SEAweb: the small RNA Expression Atlas web application

Abstract

We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.

Roles of host small RNAs in the evolution and host tropism of coronaviruses

“…To investigate the RNAi-sensitive sites on genomes of coronaviruses targeted by human miRNAs, we first downloaded the up-to-date human mature miRNA sequences from miRBase [ 28 ] with which we can infer candidate RNAi-sensitive targets for any given genome of coronavirus. As the strength of overall RNAi suppression against a virus should depend on the total amount of miRNA transcripts including all miRNA species that match their targets in the coronavirus genome, we therefore obtained the profile of miRNAs expressed in normal human lung, the common entryway of coronaviruses, from SEAweb [ 29 ], an up-to-date miRNA expression database. Using these data, we can estimate the total abundance of the coronavirus-targeting miRNA (coronavirus-targeting human miRNA) present in human lung targeting a given coronavirus genome; we hereafter refer to this information as CoVT-miRNA for convenience.…”

“…As each target can be interfered by an miRNA species at various expression levels in normal human lung, we defined the CoVT-miRNA abundance of the given strain as the sum of abundance of all the interfering miRNAs matching its targets. The expression level of all the miRNAs in different tissues were downloaded from SEAweb [ 29 ] and indicated as RPM (Reads of exon model per Million mapped reads). The abundance of each miRNA in a sample was calculated as the percentage of the miRNA’s RPM value in the total RPM of the sample, and final abundance of each miRNA species in each tissue was averaged among all samples of the same tissue type.…”

Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans

“…Although not strictly required for survival under laboratory conditions, such cell-specific miRNAs contribute to the acquisition of the phenotypic diversity that is critical for the animal’s evolutionary success in complex natural environments (e.g., by enabling development and function of diverse sensory neurons) [ 38 , 46 ]. Similarly, many miRNAs in other animals are expressed with high cell type specificity [ 47 , 48 ] and, based on a comprehensive survey in the mouse [ 1 ], seem to function in cell- or tissue-specific development or physiology. Many of these mouse miRNAs are also essential for viability, although lethality in these cases occurs late in development in correctly patterned embryos that fail to generate specific cell types, e.g., miR-1-deficient mice die shortly after birth due to cardiac muscle defects [ 49 ].…”

Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

“…SEAweb has the advantage of collecting a wide range of datasets of tissue-specific miRNAs across different conditions and dealing with pathologic information to find any association. The ability to download data on differential expression is a feature that allows comparison of one’s own data with information contained in the atlas [ 119 , 120 ].…”