starbase.sysu.edu.cn

starBase v2.0: decoding Interaction Networks of lncRNAs, miRNAs, ceRNAs, RNA-Binding Proteins and mRNAs from large-scale tumor samples and CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data

Portal, Visualize, Analyze, Discover. Is designed for decoding Pan-Cancer. Of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH). Data and tumor samples (14 cancer types, 6000 samples). Is also developed for deciphering Protein-RNA. Web tools to predict the function. Of ncRNAs (miRNAs, lncRNAs, pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA) regulatory networks. CLIP-Seq data from 37.

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starBase v2.0: decoding Interaction Networks of lncRNAs, miRNAs, ceRNAs, RNA-Binding Proteins and mRNAs from large-scale tumor samples and CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data | starbase.sysu.edu.cn Reviews

<META> DESCRIPTION

Portal, Visualize, Analyze, Discover. Is designed for decoding Pan-Cancer. Of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH). Data and tumor samples (14 cancer types, 6000 samples). Is also developed for deciphering Protein-RNA. Web tools to predict the function. Of ncRNAs (miRNAs, lncRNAs, pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA) regulatory networks. CLIP-Seq data from 37.

<META> KEYWORDS

1 starBase v2.0

2 Pan-Cancer

3 tumor

4 cancer

5 microRNA

6 lncRNA

7 lincRNA

8 circRNA

9 circular RNA (circRNA)

10 pseudogene

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clip seq pan cancer,mirna lncrna,mirna lncrna interactions,mirna circrna interactions,mirna pseudogene interactions,mirna sncrna interactions,mirna mrna,mirna target intersections,mirna mrna interactions,cerna network,pan cancer,protein rna,mirfunction

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starBase v2.0: decoding Interaction Networks of lncRNAs, miRNAs, ceRNAs, RNA-Binding Proteins and mRNAs from large-scale tumor samples and CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data | starbase.sysu.edu.cn Reviews

https://starbase.sysu.edu.cn

Portal, Visualize, Analyze, Discover. Is designed for decoding Pan-Cancer. Of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH). Data and tumor samples (14 cancer types, 6000 samples). Is also developed for deciphering Protein-RNA. Web tools to predict the function. Of ncRNAs (miRNAs, lncRNAs, pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA) regulatory networks. CLIP-Seq data from 37.

INTERNAL PAGES

starbase.sysu.edu.cn

1

MiRNA-Target Base, Pan-Cancer miRNA-target interaction maps: for searching the intersections among targets predicted by five predicted softwares(TargetScan, PicTar, PITA, miRanda and RNA22)

http://starbase.sysu.edu.cn/targetSite.php

Portal, Visualize, Analyze, Discover. Intersections from different prediction programs. Number of supporting Experiments =. Very high stringency( =5). Number of Cancer Types(Pan-Cancer). Intersections by selecting two or more programs. Gene Symbol: (e.g. "E2F1"). Intersections from different prediction programs. You can search for intersections among targets predicted by five predicted softwares(TargetScan, PicTar, PITA, miRanda/mirSVR and RNA22). Number of supporting Experiments. At least one cancer type.

2

Pan-Cancer miRNA Function, predicted miRNA functions based on Pathways, starBase: decoding miRNA-target, miRNA-ceRNA and protein-RNA interaction maps

http://starbase.sysu.edu.cn/miRFunction.php

Portal, Visualize, Analyze, Discover. Select one or multiple microRNAs( Required). Number of supporting Experiments =. Very high stringency( =5). Number of Cancer Types(Pan-Cancer). Targets predicted by programs =. You can browse enriched 13 functional terms(include: GO, KEGG, BIOCARTA, etc.). Enrichment analysis for the 13 functional terms (including: GO, KEGG, BIOCARTA, etc.) for miRNA targets was conducted using a hypergeometric test and Bonferroni/FDR correction. You can also select a microRNA gene.

