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Forum: RNA Sequencing 05-26-2018, 09:18 PM
Replies: 1
Views: 2,229
Posted By yjhua2110
A review paper that related with the functions of...

A review paper that related with the functions of RNA-binding proteins in cancers has been published in Trends in Molecular Medicine....
Forum: Epigenetics 04-16-2018, 04:39 PM
Replies: 6
Views: 24,034
Posted By yjhua2110
You can try Ensembl Plants database:...

You can try Ensembl Plants database: https://plants.ensembl.org/index.html
Forum: RNA Sequencing 01-25-2018, 07:18 AM
Replies: 1
Views: 2,229
Posted By yjhua2110
Pan-Cancer Patterns of RNA-Binding Proteins in ~7000 tumor RNA-seq samples

RNA-binding proteins (RBPs) regulate the expression of thousands of transcripts, and some are reported to be involved in human tumorigenesis.

We conducted comprehensive analyses for expression,...
Forum: RNA Sequencing 09-05-2017, 04:17 PM
Replies: 6
Views: 4,823
Posted By yjhua2110
RMBase v2.0 (http://rna.sysu.edu.cn/rmbase/) has...

RMBase v2.0 (http://rna.sysu.edu.cn/rmbase/) has been developed, RMBase v2.0 is freely available at http://rna.sysu.edu.cn/rmbase/
Forum: Bioinformatics 02-07-2017, 07:38 PM
Replies: 0
Views: 973
Posted By yjhua2110
oncoNcRNA: Exploring the ncRNAs with Oncogenic Potentials in Human Cancers

We had released oncoNcRNA (http://rna.sysu.edu.cn/onconcrna/), a web portal for explore the ncRNAs (lncRNAs, miRNAs, piRNAs, snoRNAs, tRNAs) with oncogenic potentials in 64 human cancer types (>20000...
Forum: Bioinformatics 12-11-2016, 05:11 PM
Replies: 5
Views: 3,238
Posted By yjhua2110
RNA modifications in sex determination and nervous system

two papers published in nature journal discovered RNA modifications modulate neuronal functions and sex determination in Drosophila.
(1) Lence T et al. m(6)A modulates neuronal functions and sex...
Forum: Bioinformatics 11-11-2016, 05:08 PM
Replies: 0
Views: 1,747
Posted By yjhua2110
Transcription Factor Binding Sites, Motifs and Profiles from ChIP-seq data

ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) is designed for studying transcription factor binding sites and motifs, and decoding transcriptional regulatory networks of non-coding RNAs (lncRNAs,...
Forum: Epigenetics 10-15-2016, 05:51 PM
Replies: 6
Views: 24,034
Posted By yjhua2110
ChIPBase (http://rna.sysu.edu.cn/chipbase/)...

ChIPBase (http://rna.sysu.edu.cn/chipbase/) (http://rna.sysu.edu.cn/chipbase/) has been updated to discover transcription factor binding motifs, profiles and targets (lncRNAs, miRNAs, proteins,...
Forum: Epigenetics 10-10-2016, 05:36 PM
Replies: 0
Views: 1,593
Posted By yjhua2110
Transcription factor binding profiles/motifs and targets (lncRNAs, proteins, miRNAs)

ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) (http://rna.sysu.edu.cn/chipbase/) has been developed to explore the regulatory networks between transcription factors and genes (proteins, lncRNAs,...
Forum: RNA Sequencing 07-14-2016, 01:34 AM
Replies: 6
Views: 4,823
Posted By yjhua2110
relationships between RNA-Binding Proteins and RNA modificaitons

millions of relationships between RNA-Binding Protein (RBP) binding regions and RNA modifications have been added into RMBase (http://rna.sysu.edu.cn/rmbase/index.php). We revealed that RNA...
Forum: RNA Sequencing 07-09-2016, 06:24 AM
Replies: 0
Views: 800
Posted By yjhua2110
RNA-seq reveals clinical phenotypes and driver potentials of lncRNAs from TCGA data

1. A comprehensive analyses for the expression profile, clinical outcomes, somatic copy number alterations (SCNAs) profile of long non-coding genes(lncRNAs) in ~7000 clinical RNA-Seq data/samples...
Forum: Bioinformatics 04-21-2016, 07:32 PM
Replies: 5
Views: 3,238
Posted By yjhua2110
recently, one Nature paper and one Nature...

recently, one Nature paper and one Nature Chemical biology paper have identified dynamic N1-methyladenosine (m1A) methylome in the message RNAs (mRNAs) using newly developed sequencing approaches....
Forum: RNA Sequencing 02-29-2016, 04:18 PM
Replies: 6
Views: 4,823
Posted By yjhua2110
recently, one Nature paper and one Nature...

