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Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

Zhao Z, Bai J, Wu A, Wang Y, Zhang J, Wang Z, Li Y, Xu J, Li X - Database (Oxford) (2015)

Bottom Line: However, the combinatorial effects of these molecules in a specific biological function are poorly understood.Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis.Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

No MeSH data available.


Six main modules of Co-LncRNA. (a) The ‘CEGs’ module provides the co-expressed associations between the lncRNA and protein-coding genes. (b) The ‘CEGsFuncs’ module provides the combinatorial effects of the lncRNAs in the GO annotations and KEGG pathways. (c) The ‘merge CEGsFuncs’ module provides the integrated results for the combinatorial effects of lncRNAs in multiple datasets. (d) In the ‘CEGsNet’ module, the relevant networks that were built with lncRNAs and CEGs can be visualized. (e) In the ‘Analyse your data’ module, the users can submit their own matched lncRNA and protein-coding gene expression profiles to investigate the combinatorial effects among the lncRNAs. (f) All of the internal lncRNA and protein-coding gene expression data and the lncRNA-CEG pairs can be downloaded in the ‘Download’ module for further analyses.
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bav082-F3: Six main modules of Co-LncRNA. (a) The ‘CEGs’ module provides the co-expressed associations between the lncRNA and protein-coding genes. (b) The ‘CEGsFuncs’ module provides the combinatorial effects of the lncRNAs in the GO annotations and KEGG pathways. (c) The ‘merge CEGsFuncs’ module provides the integrated results for the combinatorial effects of lncRNAs in multiple datasets. (d) In the ‘CEGsNet’ module, the relevant networks that were built with lncRNAs and CEGs can be visualized. (e) In the ‘Analyse your data’ module, the users can submit their own matched lncRNA and protein-coding gene expression profiles to investigate the combinatorial effects among the lncRNAs. (f) All of the internal lncRNA and protein-coding gene expression data and the lncRNA-CEG pairs can be downloaded in the ‘Download’ module for further analyses.

Mentions: Co-LncRNA was designed to investigate the lncRNA combinatorial effects in the GO annotations and KEGG pathways based on human RNA-Seq data, and is available at http:// www. bio- bigdata. com/ Co- LncRNA/ . Co-LncRNA currently contains 241 independent RNA-Seq datasets across 28 human tissue types/cell lines for a total of 6560 individuals (29 012 samples) (Figure 2). Detailed information of each dataset is available in the sources provided in Supplementary Table S1. Co-LncRNA currently contains six modules (Figure 3): (a) the acquisition of lncRNA co-expressed protein-coding genes (entitled ‘CEGs’); (b) the lncRNA combinatorial effects in functions, including GO annotations and KEGG pathways under a specific dataset (entitled ‘CEGsFuncs’); (c) the integrated results of lncRNA combinatorial effects from different datasets (entitled ‘merge CEGsFuncs’); (d) the visualization of lncRNA–protein-coding gene co-expression network (entitled ‘CEGsNet’); (e) the online analysis tool (entitled ‘Analyse your data’); and (f) the download module.Figure 3.


Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

Zhao Z, Bai J, Wu A, Wang Y, Zhang J, Wang Z, Li Y, Xu J, Li X - Database (Oxford) (2015)

Six main modules of Co-LncRNA. (a) The ‘CEGs’ module provides the co-expressed associations between the lncRNA and protein-coding genes. (b) The ‘CEGsFuncs’ module provides the combinatorial effects of the lncRNAs in the GO annotations and KEGG pathways. (c) The ‘merge CEGsFuncs’ module provides the integrated results for the combinatorial effects of lncRNAs in multiple datasets. (d) In the ‘CEGsNet’ module, the relevant networks that were built with lncRNAs and CEGs can be visualized. (e) In the ‘Analyse your data’ module, the users can submit their own matched lncRNA and protein-coding gene expression profiles to investigate the combinatorial effects among the lncRNAs. (f) All of the internal lncRNA and protein-coding gene expression data and the lncRNA-CEG pairs can be downloaded in the ‘Download’ module for further analyses.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4565967&req=5

bav082-F3: Six main modules of Co-LncRNA. (a) The ‘CEGs’ module provides the co-expressed associations between the lncRNA and protein-coding genes. (b) The ‘CEGsFuncs’ module provides the combinatorial effects of the lncRNAs in the GO annotations and KEGG pathways. (c) The ‘merge CEGsFuncs’ module provides the integrated results for the combinatorial effects of lncRNAs in multiple datasets. (d) In the ‘CEGsNet’ module, the relevant networks that were built with lncRNAs and CEGs can be visualized. (e) In the ‘Analyse your data’ module, the users can submit their own matched lncRNA and protein-coding gene expression profiles to investigate the combinatorial effects among the lncRNAs. (f) All of the internal lncRNA and protein-coding gene expression data and the lncRNA-CEG pairs can be downloaded in the ‘Download’ module for further analyses.
Mentions: Co-LncRNA was designed to investigate the lncRNA combinatorial effects in the GO annotations and KEGG pathways based on human RNA-Seq data, and is available at http:// www. bio- bigdata. com/ Co- LncRNA/ . Co-LncRNA currently contains 241 independent RNA-Seq datasets across 28 human tissue types/cell lines for a total of 6560 individuals (29 012 samples) (Figure 2). Detailed information of each dataset is available in the sources provided in Supplementary Table S1. Co-LncRNA currently contains six modules (Figure 3): (a) the acquisition of lncRNA co-expressed protein-coding genes (entitled ‘CEGs’); (b) the lncRNA combinatorial effects in functions, including GO annotations and KEGG pathways under a specific dataset (entitled ‘CEGsFuncs’); (c) the integrated results of lncRNA combinatorial effects from different datasets (entitled ‘merge CEGsFuncs’); (d) the visualization of lncRNA–protein-coding gene co-expression network (entitled ‘CEGsNet’); (e) the online analysis tool (entitled ‘Analyse your data’); and (f) the download module.Figure 3.

Bottom Line: However, the combinatorial effects of these molecules in a specific biological function are poorly understood.Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis.Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

No MeSH data available.