Cross-talk between competitive endogenous RNAs (ceRNAs) through shared miRNAs represents a novel layer of gene regulation that plays important roles in the physiology and development cancers. However, global view their system-level properties across various types cancers is still unknown. Here, we constructed mRNA related ceRNA–ceRNA interaction landscape 20 cancer by systematically analyzing molecular profiles 5203 tumors miRNA regulations. Our study highlights conserved features pan-cancer...

Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional remain a fundamental challenge for cancer biology. We show are widely mediated by long noncoding RNAs (lncRNAs) via integration genome-wide regulation with paired lncRNA gene expression profiles. Systematic construction an LncRNA Modulator Atlas in Pan-cancer (LncMAP) reveals distinct types molecules, which expressed multiple tissues,...

Epigenetic alterations, a well-recognized cancer hallmark, are driven by chromatin regulators (CRs). However, little is known about the extent of CR deregulation in cancer, and less their common specialized roles across various cancers. Here, we performed genome-wide analyses constructed molecular signatures network profiles functional CRs over 10 000 tumors 33 types. By integration DNA mutation, methylation, transcriptional/post-transcriptional regulation, protein interaction networks with...

Characterizing the dynamics of specific RNA levels requires real-time profiling in a single cell. We show that combination synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure real time activity any promoter prokaryotes. Using simple inducible gene expression system, we found induced within bacterium Escherichia coli exhibited pulsating profile response steady input inducer. The deletion an efflux pump key determinant antibiotic...

Abstract Background Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and play fundamental roles in various types cancer. Current developments transcriptome analyses unveiled the existence lncRNAs; however, their functional characterization remains a challenge. Methods A bioinformatics screen was performed by integration multiple omics data hepatocellular carcinoma (HCC) prioritizing novel oncogenic lncRNA, LINC01132. Expression LINC01132 HCC control...

Transfer RNAs (tRNAs) are central to protein synthesis and impact translational speed fidelity by their abundance. Here we examine the extent which viruses manipulate tRNA populations favor translation of own genes. We study two very different viruses: influenza A virus (IAV), a medium-sized (13 kB genome) RNA virus; vaccinia (VV), large (200 DNA virus. show that total cellular population remains unchanged following viral infection, whereas polysome-associated changes dramatically in...

RNA-binding proteins (RBPs) are key players of gene expression and perturbations RBP-RNA regulatory network have been observed in various cancer types. Here, we propose a computational method, RBPreg, to identify the RBP regulators by integration single cell RNA-Seq (N = 233,591) binding data. Pan-cancer analyses suggest that exhibit specificity involved hallmark-related functions. We prioritize an oncogenic RBP-HNRNPK, which is highly expressed tumors associated with poor prognosis...

// Yongsheng Li 1,* , Hong Chen Tao Pan Chunjie Jiang 1 Zheng Zhao Zishan Wang Jinwen Zhang Juan Xu and Xia College of Bioinformatics Science Technology Bio-Pharmaceutical Key Laboratory Heilongjiang Province, Harbin Medical University, Nangang, Harbin, Heilongjiang, China * These authors should be regarded as joint First Authors Correspondence to: Li, email: Xu, Keywords : long non-coding RNA, chromatin pattern, lncRNA ontology, functions, integrated model Received July 06, 2015 Accepted...

This study aimed to determine the healing effect of hydrogen-rich water (HRW) on radiotherapy-induced skin injury. Rats were irradiated with a 6 MeV electron beam from Varian linear accelerator. After wound formation, rats individually administrated distilled water, HRW (1.0 ppm) or (2.0 ppm). We measured time and observed rate wounded surface. irradiation, malondialdehyde (MDA) content superoxide dismutase (SOD) activity in tissues evaluated, as determined using an MDA SOD assay kit....

Alternative splicing (AS) plays an important role in gene regulation, and AS perturbations are frequently observed cancer. RNA binding protein (RBP) is one of the molecular determinants AS, RBP-gene network activity causally associated with cancer development. Here, we performed a systematic analysis to characterize events across 18 types. We showed that alterations were prevalent involved cancer-related pathways. Given extent perturbation was disease severity, proposed computational...

Immune system gene regulation perturbation has been found to be a major cause of the development various types cancer. Numbers mechanisms contribute expression regulation, thus, systematically identification potential regulons immune-related pathways is critical cancer immunotherapy. Here, we comprehensively chart landscape transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs in 17 across 33 cancers. The immunology are likely exhibit higher expressions immune cells,...

