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zhxq09's Content

There have been 3 items by zhxq09 (Search limited from 14-April 20)

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#175062 scanning miRNA/piRNA/siRNA targets in lncRNA, circRNA, mRNA and pseudo genes

Posted by zhxq09 on 25 May 2015 - 08:09 PM in siRNA, microRNA and RNAi

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging.
Recently, a novel tool, StarScan (sRNA target Scan) was developed for discovering potential sRNA-mediated RNA cleavage events from degradome sequencing data in plants and animals (20 species). StarScan searches sRNA (miRNA, siRNA, piRNA, etc.) targets in annotated (lncRNAs, circRNAs, pseudogenes, 5' UTR, CDS, 3' UTR and introns) and unannotated genomic regions. StarScan web server performs an ultrafast and exhaustive search for potential sRNA–target interactions in various genomic regions.
Please visit http://mirlab.sysu.edu.cn/starscan/ or read StarScan paper (Nucleic Acids Res. 2015 May 18. doi: 10.1093/nar/gkv524) for details.
By integrating 100 degradome sequencing data from 20 species, StarScan will help researchers further investigate these data and discover novel regulatory modules and rules hidden in these data.


#172634 Discovering protein–lncRNA interactions from large-scale CLIP-Seq and RNA-Seq da

Posted by zhxq09 on 15 January 2015 - 03:30 AM in siRNA, microRNA and RNAi

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown.

protein-lncRNA interaction resources:
RBP-lncRNA Base, that analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBPlncRNA regulatory relationships.

RBP-lncRNA interactions were available at http://starbase.sysu...n/rbpLncRNA.php.

An invited paper described these proteinlncRNA interactions has been published in Frontiers journal.

The genomic context distributions of binding sites for 47 human RBPs.

#170603 Pan-Cancer pattern of lncRNAs, miRNAs and their regulatory networks

Posted by zhxq09 on 04 September 2014 - 04:28 AM in siRNA, microRNA and RNAi

1. in panCancerMine, Cancer types as follows:
Urothelial bladder cancer (BLCA)
Breast cancer (BRCA)
Colon and Rectal adenocarcinoma (CRC)
Glioblastoma multiforme (GBM)
Head and neck squamous cell carcinoma (HNSC)
Chromophobe renal cell carcinoma (KICH)
Clear cell kidney carcinoma (KIRC)
Acute Myeloid Leukemia (LAML)
Lung adenocarcinoma (LUAD)
Lung squamous cell carcinoma (LUSC)
Ovarian serous cystadenocarcinoma (OV)
Cutaneous melanoma (SKCM)
Papillary thyroid carcinoma (THCA)
Uterine corpus endometrial carcinoma (UCEC)

2. in cancerMiner includes above-mentioned 12 cancer types.

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