Comprehensive databases of microRNA-disease associations are continuously demanded in biomedical researches. The recently launched version 3.0 Human MicroRNA Disease Database (HMDD v3.0) manually collects a significant number miRNA-disease association entries from literature. Comparing to HMDD v2.0, this new contains 2-fold more entries. Besides, the have been accurately classified based on literature-derived evidence code, which results six generalized categories (genetics, epigenetics,...

Abstract Sex differences are widely observed under various circumstances ranging from physiological processes to therapeutic responses, and a myriad of sex-biased genes have been identified. In recent years, transcriptomic datasets microRNAs (miRNAs), an important class non-coding RNAs, become increasingly accessible. However, comprehensive analysis sex difference in miRNA expression has not performed. Here, we identified the differentially-expressed miRNAs between males females by examining...

MicroRNAs (miRNAs) are one class of important small non-coding RNA molecules and play critical roles in health disease. Therefore, it is necessary to evaluate the functional relationship miRNAs then predict novel miRNA-disease associations. For this purpose, here we developed updated web server MISIM (miRNA similarity) v2.0. Besides a 3-fold increase data content compared with v1.0, v2.0 improved original algorithm by implementing both positive negative That is, scores could be or negative,...

A series of miRNA-disease association prediction methods have been proposed to prioritize potential disease-associated miRNAs. Independent benchmarking these is warranted assess their effectiveness and robustness.Based on more than 8000 novel associations from the latest HMDD v3.1 database, we perform systematic comparison among 36 readily available methods. Their overall performances are evaluated with rigorous precision-recall curve analysis, where 13 show acceptable accuracy (AUPRC >...

Numerous studies on discovering the roles of long non-coding RNAs (lncRNAs) in occurrence, development and prognosis progresses various human diseases have drawn substantial attentions. Since only a tiny portion lncRNA-disease associations been properly annotated, an increasing number computational methods proposed for predicting potential associations. However, traditional models lack ability to precisely extract features biomolecules, it is urgent find model which can identify with both...

Abstract Abdominal aortic aneurysm (AAA) is a permanent dilatation of the abdominal aorta and highly lethal. The main purpose current study to search for noninvasive medical therapies AAA, which there currently no effective drug therapy. Network medicine represents cutting-edge technology, as analysis modeling disease networks can provide critical clues regarding etiology specific diseases therapeutics that may be effective. Here, we proposed novel algorithm quantify relations based on large...

Menopausal hormone therapy (MHT) was widely used to treat menopause-related symptoms in menopausal women. However, MHT therapies were controversial with the increased risk of breast cancer because different estrogen and progestogen combinations, molecular basis behind this phenomenon is currently not understood. To address issue, we identified differentially expressed genes (DEGs) between plus progestogens treatment (EPT) (ET) using Gene Expression Omnibus (GEO) The Cancer Genome Atlas...

Cellular senescence is an important protective mechanism against cell proliferation and has critical roles in aging aging-related disease. Recently, one interesting observation that the protein abundance higher senescent cells than young cells. So far, some factors were presented to interpret this observation, such as active synthesis linked with autophagy, mTOR, oxidative stress. Here, applying bioinformatic analysis of microRNA profiles cells, we revealed globally show lower miRNA...

Background Effectively predicting the risk of adverse pregnancy outcome (APO) in women with systemic lupus erythematosus (SLE) during early and mid-pregnancy is a challenge. This study was aimed to identify potential markers for prediction APO SLE. Methods The GSE108497 gene expression dataset containing 120 samples (36 patients, 84 controls) downloaded from Gene Expression Omnibus database. Weighted co-expression network analysis (WGCNA) performed, differentially expressed genes (DEGs) were...

