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Pan-Cancer lncRNA, RNA-RNA and Protein-RNA networks from TCGA 14 cancer types

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  • Pan-Cancer lncRNA, RNA-RNA and Protein-RNA networks from TCGA 14 cancer types

    We're pleased to announce the release of the Pan-Cancer Analysis Platform on the starBase by mining expression profiles(RNA-Seq, miRNA-Seq) of lncRNAs, miRNAs, and mRNAs across 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal(all data available without limitations).

    We hope this platform will greatly help biologists to explore the impact of lncRNA, miRNA, mRNA, RNA-Binding Protein (RBP) genes and their regulatory networks (ceRNA, co-expression etc.) on human cancers and other diseases.

    We are looking forward to hearing your feedback!

    Overview:


    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)
    Last edited by yjhua2110; 07-25-2014, 05:22 AM.

  • #2
    How to identify lncRNA genes from TCGA level 3 dataset.


    As I know, TCGA dose not provide lncRNA annotation on level 3 dataset. How many lncRNA records have you identified? Thank you~

    Comment


    • #3
      Originally posted by xiaomagege View Post

      As I know, TCGA dose not provide lncRNA annotation on level 3 dataset. How many lncRNA records have you identified? Thank you~
      Yes, you are right. starBase just only identified a little of lncRNAs from TCGA level 3 datasets. TCGA level 3 data almost all are protein-coding genes.
      Last edited by rnaNGS; 03-19-2014, 11:10 PM.

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      • #4
        Originally posted by rnaNGS View Post
        Yes, you are right. We just only identified a little of lncRNAs (filtered by CPC software and other softwares) from TCGA level 3 datasets. TCGA level 3 data almost all are protein-coding genes.
        Would please provide the pipline how these lncRNA are identified , and which file are needed from the TCGA level3 dataset. Thanks~

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        • #5
          How can I download Pan-Cancer data (14 cancer types) of miRNA-lncRNA, protein-lncRNA, competing endogenous RNA (ceRNA) pairs from your website.

          Comment


          • #6
            Originally posted by zhxq09 View Post
            How can I download Pan-Cancer data (14 cancer types) of miRNA-lncRNA, protein-lncRNA, competing endogenous RNA (ceRNA) pairs from your website.
            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.

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            • #7
              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?

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              • #8
                Originally posted by zhxq09 View Post
                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?
                Yes. it is peak height. the values were identified from PARalyzer software.

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                • #9
                  How can i find the lncRNAs with chromosome locations but not gene names in starBase?

                  Comment


                  • #10
                    Originally posted by zhxq09 View Post
                    How can i find the lncRNAs with chromosome locations but not gene names in starBase?
                    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.

                    Comment


                    • #11
                      regarding circRNABase in Starbase I'd like to know:
                      a) in search page, which input in the field circRNA Symbol has to be inserted?
                      b) 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?

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                      • #12
                        I would also like to ask how does the circRNA-miRNA target prediction program you are offering in starbase works.
                        Last edited by zhxq09; 07-27-2014, 06:02 PM.

                        Comment


                        • #13
                          Originally posted by zhxq09 View Post
                          regarding circRNABase in Starbase I'd like to know:
                          a) in search page, which input in the field circRNA Symbol has to be inserted?
                          b) 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?
                          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 circBase (http://circbase.org/cgi-bin/downloads.cgi). This means that the circRNA is originated from the gene in circBase.

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                          • #14
                            a new paper, by analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBP–lncRNA regulatory relationships.

                            RBP–lncRNA interactions were available at http://starbase.sysu.edu.cn/rbpLncRNA.php.

                            an invited paper described these protein–lncRNA interactions has been published in Frontiers journal.

                            The genome-wide binding map of Ezh2 in mouse.
                            Last edited by rnaNGS; 05-18-2015, 03:54 AM.

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