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ALDB: a domestic-animal long noncoding RNA database.

Li A, Zhang J, Zhou Z, Wang L, Liu Y, Liu Y - PLoS ONE (2015)

Bottom Line: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes.Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, PR China; School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, PR China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs.

Results: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.

Conclusions: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.

No MeSH data available.


Related in: MedlinePlus

Screenshot of the search pages.(A) Search for transcripts or genes by their ids or names. (B) Basic information for a gene. (C) Basic information for a transcript. (D) The expression levels of genes in various tissue samples. (E) About ten genes adjacent to the current gene are represented. (F) The QTLs which overlap with the current gene or transcript. (G) Search for transcripts or genes by genomic region. (H) Search for neighboring lncRNAs of protein-coding genes.
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pone.0124003.g004: Screenshot of the search pages.(A) Search for transcripts or genes by their ids or names. (B) Basic information for a gene. (C) Basic information for a transcript. (D) The expression levels of genes in various tissue samples. (E) About ten genes adjacent to the current gene are represented. (F) The QTLs which overlap with the current gene or transcript. (G) Search for transcripts or genes by genomic region. (H) Search for neighboring lncRNAs of protein-coding genes.

Mentions: In the “Search by Id/Name” page, users can find transcripts and genes by inputting their ids or names (Fig 4A). For a transcript or gene, the following relative information will be represented: “Basic information” (Fig 4B and 4C), “Expression profile” (Fig 4D), “Neighboring genes” (Fig 4E), “Overlap with QTLs” (Fig 4F). The content panels can be expanded or collapsed when their head titles (inverted triangle icons) are clicked.


ALDB: a domestic-animal long noncoding RNA database.

Li A, Zhang J, Zhou Z, Wang L, Liu Y, Liu Y - PLoS ONE (2015)

Screenshot of the search pages.(A) Search for transcripts or genes by their ids or names. (B) Basic information for a gene. (C) Basic information for a transcript. (D) The expression levels of genes in various tissue samples. (E) About ten genes adjacent to the current gene are represented. (F) The QTLs which overlap with the current gene or transcript. (G) Search for transcripts or genes by genomic region. (H) Search for neighboring lncRNAs of protein-coding genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390226&req=5

pone.0124003.g004: Screenshot of the search pages.(A) Search for transcripts or genes by their ids or names. (B) Basic information for a gene. (C) Basic information for a transcript. (D) The expression levels of genes in various tissue samples. (E) About ten genes adjacent to the current gene are represented. (F) The QTLs which overlap with the current gene or transcript. (G) Search for transcripts or genes by genomic region. (H) Search for neighboring lncRNAs of protein-coding genes.
Mentions: In the “Search by Id/Name” page, users can find transcripts and genes by inputting their ids or names (Fig 4A). For a transcript or gene, the following relative information will be represented: “Basic information” (Fig 4B and 4C), “Expression profile” (Fig 4D), “Neighboring genes” (Fig 4E), “Overlap with QTLs” (Fig 4F). The content panels can be expanded or collapsed when their head titles (inverted triangle icons) are clicked.

Bottom Line: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes.Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, PR China; School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, PR China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs.

Results: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.

Conclusions: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.

No MeSH data available.


Related in: MedlinePlus