CLIPZ

Names
More detailed information about this field from each metasource.

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

clipz
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

Other names: clipz

Experimentally-determined binding sites of RNA-binding proteins

Webpage:

http://www.clipz.unibas.ch/

Publications:

Publications
More detailed information about this field from each metasource.

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins
PMID: 21087992
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

http://dx.doi.org/10.1093/nar/gkq940
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins PubMed citations: 77.

77 articles citing: CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression. PMID:34694601
Techniques for Characterizing Cytomegalovirus-Encoded miRNAs. PMID:33555594
Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs. PMID:31919282
Clip for studying protein-RNA interactions that regulate virus replication. PMID:31765715
Argonaute 4 as an Effector Protein in RNA-Directed DNA Methylation in Human Cells. PMID:31333722
Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs. PMID:31098334
MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. PMID:30728462
The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1. PMID:30582518
RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. PMID:30558267
Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. PMID:30527764
A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information. PMID:29858068
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. PMID:29846699
CLIP-related methodologies and their application to retrovirology. PMID:29716635
A Brief Review of RNA-Protein Interaction Database Resources. PMID:29657278
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. PMID:29156006
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. PMID:28605404
TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. PMID:28412966
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. PMID:28077065
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:28053162
High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. PMID:28031372
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner. PMID:28003477
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. PMID:27765618
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. PMID:27506469
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. PMID:27382025
Tiny giants of gene regulation: experimental strategies for microRNA functional studies. PMID:26950183
Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. PMID:26744779
PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. PMID:26463383
HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages. PMID:26226348
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. PMID:26201343
Revealing protein-lncRNA interaction. PMID:26041786
Design and bioinformatics analysis of genome-wide CLIP experiments. PMID:25958398
CLIPdb: a CLIP-seq database for protein-RNA interactions. PMID:25652745
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data. PMID:25638391
miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. PMID:25531890
Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. PMID:25515586
High-throughput characterization of protein-RNA interactions. PMID:25504152
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. PMID:25416803
Computational Methods for CLIP-seq Data Processing. PMID:25336930
Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. PMID:25301781
Computational Methods for MicroRNA Target Prediction. PMID:25153283
HITS-CLIP and PAR-CLIP advance viral miRNA targetome analysis. PMID:24940765
RBPmap: a web server for mapping binding sites of RNA-binding proteins. PMID:24829458
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
A model-based approach to identify binding sites in CLIP-Seq data. PMID:24714572
The role of miR-148a in gastric cancer. PMID:24659367
Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP. PMID:24571656
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. PMID:24451213
dCLIP: a computational approach for comparative CLIP-seq analyses. PMID:24398258
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. PMID:24393166
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. PMID:24304892
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. PMID:24297251
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. PMID:24243805
Finding the target sites of RNA-binding proteins. PMID:24217996
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression. PMID:23974436
Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins. PMID:23935075
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. PMID:23832275
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. PMID:23706177
Advances in the techniques for the prediction of microRNA targets. PMID:23591837
Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. PMID:23376935
Pharmaco-miR: linking microRNAs and drug effects. PMID:23376192
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. PMID:23368412
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. PMID:23335364
Toward a genome-wide landscape of translational control. PMID:23209130
Site identification in high-throughput RNA-protein interaction data. PMID:23024010
Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. PMID:22995832
Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PMID:22927820
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. PMID:22844102
microPIR: an integrated database of microRNA target sites within human promoter sequences. PMID:22439011
Protein-RNA interactions: new genomic technologies and perspectives. PMID:22251872
Identification of RNA-protein interaction networks using PAR-CLIP. PMID:22213601
Predicting RNA-protein interactions using only sequence information. PMID:22192482
doRiNA: a database of RNA interactions in post-transcriptional regulation. PMID:22086949
Noncoding RNAs and cancer. PMID:21958754
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. PMID:21572407
Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PMID:21423624
http://dx.doi.org/10.1093/nar/gkq940

Tags:

Tags
More detailed information about this field from each metasource.

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

databases of individual protein families
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

protein binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:00.215359

protein sequence protein family gene transcripts functional, regulatory and non-coding rna protein binding sites transcription factors and regulatory sites gene expression

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