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. 2019 Jan 1;2019:baz058.
doi: 10.1093/database/baz058.

Chickspress: A Resource for Chicken Gene Expression

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Free PMC article

Chickspress: A Resource for Chicken Gene Expression

Fiona M McCarthy et al. Database (Oxford). .
Free PMC article

Abstract

High-throughput sequencing and proteomics technologies are markedly increasing the amount of RNA and peptide data that are available to researchers, which are typically made publicly available via data repositories such as the NCBI Sequence Read Archive and proteome archives, respectively. These data sets contain valuable information about when and where gene products are expressed, but this information is not readily obtainable from archived data sets. Here we report Chickspress (http://geneatlas.arl.arizona.edu), the first publicly available gene expression resource for chicken tissues. Since there is no single source of chicken gene models, Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and Ensembl gene prediction pipelines, researchers can, for the first time, easily compare gene models from each of these prediction workflows to available experimental data for these products. We use Chickspress data to show the differences between these gene annotation pipelines. Chickspress also provides rapid search, visualization and download capacity for chicken gene sets based upon tissue type, developmental stage and experiment type. This first Chickspress release contains 161 gene expression data sets, including expression of mRNAs, miRNAs, proteins and peptides. We provide several examples demonstrating how researchers may use this resource.

Figures

Figure 1
Figure 1
Expression of mRNAs across multiple tissues from adult Red Jungle Fowl. mRNA transcripts are grouped based upon whether they are annotated by NCBI or Ensembl or if they are novel.
Figure 2
Figure 2
Expression of miRNAs across multiple tissues from adult Red Jungle Fowl. Mature miRNAs are grouped based upon whether they have been annotated in NCBI or if they are novel and are reported based upon the number of tissues in which they were identified.
Figure 3
Figure 3
Expression of proteins and peptides across multiple tissues from adult Red Jungle Fowl. Peptides are identified as mapping to NCBI and Ensembl proteins, or as novel proteogenomic peptides (which map to the genome but not to annotated proteins). All peptides included in this study have a P-value of ≤0.01.
Figure 4
Figure 4
Novel transcripts not in the current chicken gene annotation. Novel transcripts are assembled mRNAs that differ from the gene model, and this difference is shown for NCBI and Ensembl genes.
Figure 5
Figure 5
Searching for specific genes in Chickspress. (A) Searching for CLSNT2 expression in nerve tissues using the Chickspress Genome Browser main page. (B) Researchers may also directly search from the CoGe browser by entering a region or using the `Find Features’ option (red box). Identified features are displayed in the right-hand side menu.
Figure 6
Figure 6
Expression of individual transcripts in the CoGe browser. (A) Individual experiments are displayed as separate tracks, with genes in the forward orientation represented as positive value and genes in the reverse orientation represented as negative value. (B) Holding the cursor over exons displays individual transcripts and their expression values. The first value is exon expression, and the second value is expression of the full-length transcript (all expression values are calculated as FPKM). This view may be regenerated at https://goo.gl/x5vzaa.
Figure 7
Figure 7
LOC107051856 expression varies in concert with CLSTN2 transcripts. LOC107051856 is an uncharacterized ncRNA nested within CLSTN2. LOC107051856 is highly expressed in female hypothalamus but not in male hypothalamus. The XM_015277049 CLSTN2 transcript is more highly expressed in female compared to male hypothalamus, while the reverse is true for the XM_015277050 CLSTN2 transcript. This view may be regenerated at https://goo.gl/x5vzaa.
Figure 8
Figure 8
Filtering and downloading Chickspress data. (A) Chickspress data can be filtered and downloaded using the `Search and Download Data’ page. This interface allows users to filter based upon gene product type, tissue, genomic region and expression characteristics. (B) Results of a search displayed as a table with link to the genome browser. Search criteria are displayed at the top of the page, and results may be downloaded in a number of file formats.

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