recently, one Nature paper and one Nature Chemical biology paper have identified dynamic N1-methyladenosine (m1A) methylome in the message RNAs (mRNAs) using newly developed sequencing approaches. ...
Forum: RNA Sequencing 01-26-2016, 05:40 PM
Replies: 0
Views: 1,357
Posted By yjhua2110
human snoRNA atlas from small RNA sequencing data using snoSeeker

Dear All,

We identified 857 novel snoRNAs, as well as 1032 known snoRNAs from 370 million sequence reads generated by 237 small RNA sequencing data (ENCODE and GEO) using snoSeeker...
Forum: RNA Sequencing 10-16-2015, 07:43 PM
Replies: 6
Views: 4,823
Posted By yjhua2110
Decoding the landscape of RNA modifications from transcriptome sequencing data

RMBase (http://rna.sysu.edu.cn/rmbase/index.php) (RNA Modification Base) is a RNA modification database and designed for decoding the landscape of RNA modifications (>100 different RNA modification...
Forum: RNA Sequencing 06-04-2015, 12:12 AM
Replies: 9
Views: 4,127
Posted By yjhua2110
Revealing protein–lncRNA interaction

A review paper described the protein-lncRNA interaction was published in Brief Bioinform (June 2, 2015, doi: 10.1093/bib/bbv031).

Abstract:
Long non-coding RNAs (lncRNAs) are associated to a...
Forum: RNA Sequencing 05-21-2015, 05:30 PM
Replies: 0
Views: 1,134
Posted By yjhua2110
StarScan: scanning small RNA targets in lncRNA, circRNA, mRNA and pseudo genes

StarScan (http://mirlab.sysu.edu.cn/starscan/) (sRNA target Scan) is the first web-based software for discovering potential sRNA-mediated RNA cleavage events from degradome sequencing data in plants...
Forum: RNA Sequencing 01-14-2015, 06:18 PM
Replies: 0
Views: 1,275
Posted By yjhua2110
Discovery of protein–lncRNA interactions from large-scale CLIP-Seq and RNA-Seq data

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...
Forum: Bioinformatics 07-27-2014, 06:08 PM
Replies: 13
Views: 5,317
Posted By yjhua2110
You can input circRNA Id and their gene symbol...

You can input circRNA Id and their gene symbol from circbase.
We did not displayed circRNAs without miRNA target sites supported by CLIP-Seq.
RRP1B is the gene symbol that were fetched from...
Forum: Bioinformatics 07-18-2014, 12:52 AM
Replies: 13
Views: 5,317
Posted By yjhua2110
You can input your chromosome locations in our...

You can input your chromosome locations in our deepView genome browser ( http://starbase.sysu.edu.cn/browser.php ), and then determine what lncRNAs (with gene names) are located within these region.
Forum: Bioinformatics 07-06-2014, 08:47 PM
Replies: 13
Views: 5,317
Posted By yjhua2110
Yes. it is peak height. the values were...

Yes. it is peak height. the values were identified from PARalyzer software.
Forum: Bioinformatics 06-04-2014, 07:49 PM
Replies: 13
Views: 5,317
Posted By yjhua2110
Analysis results from starBase can be downloaded...

Analysis results from starBase can be downloaded at each search web page use export button. CLIP-Seq Data generated by starBase v2.0 can be downloaded at download web page.
Forum: RNA Sequencing 05-26-2014, 11:33 PM
Replies: 9
Views: 4,127
Posted By yjhua2110
in starBase, all lncRNAs from GENCODE v17 were...

in starBase, all lncRNAs from GENCODE v17 were included.
Forum: Bioinformatics 03-03-2014, 02:38 AM
Replies: 6
Views: 3,379
Posted By yjhua2110
pan-cancer ceRNA networks

starBase also provides scatter and boxplot charts (http://starbase.sysu.edu.cn/pcCeRNAInfo.php?database=hg19&name=PTEN&cernaName=C16orf72&autoId=361608#expTabs) and statistic test to display ceRNA...
Forum: Bioinformatics 02-17-2014, 08:36 PM
Replies: 6
Views: 3,379
Posted By yjhua2110
starBase have constructed pan-cancer ceRNA...

starBase have constructed pan-cancer ceRNA networks (http://starbase.sysu.edu.cn/mrnaCeRNA.php) from tumor miRNA and mRNA expression profiles (TCGA 14 cancer types with >6000 tumor and normal...
Showing results 1 to 25 of 67

 


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