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[QUICK SEARCH] [QUERY MASK] [SEARCH PAGE RESULTS] [FEATURE PAGE] [FILE FORMAT] [TEXT AREA FORMAT] [PERFORMANCE AND REQUIREMENT] [EXTERNAL DB REFERENCES]
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QUICK SEARCH

In the home page there is the possibility to sumbit a quick search using as keyword the name of the microRNA (e.g. 'hsa-mir-211' or 'mir-211'),
writing a list of microRNAs in a text area (example).
or uploading a file with a list of microRNA in the appropriate format with a list of microRNA.

QUERY MASK

The query mask allows the user to perform more complex queries. In the advanced search all the options are available.
In the main search page the query became more and more specific, depending on the user's choice.
MICRO RNA
It is possible to choose from the pop-up menu either a specific microRNA, e.g. mir-1 or mir-1a or to perform a broader search by selecting a "group", i.e., all microRNAs sharing the same 'root' number.
For instance, by using the term "let-7?", it is possible to retrieve microRNAs let-7a, let-7b, let-7c, etc.
By default, the query is aimed at the specific microRNA, but using the radio button it is possible extend the selection to a family of microRNAs.
SPECIES
The query can run on all species present in the database or on a selected species or a clade of species
Choose species Choose species
ANNOTATION
Checking the appropriate box the user can choose the annotation to display.
Some annotation are shown by default, whereas the display of other depends from the query.
Choose the annotation to display
APPLICABLE FILTERS
If the result of the query include more than one microRNA, some filters are applicable.
GENOMIC CONTEST FILTER
STATUS
You can filter the search by the status of microRNA in the database
Choose status
Filter prediction
The annotated microRNAs are those which are present in miRBase as experimentally tested.
These also included the PUTATIVE MicroRNAs, which are annotated in miRBase but not are experimentally tested.
The Ensembl Predictions are the microRNAs that are not present in miRBase but are predicted by EnsEMBL.
The CoGemiR Predictions are the microRNAs that are only predicted by CoGemiR.
For further details please refer to the work flow of the prediction pipeline on the workflow page
LOCALIZATION
Radio buttons allow you to filter your query by microRNA localization.
1) by choosing to filter for intergenic or intragenic microRNA All Intergenic Intragenic
2) by choosing the direction of the overlapping gene transcription
Where sense means that the transcription direction of the gene is the same as the microRNA and antisense means that the transcription direction of the gene is opposite with respect to the microRNA
3) by choosing to restrict queries to intragenic microRNAs with either an overlapping annotated GENE or overlapping ESTs.
4) by choosing a sublocalization (exonic or intronic) for intragenic microRNAs
OTHER FEATURES FILTERS
5) by choosing the extent of overlap with exons for exonic microRNAs:
"Exon left" and "exon right" means that a microRNA partially overlaps with an exon,
"over_exon" means that the exon is smaller than the microRNA,
"inside_exon" means that a microRNA falls entirely within an exon.
OVERLAPPING GENE
This search allows you to verify whether a gene overlaps one or more microRNAs (please use gene symbols or EnsEMBL gene IDs)
Search by specific hostgene
EXPRESSION DATA
For Human and Mouse it is possible to earch a microRNA by the expression profile of its overlapping gene
Search by tissue
The data are extracted from SymAtlas and are available only for Human and Mouse.
The result is sort in descending expression level order.
For details see SymAltas references
Note that we list ONLY the tissues which show an expression that is greater than the mean plus 3 standard deviation values
AND ONLY if the number of tissues that pass this threshold is lower or equal to 30% of the
total number of tissues analyzed.
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SEARCH PAGE RESULTS

