Tool:Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data

Question

[lsp03yjh]

We had released starBase v3.0 Pan-Cancer Analysis and Networks Platform to decipher Pan-Cancer Interaction Networks of lncRNAs, miRNAs, circRNAs, competing endogenous RNAs (ceRNAs) and RNA-binding proteins (RBPs) by mining clinical and expression profiles of TCGA 32 cancer types (~10,000 RNA-seq and ~9,900 miRNA-seq samples) and hundreds of CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH), degradome-seq, RNA-RNA interactome datasets on the starBase platform (http://starbase.sysu.edu.cn/).

Pan-Cancer Analysis website: http://starbase.sysu.edu.cn/panCancer.php

starBase platform provides the following Pan-Cancer and Interaction Analysis Services:

1. starBase generated Pan-Cancer networks of CLIP-Se q experimentally supported miRNA-lncRNA and miRNA-mRNA interactions.
2. starBase identified Pan-Cancer ceRNA networks involving lncRNAs and mRNAs.
3. starBase firstly provided Pan-Cancer maps of interactions between RNA-binding proteins (RBPs) and RNAs(lncRNAs, mRNAs).
4. starBase provided Pan-Cancer Differential Expression of lncRNAs, mRNAs, ncRNAs.
5. starBase provided Pan-Cancer Survival Analysis of of lncRNAs, mRNAs, ncRNAs.
6. starBase provided Pan-Cancer Target CoExpression of lncRNAs, mRNAs, ncRNAs.
7. starBase provided Pan-Cancer miRNA Differential Expression.
8. starBase provided Pan-Cancer miRNA Survival Analysis.
9. starBase provided Pan-Cancer miRNA-Target CoExpression.

starBase v3.0 Pan-Cancer Analysis:

starBase paper is available at (1) http://nar.oxfordjournals.org/content/42/D1/D92.full and (2) http://nar.oxfordjournals.org/content/39/suppl_1/D202.full

[zhangjunpeng_411]

In the miRNA-lncRNA interactions of starBase, you mean that miRNA regulate lncRNA? In starBase, if we can obtain lncRNA-miRNA interactions, lncRNA-mRNA interactions, lncRNA-TF, and TF-lncRNA? Thanks in advance.

[Istvan Albert]

Don't ask questions in the answer section of the post, create a new question

[zhangjunpeng_411]

In the miRNA-lncRNA interactions of starBase, you mean that miRNA regulate lncRNA? In starBase, if we can obtain lncRNA-miRNA interactions, lncRNA-mRNA interactions, lncRNA-TF, and TF-lncRNA? Thanks in advance.

[lsp03yjh]

Yes, miRNAs regulate lncRNAs. In starBase, you can obtain miRNA-lncRNA, miRNA-mRNA, miRNA-pseudogene, and RBP(RNA-Binding protein)-lncRNA interactions. In our ChIPBase, you can find the TF-lncRNA interaction.

Answer 1

[zhxq09]

How can I download Pan-Cancer data (14 cancer types) of miRNA-lncRNA, protein-lncRNA, competing endogenous RNA (ceRNA) pairs from your website.

[lsp03yjh]

Analysis results from starBase can be downloaded at each search web page use export button.

Answer 2

[lsp03yjh]

starBase Pan-Cancer and Interaction Analysis Workflow:

Answer 3

[lsp03yjh]

An invited paper described protein-lncRNA interactions has been published in Frontiers journal.

We released starBase RBP-lncRNA Platform to decode interaction between lncRNAs and RNA-binding proteins (RBPs) by mining 111 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) datasets.

Distinct features as follows:

1. We provide interactive web-page to display the 22,735 RBP-lncRNA regulatory relationships identified from 117 CLIP-Seq datasets generated by 50 independent studies.
2. We discovered hundreds of disease-related single nucleotide polymorphisms (SNP) resided in the RBP binding sites of lncRNAs.
3. We also revealed the expression correlation of RBP-lncRNA interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types.
4. We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulate gene expression.

Answer 4

[zhxq09]

in starBase, what methods were used to identify CLIP-Seq peaks?

[lsp03yjh]

we identified PAR-CLIP peaks using PARalyzer software. You can see details from our starBase v2.0 paper (Li et al. Nucleic Acids Res. 2014;42:D92-7).

Answer 5

[zhxq09]

in starBase download page, what a numerical value (displayed in the score column of bed files) means? Is it CLIP-Seq peak height? It can be further used to filter Protein-RNA interactions???

[lsp03yjh]

Yes. it is peak height. the values were identified from PARalyzer software.

[Giovanni M Dall'Olio]

Hi, can you please add your answers to specific questions as comments, instead of new answers? Otherwise it is difficult to follow the conversation.

[lsp03yjh]

Ok.Thank you for your reminding.

Answer 6

[zhxq09]

How can i find the lncRNAs with chromosome locations but not gene names in starBase?

[lsp03yjh]

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.

Answer 7

[zhxq09]

what is mean for bioComplex and clipReadNum in starBase?

[lsp03yjh]

bioComplex means Number of supporting Experiments, clipReadNum means the read number of CLIP-Seq。

Answer 8

[zhxq09]

I am trying to using starBase in order to look for miR-lncRNA interactions.

Is the lncRNAs list that are available on site is complete?

[Istvan Albert]

please use comments (like this one) to respond to a post, individual answers may be ranked differently

Answer 9

[yangyy9999]

regarding circRNABase in Starbase I'd like to know:

1. in search page, which input in the field circRNA Symbol has to be inserted?
2. When I select a specific miRNA(hsa-let-7a-5p) the output target is RRP1B_hsa_circ_001854, what does the name before the circRNA name (e.g. RRP1B) mean?

Answer 10

[lsp03yjh]

We released starBase miRNA-circRNA Platform to decode interaction between circRNAs and microRNA by mining AGO CLIP-seq datasets. miRNA-circRNA Interaction web site: http://starbase.sysu.edu.cn/mirCircRNA.php