae/ToNER).

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A tutorial and tool for exploring feature similarity gradients with MRI data.

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