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starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data rnaNGS RNA Sequencing 7 02-14-2013 08:38 PM
Discovery of miRNA Regulatory Networks by Integrating High-Throughput Data rnaNGS Literature Watch 0 02-14-2013 08:12 PM
starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data yjhua2110 Bioinformatics 8 09-27-2011 08:45 AM
starBase: explore microRNA–mRNA interaction maps from CLIP-Seq and Degradome-Seq data yjhua2110 Literature Watch 1 02-02-2011 08:50 AM

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Old 09-18-2013, 03:55 AM   #1
yjhua2110
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Default deciphering ceRNA regulatory networks from CLIP-seq data in starBase

Competing endogenous RNAs(ceRNAs) hypothesis: ceRNAs regulate other RNA transcripts (e.g., PTEN) by competing for shared microRNAs. They are playing important roles in pathological conditions, such as cancer. (Salmena et al. 2011 Cell)

We identified ~200,000 (P<0.05) and ~10,000 (FDR<0.05) ceRNA pairs from CLIP-supported miRNA target sites . We developed ceRNAFunction tool to predict the functions of lncRNAs and protein-coding genes from ceRNA regulatory networks.

We are looking forward to hearing your feedback and hope you enjoy it.

Last edited by yjhua2110; 12-12-2013 at 07:52 AM.
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Old 12-04-2013, 06:16 PM   #2
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Default HMGA2 functions as a ceRNA to promote lung cancer progression

A Nature paper has described ceRNA interactions between HMGA2 and TGFBR3. They show that Hmga2 promotes lung cancer progression in mouse and human cells by operating as a competing endogenous RNA (ceRNA) for the let-7 microRNA (miRNA) family.

reference: HMGA2 functions as a competing endogenous RNA to promote lung cancer progression (Nature, 2013 Dec 5)
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Old 12-08-2013, 10:58 PM   #3
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Quote:
Originally Posted by rnaNGS View Post
A Nature paper has described ceRNA interactions between HMGA2 and TGFBR3. They show that Hmga2 promotes lung cancer progression in mouse and human cells by operating as a competing endogenous RNA (ceRNA) for the let-7 microRNA (miRNA) family.

reference: HMGA2 functions as a competing endogenous RNA to promote lung cancer progression (Nature, 2013 Dec 5)
ceRNABase captured the above-mentioned HMGA2-TGFBR3 ceRNA pair.

Last edited by yjhua2110; 12-12-2013 at 07:54 AM.
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Old 12-12-2013, 07:51 AM   #4
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ceRNABase also recaptured PTEN-TNRC6A, PTEN-TNRC6B, PTEN-ZEB2, PTEN-NRAS, PTEN-CNOT6L, PTEN-CCDC6, PTEN-LRCH1, PTEN-JARID2, PTEN-SERINC1, PTEN-KLF6, PTEN-MBNL1 etc. ceRNA pairs that reported by three Cell papers(Tay et al. Cell. 2011;147:344-57., Karreth et al. Cell. 2011;147:382-95., Sumazin et al. Cell. 2011;147:370-81.).
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Old 01-20-2014, 12:00 AM   #5
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Default The multilayered complexity of ceRNA crosstalk and competition

A review paper about ceRNAs and their functions has been published in Nature Journal.

Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16;505(7483):344-52.

Abstract
Recent reports have described an intricate interplay among diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs. These RNA transcripts act as competing endogenous RNAs (ceRNAs) or natural microRNA sponges - they communicate with and co-regulate each other by competing for binding to shared microRNAs, a family of small non-coding RNAs that are important post-transcriptional regulators of gene expression. Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
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Old 02-17-2014, 08:36 PM   #6
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starBase have constructed pan-cancer ceRNA networks from tumor miRNA and mRNA expression profiles (TCGA 14 cancer types with >6000 tumor and normal samples).

For example: known PTEN-ZEB2 ceRNA interactions can be supported in 13 cancer types.

Last edited by yjhua2110; 03-03-2014 at 02:36 AM.
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Old 03-03-2014, 02:38 AM   #7
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Default pan-cancer ceRNA networks

starBase also provides scatter and boxplot charts and statistic test to display ceRNA interactions.

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