EmExplorer has six functional divisions, each of them has its unique application. Homepage uses an intuitive icon of human ovary to show the preimplantation process. Three main functional module, Search, Browser and Analysis, are designed for users to obtain the information they focus on. The graphics in Statistics module illustrate the distribution of the data which we stored in current version of EmExplorer. Download module provides data resource for diverse organisms in particular development stages.
There are 3 entries to perform visualization and analysis for A database of Spatio-Temporal Expression in Preimplantation Embryos with EmExplorer:
Search: The users can view the detail information of single data and obtain analysis entry to each data via Database ID,Official Symbol,Organism,Pathway,Pathway Name and GO Annotation.
Browser: The user can filter a particular class of data through the embryonic stage,Organism,Function,Pathway, and then selects the corresponding single gene or path in preimplantation embryos through the list.
Analysis: Users analyze spatiotemporal expression in preimplantation embryos through two different ways: By Gene,By Pathway.
The human ovary displayed in homepage vividly shows the preimplantation process. While the structure of which may quite different between diverse species, we just use it as an icon to help users generally understand the early development process. When click on a particular embryo the experimentally-validated pathways appear.
By using the search tool, users can directly obtain the entries via database ID, official symbol, organism, pathway ID, pathway name and function annotation. Fuzzy match was masterly applied to cover all query possibilities. The filter can greatly help users obtain entries which meet their needs among the massive information.
Search: The search tool allows users efficiently obtain the entries, which maximally meet their needs, via database ID, official symbol, organism, pathway ID, pathway name and function annotation.
1: Choose a search method.
2: Click the 'Search' button.
3: The filter above the returning table helps users efficiently acquire the entries maximally meet with their need.
The browser connecting to the MySQL backend allows users to select multi-species, multi-function annotations, and multi-pathways in a particular developmental stage. The Browser is useful for the users who initially access to the database and users whose search purpose is not clear.
Browser: The Browser is useful for the users who initially access to the database and users whose search purpose is not clear. The mechanism of the Browser module is taking the intersection of embryonic stage, organisms and function annotations.
1: Choose a development stage from the checkbox.
2: The Browser module support multi-organism selection, it mean users can get simultaneously obtain result for different organisms.
3: Similar to the organism selection. The Browser tool allows visitors to choose diverse functions.
4: Click the 'Browser' button.
5: The filter above the returning table helps users efficiently acquire the entries maximally meet with their need.
This module consists of two different analyzing tools. These two tools were designed for making comparison on single gene level and pathway level, respectively. The usage for each tool displayed as follows.
The analysis on single gene level allows users make comparison between diverse species. The normalization method made it possible to compare the expression value of different organisms at the same level.
1: Click input box.
2: Choose the gene you want to analysis if it exists in Hot search area or users allows to enter the official symbol in the query box.
3: Click the 'Go' button
4: The results are shown in histogram, in which each color represents a kind of species. Through the intuitive graphic, users can find the similarity of specificity of a gene cross different organisms.
This tool implements the comparison cross different pathways. We defined the pathway expression level as the overall expression level of genes in a particular pathway. The result shows in box figure, and we further distinguished the high and low expressed genes by the middle line which is the average value of gene expression. The number Q2 is the average expression value of high expressed genes. The changes of ratio of high expressed genes and Q2 imply the dynamic expression on pathway level.
By Pathway:
1: Select the organism to analysis.
2: Select the pathway to analysis.
3: Click the 'Go' button
4: The results are shown in box figure, in which each color represents a development stage. Through the intuitive graphic, researchers can understand the overall expression tendency of genes under a particular pathway.
The graphics in this module aim to answer the question, how many genes stored in current version of EmExplorer and how is the storage distributed. The dynamic figures provide comprehensive information.
The processed data was divided into different stages. Users can get the dataset in free for doing their own researches. We listed the data origin which we used to establish EmExplorer at the button of this module.