MICRORNA SUMMARY TABLE
MIRNA MIRNA This column shows a list of MicroRNAs which satisfy the query
MICRORNA DETAILED TABLE
MICRORNALink to a page with a summary of additional attributes and features.
CONSERVATIONList of  all species in which the queried microRNA is present.
FAMILYList of all microRNAs in all species belonging to the queried microRNA family..
MIRBASELink to miRBase
GENOMIC COORDINATESLink to the microRNA genomic region in EnsEMBL. Note: the release is the one indicated in the home page.
OVERLAPPING GENE
Link to the overlapping gene in EnsEMBL. Note: the release may not be the most recent.
The direction of transcription of the overlapping gene with respect to the microRNA is also indicated.
# INTRON/EXONRanking of the overlapping intron or exon
STATUS
see above
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FEATURE PAGE

GENOMIC INFORMATION
This section provides information on the position of the microRNA on the genome and on the overlapping gene, if present.
GENOMIC LOCATIONGenomic coordinates of the microRNA.
FLANKING REGIONSFor intergenic microRNA the closest upstream and downstream gene are indicated.
ADDITIONAL ANNOTATIONIf there are evidence of additional overlapping elements, as VEGA gene or EST gene, these are listed here.
LOCALIZATIONClassification of the microRNA according to its possible overlap with other genes.
If the microRNA is intragenic, a list of the overlapping transcript is provided.
If there are other microRNA overlapping the same gene of the inquired microRNA
MicroRNA CLUSTER
List of other microRNAs present within the 18kb region surrounding the selected microRNA,
together with their genomic coordinates and links to EnsEMBL.
SEQUENCE INFORMATION
Both the precursor and the mature microRNA sequences are shown.
If the microRNA is a CoGemiR prediction, the hit string is showed.
If it is a high confidence prediction, also the putative mature sequenced is shown.
The mature sequence is colored in green within the precursor sequence.
pre-mirna:PREMATURECURSOR
Hit sequence:HITMATURESEQUENCE
Mature sequence:MATURE
EXPRESSION DATA
Expression profileA list of tissue in which the overlapping gene is expressed, according to the SymAtlas database.
Note that we list ONLY the tissues which show an expression that is greater than the mean plus 3 standard deviation values
AND ONLY if the number of tissues that pass this threshold is lower or equal to 30% of thetotal number of tissues analyzed.
AP callsA list of tissue in which the hostgene is annotated as 'P' present, 'A' absent or 'M' marginal
FEATURE
A list of additional feature of the microRNA is summarized here: species-specificity of the microRNA, a list of significative paper references etc.
LINK
This section represent a list of links to a related external database.
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TEXT AREA FORMAT

Type a list of microRNA separated by tab or newline (max 50). If you want submit more than 50 microRNAs, please upload a file.
The complete name (e.g. 'hsa-mir-211') should be indicate for a search on specific species.
Otherwise a search on all species in the database will be run.
If your list is long or you want to restrict the query to some species only, please upload a file.
Example:
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FILE FORMAT

DOWNLOAD
The file contains all the data retrieved by the query, with the annotation selected by the user, separate by tab.
It has the .xls extension and it can be open directly by a spreadsheet editor or as a text file with a text editor.
UPLOAD
The file must contain a list of microRNA separated by tab or newline. The complete name (e.g. 'hsa-mir-211') should be indicate for a search on specific species.
Otherwise a search on all species in the database will be run. To restrict the query to some species only, these are to be indicated at the top of the file, in a single row, starting with # and separated by tab.
Click here to see some examples.
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PERFORMANCE AND REQUIREMENT

For a best view, we suggest to use one of the following web browsers: Firefox, Explorer, Camino or Netscape Navigator.
When using other browser, make sure that the visualization of cgi files is enabled.
Due to the complexity of some queries, for a better performance, it is suggested to click Reset before submitting a completely new query.
It is not necessary to do so when additional filters  have been chosen..
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EXTERNAL DB REFERENCE

DATABASERELEASEREFERENCE
miRBase11.0 April 2008Griffiths-Jones, S., et al (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36, D154-D158.
EnsEMBL48 December 2007Hubbard, TJ., et al (2007) Ensembl 2007 Nucleic Acids Res 35, D610-7.
SymAtlasv1.2.4HG_U133A/GNF1H and GNF1M Tissue Atlas Datasets.
Su AI, et al (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A.