3

starBase Download Center.download PAR-CLIP, HITS-CLIP, CLIP-Seq, CLASH, iCLIP data, for decoding miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-circRNA, ceRNA regulatory networks and protein-RNA interaction maps

http://starbase.sysu.edu.cn/download.php

Portal, Visualize, Analyze, Discover. Download starBase v2.0 Tutorial. If you make use of the data and web-server presented here,. Please cite our starBase paper. Li et al. Nucleic Acids Res. 2014. Yang et al. Nucleic Acids Res. 2011). In addition to the primary data sources. Analysis results from starBase can be downloaded at each web page use. CLIP-Seq Data generated by starBase v2.0. Or publications for Human(hg19), Mouse(mm9) and C.elegans(ce6). Can be downloaded as follows:. 4-thiouridine, RNase T1.

4

miRNA-mRNA Base, Pan-Cancer miRNA-mRNA interactions: for searching targets predicted by five predicted softwares(TargetScan, PicTar, PITA, miRanda and RNA22)

http://starbase.sysu.edu.cn/mirMrna.php

Portal, Visualize, Analyze, Discover. Number of supporting Experiments =. Very high stringency( =5). Number of Cancer Types(Pan-Cancer). Gene Symbol: (e.g. "E2F1"). Browse the predicted miRNA-target interactions processed from five miRNA prediction software programs (TargetScan, PicTar, PITA, miRanda and RNA22). By entering the gene name or selecting a miRNA name. Here, we list predicted miRNA-target interactions overlapped with CLIP-Seq data. You can input the gene name. You can select a microRNA gene.

5

LncRNABase, Pan-Cancer miRNA-lncRNA interactions: decoding Pan-Cancer miRNA-lncRNA interaction maps from large-scale tumor samples and CLIP-Seq data.

http://starbase.sysu.edu.cn/mirLncRNA.php

Portal, Visualize, Analyze, Discover. Number of supporting Experiments =. Very high stringency( =5). Number of Cancer Types(Pan-Cancer). LncRNA Gene Symbol: (e.g. "HOTAIR"). LncRNABase: miRNA-lncRNA interaction Descriptions. View the predicted miRNA-lncRNA interactions by scanning lncRNA sequences overlapping with CLIP-Seq peaks for potential microRNA targets (miRanda/mirSVR) and then output the detailed information. Here, we list predicted miRNA-target interactions overlapped with CLIP-Seq data.

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aura.science.unitn.it

AURA - Atlas of UTR Regulatory Activity

http://aura.science.unitn.it/cite

How to cite AURA. Please cite AURA in your publications as follows:. Dassi E, Re A, Leo S, Tebaldi T, Pasini L, Peroni D and Quattrone A. (2014). AURA 2: Empowering discovery of post-transcriptional networks. The paper is open access and can be downloaded here. AREsite: a database for the comprehensive investigation of AU-rich elements. A compendium of RNA-binding motifs for decoding gene regulation. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

ajay-microrna.blogspot.com

microRNA: May 2011

http://ajay-microrna.blogspot.com/2011_05_01_archive.html

Tuesday, 17 May 2011. Quantitative Stem-Loop RT-PCR for Detection of MicroRNAs. Methods Mol Biol. Real-time quantification of microRNAs by stem-loop RT-PCR. 2005 Nov 27;33(20):e179. Tuesday, 10 May 2011. Artificial microRNA (amiRNA) technology is a novel tool in reverse genetic research for discovering or validating gene functions in plants. A convenient cloning strategy has been developed to construct plant amiRNA vectors based on lacO. AmiRNA vectors – Blue–white screening – lac. Saturday, 7 May 2011.

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starBase v2.0: decoding Interaction Networks of lncRNAs, miRNAs, ceRNAs, RNA-Binding Proteins and mRNAs from large-scale tumor samples and CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data

Portal, Visualize, Analyze, Discover. Is designed for decoding Pan-Cancer. Of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH). Data and tumor samples (14 cancer types, 6000 samples). Is also developed for deciphering Protein-RNA. Web tools to predict the function. Of ncRNAs (miRNAs, lncRNAs, pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA) regulatory networks. CLIP-Seq data from 37.

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