Abstract To dig critical microRNAs (miRNAs) from the big miRNAome, it is becoming emergent to quantify importance of miRNAs. However, computational methods for this purpose are still not available. Some sequence features associated with miRNA conservation revealed and disease spectrum width (DSW) defined as a score measure miRNAs some extent. Here, random forest based regression model, microRNA calculator (MIC), proposed estimate relationship between DSW score. The result shows that MIC fits...

Physiological and pathophysiological differences widely exist in paired organ systems. However, the molecular basis for these remains largely unknown. We previously reported that there differentially expressed miRNAs (DEMs) left right kidneys of normal mice. Here, we identified DEMs eyes, lungs, testes mice via RNA sequencing. As a result, 26 with 23 higher 3 lower eyes compared eyes; 21 15 6 lungs lungs; 54 testes, 48 testes. Ten microRNAs (miRNAs) were further examined by quantitative PCR...

Colon cancer (COAD) is a common malignancy, yet its etiology not fully elucidated. This study gathered endocytosis-related genes, using gene expression profiles from TCGA databases to categorize molecular subtypes of COAD into Cluster1 and Cluster2 based on genes related endocytosis, further explored the connection between two prognostic characteristics. Differential analysis revealed 3412 differentially expressed (DEGs), whose functions were remarkably enriched in cellular metastasis...

Disease causative non-coding RNAs (ncRNAs) are of great importance in understanding a disease, for they directly contribute to the development or progress disease. Identifying ncRNAs can provide vital implications biomedical researches. In this work, we updated long RNA disease database (LncRNADisease) with (lncRNA) causality information manual annotations causal associations between lncRNAs/circular (circRNAs) and diseases by reviewing related publications. Of total 11 568 experimental...

MicroRNAs (miRNAs) are an important class of small noncoding RNA molecules that serve as excellent biomarkers various diseases. However, current miRNA biomarkers, including those comprised multiple miRNAs, work at a single-miRNA level but not miRNA-set level, which is defined group miRNAs sharing common biological characteristics. Given the rapidly accumulating omics data, we believe analysis could be supplement to analysis. Therefore, present sTAM (http://mir.rnanut.net/stam), computational...

Abstract Abdominal aortic aneurysm (AAA) is a highly lethal vascular disease characterized by permanent dilatation of the abdominal aorta. The main purpose current study to search for noninvasive medical therapies (AAA), which there currently no effective drug therapy. Network medicine represents cutting-edge technology, as analysis and modeling networks can provide critical clues regarding etiology specific diseases therapeutics may be effective. Here, we proposed novel algorithm quantify...

In article number 1900083, Chunmei Cui, Qinghua and co-workers design a ‘computational model’, MIC, to quantify miRNA essentiality identify the important ones from huge of miRNAs in human genome using sequence information. For cover figure, MIC model is like superman (or archmage/magician) who can precisely select he/she needs ball.

Abstract microRNAs (miRNAs) are one class of important small noncoding RNA molecules, which have shown their excellent ability as biomarkers various diseases. However, current miRNA including those comprised multiple miRNAs work at a single-miRNA level but not set level. Given the rapidly accumulated omics data, it is believed that analysis could be an supplement to single analysis. For doing so, here we presented computational method for single-sample enrichment and developed sTAM tool (...

Highlights ● We presented a computational model to built human disease network from miRNA-disease association data; Applying the model, we miRNA-derived which covers 15 classes and includes 304 diseases; revealed number of patterns for network, example diseases tend be clustered coherent in network; repurposed methotrexate, drug autoimmune disease, possible prevent formation inhibit development AAA, common serious without drugs clinics.

The sex chromosomes play central roles in determining the of almost all multicellular organisms. It is well known that meiosis mammalian spermatogenesis produces ~50% Y- and X-chromosome-bearing sperm, a 1:1 ratio. Here we first reveal X-chromosome-encoded miRNAs show lower expression levels left testis than right healthy mice using bioinformatics modeling miRNA-sequencing data, suggesting Y:X ratio could be unbalanced between testis. We further significantly elevated but balanced flow...