ReCGiP: Database of Reproduction Candidate Genes in Pigs based on bibliomics

Tutorial

A detailed tutorial on how to use the Database
Please take this tutorial before accessing the database

Taking BMP2 gene on 'Embryo Implantation' topic for example, a usage of ReCGiP is described.

Following pages in ReCGiP are used:
    Gene page
    Topic gene page
    Different topic of network page

(1) Gene search

Search human BMP2 gene in 'Embryo Implantation' topic using search form in ReCGiP.

(2) Gene symbol search result

The resulting page contains the gene function annotated by NCBI with links to the gene pages. Entrez Gene ID and e logo hyperlink to Entrez Gene are also provided for users to be easy to make use of it. In order to offer more information on reproductive genes in livestock, homologous gene pages are provided. Click pig logo, cow logo and sheep logo, respectively, to move homologous gene page for pig BMP2, cow BMP2 and sheep BMP2. Click the symbol of "BMP2" to go the gene page.

(3) Gene page

Gene page is the main page of ReCGiP. It is mainly composed of two parts.
    1. functional annotation part
    2. internal gene(s) or external gene(s) part

The name of each part is highlighted by aquamarine blue bar.
IDs for others DBs are also provided as the forth part.

The functionsl annotation part provides functional gene annotations gene biomedical literatures as evidence obtained from NCBI, GO, KEGG and OMIM.

Internal gene(s) or external gene(s) section provides the cooccurrence gene list relevant to this gene on the right of the page.

(4) Topic gene page

Topic gene page is the central page of ReCGiP. For each topic gene page, internal genes in GGCON are sorted by their descending CR and are displayed, and the literature containing this gene is also presented. Ten internal genes are presented in each page. The details of the internal gene can be seen by following the link to this gene of gene page. Click the symbol of "BMP2" to go the gene page.

Moreover, pig topic gene page is constructed for spermatogenesis, oogenesis, fertilization, pre-implantation development, embryo implantation, placentation and reproductive traits. For each page, curator genes and their related literatures are presented.

(5) Different topic of network page

In order to consult the gene cooccurrence networks in these reproductive topics, the co-occurred gene networks for six mainly processes of reproduction are provided (embryo implantation topic in this example). We employed jSquid API to navigate the huge cooccurrence network in a topic.

Zoom-out view can be obtained by sliding a zoom slider at the bottom panel.

In the zoom-out view, cooccurrence genes of BMP2 include BMPR2, BMP4, BMP7, MGP, RUNX2, SMAD1, PTEN, TGFB2 and COL2A1 in embryo implantation topic.

The significant genes can be identified by gene-gene cooccurrence network. For example, there are 344 genes that co-occurred with EGFR in the 'Embryo Implantation' topic.

Mostly information can be obtained by hitting navigation bars in home page. Thank you for taking the Tutorial.

ReCGiP team hopes that this demo will help you to efficiently use this database. Any time, you may contact us directly when having questions, remarks or problems.