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Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell.

Tang X, Hou M, Ding Y, Li Z, Ren L, Gao G - BMC Genomics (2013)

Bottom Line: To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively.In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools.By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these novel regulators but also shed light on their functionalities.

Results: Based on multiple RNA-Seq datasets, we systematically identified 300 human embryonic stem cell lincRNAs (hES lincRNAs). Of which, one forth (78 out of 300) hES lincRNAs were further identified to be biasedly expressed in human ES cells. Functional analysis showed that they were preferentially involved in several early-development related biological processes. Comparative genomics analysis further suggested that around half of the identified hES lincRNAs were conserved in mouse. To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively. In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools.

Conclusions: By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs. A full functional web portal is available freely at http://scbrowse.cbi.pku.edu.cn. As the first global profiling and annotating of human embryonic stem cell lincRNAs, this work aims to provide a valuable resource for both experimental biologists and bioinformaticians.

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Related in: MedlinePlus

Web portal interface. (a) Welcome page; (b) main canvas for genome browse; (c) control panel to see detailed annotations; (d) find lincRNAs through user-specified expression pattern.
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Figure 4: Web portal interface. (a) Welcome page; (b) main canvas for genome browse; (c) control panel to see detailed annotations; (d) find lincRNAs through user-specified expression pattern.

Mentions: User can start his/her navigation by either choosing a hES lincRNA on the chromosome map, or jumping to interested genes directly (Figure 4a). The main interface is presented as a typical genome browse, with heading navigation bar, control panel (at the left) (Figure 4c) and the main browsing canvas (Figure 4b). Multiple tracks could be displayed simultaneously after turning them on in the "Tracks" box. Currently, twelve tracks covering gene model, transcription regulation and comparative genomics are available (see http://scbrowse.cbi.pku.edu.cn/tutorial/index.jsp for detailed descriptions for all tracks).


Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell.

Tang X, Hou M, Ding Y, Li Z, Ren L, Gao G - BMC Genomics (2013)

Web portal interface. (a) Welcome page; (b) main canvas for genome browse; (c) control panel to see detailed annotations; (d) find lincRNAs through user-specified expression pattern.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852230&req=5

Figure 4: Web portal interface. (a) Welcome page; (b) main canvas for genome browse; (c) control panel to see detailed annotations; (d) find lincRNAs through user-specified expression pattern.
Mentions: User can start his/her navigation by either choosing a hES lincRNA on the chromosome map, or jumping to interested genes directly (Figure 4a). The main interface is presented as a typical genome browse, with heading navigation bar, control panel (at the left) (Figure 4c) and the main browsing canvas (Figure 4b). Multiple tracks could be displayed simultaneously after turning them on in the "Tracks" box. Currently, twelve tracks covering gene model, transcription regulation and comparative genomics are available (see http://scbrowse.cbi.pku.edu.cn/tutorial/index.jsp for detailed descriptions for all tracks).

Bottom Line: To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively.In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools.By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these novel regulators but also shed light on their functionalities.

Results: Based on multiple RNA-Seq datasets, we systematically identified 300 human embryonic stem cell lincRNAs (hES lincRNAs). Of which, one forth (78 out of 300) hES lincRNAs were further identified to be biasedly expressed in human ES cells. Functional analysis showed that they were preferentially involved in several early-development related biological processes. Comparative genomics analysis further suggested that around half of the identified hES lincRNAs were conserved in mouse. To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively. In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools.

Conclusions: By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs. A full functional web portal is available freely at http://scbrowse.cbi.pku.edu.cn. As the first global profiling and annotating of human embryonic stem cell lincRNAs, this work aims to provide a valuable resource for both experimental biologists and bioinformaticians.

Show MeSH
Related in: MedlinePlus