Phenotype of an organism is determined by the complex interactions between genetic factors and environmental factors. miREnvironment is a database that curated and collected experimentally supported microRNA (miRNA), one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes. Information such as conditions of environmental factors, samples treated by environmental factors, species, detailed evidences of the experiments and references are also given. The users can
Last update: Sep-9, 2012
Statistics:
miREnvironment integrated more than 3857 entries, 1242 miRNAs, 394 environmental factors, 305 phenotypes, 24 species from 557 publications.
Links:
HMDD: the Human microRNA Disease database
miRBase: the microRNA database
DrugBank: the Open Data Drug & Drug Target Database
History:
1. Feb-29, 2012, a paper for analyzing and modeling the interactions between miRNAs and environmental factors and their relationship to human disease was accepted by Scientific Reports.
2. Oct-7, 2011, the paper for the miREnvironment database was online in Bioinformatics.
3. June-28, 2011, the original miREnvironment Database was released.
Contact us
Email: cuiqinghua@hsc.pku.edu.cn
Homepage: http://www.cuilab.cn/
You can search the entries by such keywords:
In the "Search" result, each entry has ten items.
(1) miRNA gene - the annotated miRNA gene name based on miRBase Release 17.
(2) miRNA product - the annotated miRNA product name based on miRBase Release 17.
(3) miRNA product original - the miRNA gene product reported in the original reference.
(4) phenotype - the annotated phenotype reported in the original reference.
(5) environmental factor (EF) - the annotated environmental factor reported in the original reference.
(6) Condition of EF - the condition environmental factor. This item indicates how the environmental factor acts on the experimental objects.
(7) Sample - the samples treated by the environmental factor.
(8) Species - the species selected in the experiment
(9) Evidence - this item indicates the detailed association result among the miRNA, environmental factor, and phenotype.
(10) PubMed ID - the reference ID in PubMed database.
All data of miREnvironment can be downloaded here. TXT or EXCEL
The list of miRNAs: TXT or EXCEL
The list of phenotypes: TXT or EXCEL
The list of environmental factors: TXT or EXCEL
The miRNA DSW (Disease Spectrum Width) data: TXT
The predicted EF-disease association data: EXCEL
Welcome to submit new entries to the database.
The interaction between genetic factors and environmental factors has critical roles in determining the phenotype of an organism. In recent years, increasing evidences have shown that microRNAs (miRNAs), one class of newly identified genetic factors, also show complex interactions with various environmental factors. Dysfunctions on miRNAs, environmental factors, and their interactions thus have strong affects on phenotypes and even may result in abnormal phenotypes and diseases. This database provided researchers in this field a bridge to link miRNAs, environmental factors, and phenotypes. In order to understand this field more easily, we collected a list of review papers in this field. The users could have a quick understanding on this field by having a look at these reviews.
This tool aims to predict the result of cancer treatment through evaluating the enrichment of the miRNA signatures in two predefined miRNA sets: miRNA oncogenes and miRNA suppressors. The hypothesis is that a succesfull therapy of cancer should inhibit the activity of oncogenes and amplify the activity of tumor suppressors, and vice versa.
This tool aims to predict associations between environmental factors (drugs) and human disease through enrichment analysis of their miRNA signatures. The users input the miRNA signature of an environmental factor. The tool integrated the miRNA signatures of human disease from the Human microRNA Disease Database (HMDD). After evaluaitng the enrichemnt, this tool output the potential disease associated with the given environmental factor.
Analysis Result will be shown here.
miREnvironment is a database that curated and collected experimentally supported miRNA and environmental factor interplays and their associated phenotypes.
miREnvironment presents functions of "browse", "search", "download", and "submit" for users.
The detailed usage of the database is as followings:
[1] Visiting miREnvironment: Log on miREnvironment at http://www.cuilab.cn/miren.
[2] To browse data in the database, select the menu "Browse". And then select corresponding items to browse the entries you are interested. For example, if you want to get entries about the drug "Tamoxifen", you can click "environmental factors" first and then select "Tamoxifen". The corresponding entries will be shown on the right panel.
[3] To search data in the database, select the menu "Search". miREnvironment provides functions of "search" by multiple keywords, such as miRNA name, environmental factor name, and species. Input your candidate keywords into corresponding blanks and submit the query. In the "Search" result, each entry has ten items.
(1) miRNA gene - the annotated miRNA gene name based on miRBase Release 17.
(2) miRNA product - the annotated miRNA product name based on miRBase Release 17.
(3) miRNA product original - the miRNA gene product reported in the original reference.
(4) phenotype - the annotated phenotype reported in the original reference.
(5) environmental factor (EF) - the annotated environmental factor reported in the original reference.
(6) Condition of EF - the condition environmental factor. This item indicates how the environmental factor acts on the experimental objects.
(7) Sample - the samples treated by the environmental factor.
(8) Species - the species selected in the experiment
(9) Evidence - this item indicates the detailed association result among the miRNA, environmental factor, and phenotype.
(10) PubMed ID - the reference ID in PubMed database.
[4] To download data in the database, select the menu "Download". miREnvironment provides two formats of downloadable file for the whole data in TEXT and Excel formats, respectively. Moreover, files for the lists of miRNAs, environmental factors, and phenotypes are also given. Right click any of the file, and then click "save as" to save the file to your local computer.
[5] To submit new entries to the database, select the menu "Submit". The users need to input their data into corresponding blanks and then submit the query. We will further curate the submitted information to determine whether to add the new entries to the database or not.
If there are any comments or suggestions, please contact Dr. Qinghua Cui at cuiqinghua@hsc.pku.edu.cn
Citation: Yang Q, Qiu C, Yang J, Wu Q, and Cui Q*. miREnvironment Database: providing a bridge for microRNAs, environmental factors, and phenotypes. Bioinformatics 2011 27: 3329-3330.
Qiu C, Chen G, and Cui Q*. Towards the understanding of microRNA and environmental factor interactions and their relationships to human diseases. Scientific Reports 2012, 2:318.