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DGIL Porcine Translational Research Database

PINdb

 

 

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As of March 2020, the database has been online for 15 years. It is used by research scientists working with pigs worldwide as well as commercial and public developers of new reagents. This database is the largest manually curated database for any agriculture species and is unique among porcine gene databases by linking gene expression to gene function, identification of related gene pathways, and connectivity with other porcine/human gene databases. It is referenced in more than 90 manuscripts or websites and used as an information resource for several reagent vendors.

 

What is new?

  1. Content

The database currently has 17,880 entries (pig, mouse and/or human) and transcript information for 11,547 pig genes. This represents an increase of 1,848 entries from the previous update. 4,747 entries have also been updated in that time frame. Each entry now has 103 data fields. We have also added 2 dimensional, and on a limited basis, 3-dimensional structural comparisons between the 3 species (pig, mouse, and human). The database now contains 3,327 real-time PCR assay (Taqman and SYBR green). The database also contains antibody or protein assay data for 965 proteins including 982 monoclonal antibodies, 994 polyclonal antibodies and 450 enzyme-linked immunosorbent assays.

  1. Splice variant analysis

We have numbered pig splice variants according to their human counterpart when possible. Although splice variant conservation of major isoforms is generally conserved, our comparison of 7,822 corresponding splice variants revealed that pigs lack the exon to make 9.3% of human splice variants. Possible differences in the functional capabilities of splice variants have also been added to our notes field.

  1. Error determination

Information in the database identifies and corrects > 7,000 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) in the current genome builds (NCBI and Ensembl build 11.1). Our analysis of 6,518 Ensembl locus reveals that only 46.1% are correctly assembled and annotated. We have recently extended this analysis to the Ensembl assembly of MARC 1.0 build. An error analysis of the 150 largest proteins show that the percentage correctly assembled genes for for NCBI build 11.1, Ensembl build 11.1 and Ensembl MARC build is, respectively, 37%, 20% and 18%. Our preliminary analysis of 1,032 genes from the Ensembl assembly of MARC build 1.0 also reveals 61 genes that are not annotated and 52 genes that are missing from chromosomes 1, 2, 3, 7 and 13.

  1. Porcine Immunome

The 7th and 8th comparative genome manuscripts were published in 2019-2020. One describing porcine CD markers (PMID: 29518710) and another describing porcine cytokines, chemokine and growth factors (PMID: 32442727). The latter paper fills in certain gaps in sequence information (chemokines, IL-1 Family) in the porcine genome necessary for understanding inflammation. To date, we have identified 3,696 genes (or their paralogs) that have a documented role in the immune or inflammatory response. We have identified 3,163 of these genes in pigs. Three species (pig, mouse, human) comparisons (presence/absence, splice variant and structural domain conservation) have been made for 17 recently described families of genes (B7-related MG Family, Butyrophilins, C-type Lectins, Chckpoint Receptors and Ligands, Chitinases, Complement-Related Genes, DeAD Box helicases, Defensins and Antimicrobial Peptides, IAP and IAP-Related Genes, Immunity-related GTPases, Immunoglobulin Receptors, Intelectins, Non-coding RNA, Ly49 Superfamily, LY9 Superfamily, PYHIN Superfamily and SIRPs). The number of genes identified and annotated are more than twice the number found in our previous immunome investigation (PMID: 23676093).

  1. Porcine Nutrigenomics

To date, we have identified 3,426 genes (or their paralogs) associated with porcine, murine, and human macro and micronutrient metabolism, including Zn metalloproteins. Preliminary analysis reveal that pigs have roughly 4-fold fewer unique genes than the mouse and human. The great majority of these unique genes were zinc-containing members of the KRAB-A box Transcription Factor Superfamily. An analysis of 142 non-orthologous genes revealed that these genes were about 10 times more likely to be present in only pigs and humans (120) than only in mice and humans (17). Genes involved in vitamin A and lipid metabolism were more highly conserved between pigs and humans. Notable, differences were found between humans and pigs in regard to genes encoding digestive enzymes and nutrient sensing genes.  In some cases, mechanistic data were obtained to explain for previously described differences in physiology. For example, the lack of porcine salivary lipase and amylase activities is likely related to the absence of these genes in the pig. An analysis of 888 orthologous proteins indicated a greater pig-human protein similarity for almost every gene examined.

The sequences in this database (and associated informatics) are available (in bulk) to extramural laboratories, via MTA, that are looking to supplement their analysis of the porcine genome. Please contact us if you are interested in this.

Disclaimer

This database is currently in a beta version, there are some incomplete annotations. We cannot guarantee the performance of the antibodies or PCR assays that have not been tested in our lab under conditions not specified in the published literature.


Last Modified: 09/15/2020.