Dengue infection is one of the most prevalent arthropod-borne viral diseases, which can result in severe complications. Identification genes and long non-coding RNAs (lncRNAs) involved dengue would help deciphering potential mechanisms responsible for disease progression. We comprehensively analyzed dynamic transcriptome during progression identified critical lncRNAs with expression perturbations. Our findings revealed that (i.e., CCR10 GNG7) CTBP1-AS MAFG-AS1) were potentially regulated by...

The protein-protein interactions (PPIs) between human and viruses play important roles in viral infection host immune responses. Rapid accumulation of experimentally validated human-virus PPIs provides an unprecedented opportunity to investigate the regulatory pattern infection. However, we are still lack knowledge about patterns interactions. We collected 27,293 PPIs, covering 8 virus families, 140 proteins 6059 proteins. Functional enrichment analysis revealed that interacting were likely...

Transient-receptor potential (TRP) channels comprise a diverse family of ion channels, which play important roles in regulation intracellular calcium. Emerging evidence has revealed the critical TRP tumor development and progression. However, we still lack knowledge about genetic pharmacogenomics landscape genes across cancer types. Here, comprehensively characterized transcriptome alterations >10,000 patients 33 We prevalent somatic mutations copy number variation genes. In particular,...

Semaphorins have been found to play important roles in multiple malignancy-related processes. However, the role of Semaphorin 4B (SEMA4B) lung cancer remains unclear. Here, we aimed explore biological functions SEMA4B through bioinformatic analysis, vitro and vivo assays. In present study, possible mechanism by which affected tumor growth microenvironment adenocarcinoma (LUAD) were investigated.The expression LUAD was analyzed analysis verified immunohistochemistry staining. The prognostic...

RNA methylation plays a vital role in the pathogenesis of variety diseases including cancer, and aberrant levels modified nucleosides were revealed to be related cancer. Urine is favored source for biomarker discovery due non-invasion patients. Herein, we developed sensitive hydrophilic interaction liquid chromatography tandem mass spectrometry (HILIC-MS/MS) method combined with stable isotope dilution accurate quantification methylated human urine. With this method, successfully quantified...

Large-scale cancer genome sequencing has enabled the catalogs of somatic mutations; however, mutational impact on intrinsically disordered protein regions (IDRs) not been systematically investigated to date. Here, we comprehensively characterized landscapes IDRs and found that have higher mutation frequencies across diverse cancers. We thus developed a computational method, ROI-Driver, identify putative driver genes enriching IDR domain hotspots in cancer. Numerous well-known cancer-related...

Thalassemia is a genetic blood disorder characterized by decreased hemoglobin production. Severe anemia can damage organs and severe threat to life safety. Allogeneic transplantation of bone marrow-derived hematopoietic stem cell (HSCs) at present represents promising therapeutic approach for thalassemia. However, immune rejection lack HLA-matched donors limited its clinical application. In recent years, human-induced pluripotent cells (hiPSCs) technology offers prospects autologous...

Background: The heterogeneity and dynamic changes of endometrial cells have a significant impact on health as they determine the normal function endometrium during menstrual cycle. Dysfunction can lead to occurrence various gynecological diseases. Therefore, deconvolution immune microenvironment that drives transcriptional programs throughout cycle is key understand regulatory biology endometrium. Methods: Herein, we comprehensively analyzed single-cell transcriptome 59,397 across ten human...

Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors genome transcriptome. Advances in next-generation sequencing have identified thousands genomic transcriptomic aberrations that generate variant peptides assemble hidden proteome, further expanding immunopeptidome. Emerging technologies number computational methods estimated abundance infiltration from bulk transcriptome advanced our understanding microenvironments. Here, we will characterize...

The tripartite motif (TRIM) proteins function as important regulators in innate immunity, tumorigenesis, cell differentiation and ontogenetic development. However, we still lack knowledge about the genetic transcriptome alterations landscape of TRIM across cancer types. We comprehensively reviewed characterized perturbations genes > 10,000 samples 33 Genetic mutations were analyzed by diverse computational methods. A TRIMs score index was calculated based on expression genes. correlation...

Pediatric central nervous system (CNS) tumors are the second most common cancer diagnosis among children. Long noncoding RNAs (lncRNAs) emerge as critical regulators of gene expression, and they play fundamental roles in immune regulation. However, knowledge on epigenetic changes lncRNAs diverse types pediatric CNS is lacking. Here, we integrated DNA methylation profiles 2,257 across 61 subtypes with lncRNA annotations presented epigenetically regulated landscape lncRNAs. We revealed...