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#44 The Improved Database Of Chimeric Transcripts and RNA-Seq Data

open
nobody
ChiTaRS (1) Chimera (1) Fusion (1)
2017-01-16
2016-12-30
Alessandro Gorohovski
No

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are highly tissue specific in normal cells. Here we present the improved version of the ChiTaRS database (ChiTaRS-3.1) of about 40,000 chimeric transcripts in humans, mice, fruit flies, zebrafishes, cows, rats, pig and yeast. In the current version we extended the experimental data evidence as well as included a novel type of the sense-antisense chimeric transcripts of the same gene confirmed experimentally by RT-PCR, qPCR, RNA-sequencing and mass-spec peptides. In addition, we collected about 11,700 human cancer breakpoints with the expression levels of chimeric RNAs confirmed by the paired-end RNA-sequencing experiments in different tissues in humans, mice and fruit flies.

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Discussion

  • Nick Juty

    Nick Juty - 2016-12-30

    Hi Alessandro,
    I had a look at this site, but can't find a way to link to individual records. Is there anything more specific than a link to search results for example? Do ChiTaRS have their own identifiers (rather than using taxonomy, ncbi ids, etc) that reference specific information? We don't really link to search results as they may change between versions. Also, do you know what is different from the previous version of the database (2.1)?

    cheers and happy holidays,

    Nick

     

    • Alessandro Gorohovski

      Alessandro Gorohovski - 2016-12-30

      Hi Nick,

      Yes, in spite of your critical spirit, I'm glad your letter,
      because I like your sense of humor.

      2016-12-30 17:04 GMT+03:00 Nick Juty njuty@users.sf.net:

      Hi Alessandro,
      I had a look at this site, but can't find a way to link to individual
      records.

      It happens.

      Is there anything more specific than a link to search results for example?
      Do ChiTaRS have their own identifiers (rather than using taxonomy, ncbi
      ids, etc) that reference specific information?

      Yes, sure. We have own identifiers for inner targets and this data isn't
      meant for the public use.
      I think they have no advantages over well-known IDs such as NCBI Entrez
      Gene ID, Gene UniProtKB AC, etc.
      Alas, we do not aspire to the creation of new beings. It was not our goal.
      For reference specific information each can use the ChimeraID,
      e.g.: ChimeraID = AB795239 as

      http://chitars.md.biu.ac.il/bin/search.pl?searchtype=chimera_id&searchstr=AB795239

      here ChimeraID is \w{1,2}\d{5,6} (the designation of perl regex)

      We don't really link to search results as they may change between
      versions. Also, do you know what is different from the previous version of
      the database (2.1)?

      Yes, of course.
      There are a lot of them.
      Sorry, if you insist, please don't be angry and see:
      http://nar.oxfordjournals.org/content/early/2014/11/20/nar.gku1199.full
      http://nar.oxfordjournals.org/content/early/2016/11/29/nar.gkw1127.full

      cheers and happy holidays,

      Nick

      Thank you for your kind words :)

      I hope you and all your coworkers, family, and friends have a lovely
      holiday season
      filled with joy and meaning. Best wishes for a prosperous new year!

      Kind regards,
      Alessandro

      Status: open
      Labels: ChiTaRS Chimera Fusion
      Created: Fri Dec 30, 2016 11:06 AM UTC by Alessandro Gorohovski
      Last Updated: Fri Dec 30, 2016 11:06 AM UTC
      Owner: nobody

      The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs
      of two or more different genes. By analyzing thousands of chimeric ESTs by
      RNA sequencing, we found that the expression level of chimeric ESTs is
      generally low and they are highly tissue specific in normal cells. Here we
      present the improved version of the ChiTaRS database (ChiTaRS-3.1) of about
      40,000 chimeric transcripts in humans, mice, fruit flies, zebrafishes,
      cows, rats, pig and yeast. In the current version we extended the
      experimental data evidence as well as included a novel type of the
      sense-antisense chimeric transcripts of the same gene confirmed
      experimentally by RT-PCR, qPCR, RNA-sequencing and mass-spec peptides. In
      addition, we collected about 11,700 human cancer breakpoints with the
      expression levels of chimeric RNAs confirmed by the paired-end
      RNA-sequencing experiments in different tissues in humans, mice and fruit
      flies.

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/identifiers-org/new-collection/44/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

       

      Related

      Request new collection: #44

  • Nick Juty

    Nick Juty - 2017-01-16

    Hi Alessandro,

    Thanks for your message!
    I just wanted to clarify - do you wish to create a link using your internal IDs? Or using "well-known IDs such as NCBI Entrez Gene ID, Gene UniProtKB AC, etc". Is there any way to link directly rather than by using a search?

    Thanks in advance,

    regards,

    Nick

     

    • Alessandro Gorohovski

      Alessandro Gorohovski - 2017-01-16

      Hi Nick,

      I'm very glad to hear you again.

      2017-01-16 15:50 GMT+03:00 Nick Juty njuty@users.sf.net:

      Hi Alessandro,

      Thanks for your message!
      I just wanted to clarify - do you wish to create a link using your
      internal IDs? Or using "well-known IDs such as NCBI Entrez Gene ID, Gene
      UniProtKB AC, etc". Is there any way to link directly rather than by using
      a search?

      Sorry, I'm confused but
      I don't understand what form you would like to see or get a result?

      Please give me simple example.
      Yeah, sure: Will Smith will smith!

      Thanks in advance,

      regards,

      Nick

      Have no fear of perfection: You'll never reach it,
      Alessandro

      Status: open
      Labels: ChiTaRS Chimera Fusion
      Created: Fri Dec 30, 2016 11:06 AM UTC by Alessandro Gorohovski
      Last Updated: Fri Dec 30, 2016 02:04 PM UTC
      Owner: nobody

      The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs
      of two or more different genes. By analyzing thousands of chimeric ESTs by
      RNA sequencing, we found that the expression level of chimeric ESTs is
      generally low and they are highly tissue specific in normal cells. Here we
      present the improved version of the ChiTaRS database (ChiTaRS-3.1) of about
      40,000 chimeric transcripts in humans, mice, fruit flies, zebrafishes,
      cows, rats, pig and yeast. In the current version we extended the
      experimental data evidence as well as included a novel type of the
      sense-antisense chimeric transcripts of the same gene confirmed
      experimentally by RT-PCR, qPCR, RNA-sequencing and mass-spec peptides. In
      addition, we collected about 11,700 human cancer breakpoints with the
      expression levels of chimeric RNAs confirmed by the paired-end
      RNA-sequencing experiments in different tissues in humans, mice and fruit
      flies.

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/identifiers-org/new-collection/44/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

       

      Related

      Request new collection: #44

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