USAGE:
The SpermatogenesisOnline 1.0 provides the search option and advanced options.
1. Search You can input keywords to search the FollADO database. The search fields include ADO ID, UniProt Accession, Protein Names, Gene Names, Functional Stage and Functional Type.
Example: Please click on the Species field in the combo box to search "Mus musculus". By clicking on the "Submit" button, the related SG proteins will be shown.
2. Advanced Four advanced options are provided, including advanced search, browse, BLAST search, orthologous search.
(1) Advanced search: Advanced search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if fewer terms were needed. The three terms could be connected by the following operators:
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)
exclude: If selected, the term following this operator must be not contained in the specified field(s)
Example: You can click on the "Example" button to load an instance, which could search "Sycp2" and "spermatocyte" in mouse. The mouse Sycp2 (SG00001587) will be shown by clicking on the "Submit" button.
(2) Browse: You can browse the SpermatogenesisOnline 1.0 database by species, functional stage and functional type. With the default setting, you can directly click on the "Submit" button to browse all the protein involved in Spermatogenesis.
(3) BLAST Search: BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and quickly. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined. The BLAST results will be parsed and shown by clicking on the "Submit" button.
Example: You can click on the "Example" button to load the protein sequence of mouse Peroxisome proliferator-activated receptor gamma coactivator-related protein 1. By clicking on the "Submit" button, you can find the related homologues in SpermatogenesisOnline 1.0 database.
(4) Orthology Search: In SpermatogenesisOnline 1.0 database, the pairwise orthologous information was computed with the Panther and InParanoid program (Mi H.et al., 2010; Remm M et al., 2001; Kevin P et al., 2005). Two operators are provided:
(a) Simple: You can input a specified uniport Accession that include in SpermatogenesisOnline 1.0 database. The Identity, E-value and BLAST Score thresholds could be user-defined.
Example: You can click on the "Example" button to browse the ENSG00000139351 (Synaptonemal complex protein 3) orthologous in SpermatogenesisOnline 1.0 database.
(b) Advanced: The pairwise orthologous information could also be viewed in details. The Score (bits), E-value, Identities and Positives from BLAST results are provided.
Example: You can click on the "Example" button to browse the Spermatogenesis proteins conserved between Homo spaines and Mus musculus.
(5) Chromosome Location: In SpermatogenesisOnline 1.0 database, users can search the spermatogenesis-related genes by entry the chromosome location of different species.
Example: You can click on the "Example" button to browse the Spermatogenesis genes that locate at 19000000-200000 in mose chromosome 16.
3. Prediction
In SpermatogenesisOnline 1.0, spermatogenesis-related genome-wide transcriptional data are also collected for data mining. Based on the identified genes and transcriptional data, functional candidate genes which may participate in regulation of spermatogenesis are predicted by the GAS (Greed AUC Stepwise) model.
The probability was calculated by GAS algorithm, ranging from 0 to 1. The closer it is to 1, the more possibly it functions in spermatogenesis. Without enough prior information to optimize the critical point, we suggest to use 0.5 as the cut-off. At that point, both the FPR and FNR are relative low according to our simulation study. The users could sort the lsit of predicted genes by click on the "Arrow" button on the side of SG ID, Chromosome, and Probabitity. Detatils of GAS algorithm
4. Feedback
Users are welcome to review records in SpermatogenesisOnline 1.0. You can revise the existed recrods or submit new gene/protein or gene/protein with new function in Spermatogenesis. We are grateful to you for your advice!
5. Expression
As a source of expression information for SpermatogenesisOnline 1.0 and to prepare for the prediction of genes with novel functions, the ArrayExpress database was used as a resource. After the whole ArrayExpress database browse, eighteen mouse whole transcript microarray experiment datasets using Affymetrix GeneChip Mouse Genome 430 2.0 platform were downloaded. These eighteen datasets were divided into four categories. The 'developmental stages' category contains dataset of gene expression in testes in a developmental time course. Dataset in the 'gene disturbance' category is gene expression information in testes of gene modified mice. The 'before and after treatment' category contains gene expression information in testes of laboratory mice before and after received chemical treatment, and the 'tissues and cell types' category contains gene expression information in different tissues or cell types of testes.