deepBase

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deepBase

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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deepbase

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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Other names: deepbase

Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates.

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Publications

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deepBase: a database for deeply annotating and mining deep sequencing data
PMID: 19966272

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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• deepBase: a database for deeply annotating and mining deep sequencing data PubMed citations: 81.

  81 articles citing: deepBase: a database for deeply annotating and mining deep sequencing data

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  Current Understanding of Exosomal MicroRNAs in Glioma Immune Regulation and Therapeutic Responses. PMID:35095909

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  Computational Methods and Online Resources for Identification of piRNA-Related Molecules. PMID:33886096

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  Advances in the Identification of Circular RNAs and Research Into circRNAs in Human Diseases. PMID:33815488

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  Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development. PMID:33809566

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  Review on circular RNAs and new insights into their roles in cancer. PMID:33598105

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  lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484

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  ZNF139/circZNF139 promotes cell proliferation, migration and invasion via activation of PI3K/AKT pathway in bladder cancer. PMID:32454461

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  GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm. PMID:32433655

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  iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation. PMID:32421715

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  Online Databases and Non-coding RNAs in Cardiovascular Diseases. PMID:32285405

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  The bioinformatics toolbox for circRNA discovery and analysis. PMID:32103237

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  E2F1-directed activation of nc886 mediates drug resistance in cervical cancer cells via regulation of major vault protein. PMID:31966795

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  Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer. PMID:31579577

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  Biogenesis, functions and clinical significance of circRNAs in gastric cancer. PMID:31519189

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  Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders. PMID:31052326

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  Role of flow-sensitive microRNAs and long noncoding RNAs in vascular dysfunction and atherosclerosis. PMID:30300747

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  Computational Characterization of ncRNA Fragments in Various Tissues of the Brassica rapa Plant. PMID:29657288

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  Long non-coding RNA and microRNA-675/let-7a mediates the protective effect of melatonin against early brain injury after subarachnoid hemorrhage via targeting TP53 and neural growth factor. PMID:29367587

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  Repertoire of noncoding RNAs in corpus luteum of early pregnancy in buffalo (Bubalus bubalis). PMID:29062204

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  Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation. PMID:28951743

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  The Function and Therapeutic Potential of Long Non-coding RNAs in Cardiovascular Development and Disease. PMID:28918050

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  Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease. PMID:27872161

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  Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression. PMID:27643433

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  Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. PMID:27590724

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  Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster. PMID:27558137

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  piRNAs and Their Functions in the Brain. PMID:27512315

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  An updated human snoRNAome. PMID:27174936

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  deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. PMID:26590255

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  microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment. PMID:26501795

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  Regulation of p53 expression and apoptosis by vault RNA2-1-5p in cervical cancer cells. PMID:26318295

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  A Novel Type of Non-coding RNA, nc886, Implicated in Tumor Sensing and Suppression. PMID:26175659

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  Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma. PMID:26104160

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  Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization. PMID:25805854

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  LncRBase: an enriched resource for lncRNA information. PMID:25233092

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  piRNAQuest: searching the piRNAome for silencers. PMID:24997126

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  Silencing of LINE-1 retrotransposons contributes to variation in small noncoding RNA expression in human cancer cells. PMID:24980824

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  Next Generation Sequencing of miRNAs - Strategies, Resources and Methods. PMID:24710011

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  Single molecule fluorescence approaches shed light on intracellular RNAs. PMID:24417544

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  miRspring: a compact standalone research tool for analyzing miRNA-seq data. PMID:23775795

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  MicroRNAs and Drug Addiction. PMID:23717324

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  A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. PMID:23368412

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  Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. PMID:23329697

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  miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. PMID:23221645

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  YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. PMID:23203880

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  MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. PMID:23193297

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  ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. PMID:23161675

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  DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. PMID:23064648

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  Non-coding RNAs in Alzheimer's disease. PMID:23054683

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  Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648

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  Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. PMID:22871084

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  The rectal cancer microRNAome--microRNA expression in rectal cancer and matched normal mucosa. PMID:22850566

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  Induction of hepatocellular carcinoma by in vivo gene targeting. PMID:22733778

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  Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data. PMID:22705792

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  The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. PMID:22684254

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  Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation. PMID:22470567

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  Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development. PMID:22457835

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  Bioinformatic Resources of microRNA Sequences, Gene Targets, and Genetic Variation. PMID:22403585

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  Conservation of the relative tRNA composition in healthy and cancerous tissues. PMID:22357911

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  MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review. PMID:22351564

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  Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function. PMID:22319597

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  Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs. PMID:22282338

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  miRNEST database: an integrative approach in microRNA search and annotation. PMID:22135287

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  Gene regulation in Giardia lambia involves a putative microRNA derived from a small nucleolar RNA. PMID:22028939

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  Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes. PMID:21884594

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  The therapeutic potential of microRNAs: disease modulators and drug targets. PMID:21818713

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  Overexpression of the lung cancer-prognostic miR-146b microRNAs has a minimal and negative effect on the malignant phenotype of A549 lung cancer cells. PMID:21789255

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  A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. PMID:21712401

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  Sequencing technologies and genome sequencing. PMID:21698376

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  The characterisation of piRNA-related 19mers in the mouse. PMID:21672259

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  DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. PMID:21622957

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  Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. PMID:21531904

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  Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. PMID:21518807

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  Shielding the messenger (RNA): microRNA-based anticancer therapies. PMID:21514318

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  Databases and resources for human small non-coding RNAs. PMID:21504869

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  Non-coding RNA networks underlying cognitive disorders across the lifespan. PMID:21411369

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  Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. PMID:21295131

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  starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. PMID:21037263

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  Geoseq: a tool for dissecting deep-sequencing datasets. PMID:20939882

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  ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. PMID:20801769

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  Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PMID:20498841

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  mirTools: microRNA profiling and discovery based on high-throughput sequencing. PMID:20478827

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More detailed information about this field from each metasource. ×

functional, regulatory and non-coding rna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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rna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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transcriptomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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mapping

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:47.988817

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functional, regulatory and non-coding rna rna transcriptomics mapping model organisms