How to Use mirtronDB

WELCOME to mirtronDB
mirtronDB is a comprehensive database about mirtrons.
Its resources allows users query mirtrons data and download them in
several formats.

To access mirtronDB Home Page use: http://mirtrondb.cp.utfpr.edu.br/

#HOME: Presents to users basic informations about the repository.

#ABOUT: Orientations about how to cite us and repository build process scheme.

#SEARCH: The users can query mirtron data in 2 different methods:
Simple or Specifically.

#SEARCH:
In the “Simple” search the users can query mirtron data in two different ways: (i) Simple
Search by ORGANISM and (ii) Simple Search by PAPER.
Searching by ORGANISM, the user can query mirtron by organism or by organism group
(chordates, invertebrates and plants). In both cases the users are recommended to select at
least one option in the organism or organism group list. In this search method the users can
also query for precursor or/and mature mirtrons. Searching by PAPER the user must just
select the paper and the mirtrons originated from the paper or papers will be presented.
In the “Specific” search the users can query mirtron data by mirtron name. For this, the
user must first choose the organism and wait the “mirtronDB name” and “miRBase or Paper
ID” be filled. Then, the user can choose one or more mirtron name. The mirtrons
nomenclature in mirtronDB are standardized as "organism name abbreviation + the word
‘mirtron’ + ID, and for mature mirtrons we add the arm" and “miRBase or Paper ID” are the
name collected from the mirtrons origin paper.

#SEARCH: Users can query mirtrons by organism, organism group,
mirtron type and mirtron name.
If necessary,
3. Choose a “Mirtron Type”
4. Click in “Search”
1. Choose Search Method: by “Organism” or “Organism Group”
SIMPLE SEARCH BY ORGANISM
2. Choose one or more “Organism”
or “Organism Group”

#SEARCH: Users can query mirtrons by paper.
1. Choose one or more papers.
SIMPLE SEARCH BY PAPER

#SEARCH: Users can query mirtrons by organism and mirtronDB name or
miRBase ou Paper Id.
SPECIFIC SEARCH
1. Choose an “Organism”
2. Choose the Search Method:
“mirtronDB name” or
“miRBase or Paper Id”
3. Choose one or more
mirtron name.

#SEARCH: QUERY RESULT
In the query result are presented some basic mirtron data, such as mirtron organism
origin, name, type (precursor or mature), miRBase or paper id, hairpin origin and host
gene. The result query table content can be downloaded clicking in the “Download
Table” button (a CSV file will be generated).
To download specific mirtron sequence data, the user must select the respective
mirtron box in the FETCH column, and click em “Fetch” button. The FASTA file will be
generated. The user can download several sequences on the same requisition.
To search in the result table the user can use the “Search” field. The term typed in this
field will be searched in all table fields. The user can also sort the data table clicking in
the desired column label.

Click in “Download Table” to
download the data table result
in CSV format.
DOWNLOAD RESULT TABLE

2. Click in “Fetch” button and a
FASTA file will be downloaded
1. select the respective
mirtron box
DOWNLOAD SPECIFIC
MIRTRON SEQUENCE

The term typed in this
field will be searched in all
table fields
SEARCHING IN THE RESULT
TABLE

To acess more
information about one
specific mirtron

In the status column you must consider:
 Known: Mirtrons that have convincing classification evidence.
 Candidate: Mirtrons that have compelling classification evidences but
the origin paper consider prudent reserve them as candidates.
 Reclassified: Structure that were firstly considered as miRNA and
after specific studies were reclassified as mirtron.

#SEARCH: MIRTRON DETAILS
In the “+” button are presented all the functional data collected about the specific
mirtron, including the information if the mirtron was identified in miRBase and his paper
origin (with PubMed and miRBase link).
In this section is possible download all these table information in CSV format and
access the analysis results, if available. The query result table can be downloaded
using the “Download Details” button.
The analysis result are referent to BLAST alignment, alignment between all precursor
mirtrons against all other species genomes with mirtrons identified; the TargetScan and
psRNATarget results are referent to target gene prediction for humans and plants,
respectively; and TAPIR refers to a potential ceRNA interactions of mirtrons in plants.
All these results can be accessed using his respective button (tool name labeled).

MIRTRON DETAIL SCREEN
miRBase link
Link to details about
others related mirtrons

MIRTRON DETAIL SCREEN
Download mirtron details
in CSV format
Network interactions
shortcut.
Analysis results, if available,
can be accessed in the
respective button.
Link to mirtron
location in JBrowse

#BROWSER: Users can view mirtron data sorted by organism.
Click in an organism
image and access
mirtron data.

#BROWSER: Users can view mirtron data sorted by organism.
Details about a
specific mirtron
Search in all data
presented

#NETWORK: Users can build mirtrons/target-specific
network choosing specific mirtron.
In “Network” the users can visualize the potential network interaction provided by a
mirtron. The users can select between target gene and ceRNA interactions.
To build a mirtron network interaction the user must first select the organism group.
Then, the organism list will be refreshed. The prediction tool will be filled according
with the organism selected and his analysis result availability. To visualise target
gene interactions the user must select “Target Scan” or “psRNA Target”, for human
and plants, respectively. To visualize mirtrons that potentially acting as ceRNA, the
user must select “TAPIR” as tool in “predicted by” field. The ceRNA network and the
its combination between target gene interactions is available just for plants. A mirtron
name is mandatory to generate the network visualization.

1. Choose an “Organism Group”
2. Choose an “Organism”
3. Choose the “Prediction Tool”:
psRNA Target, Target Scan or TAPIR
4. Choose the “Mirtron Name”
Steps to build network visualization
5. Choose the number of interactions

Tool to navigate in
the visualization.
Data query used.
Network visualization
captions.
The psRNATarget and
TargetScan nodes are clickable.
They are hyperlinked to Ensembl
and mirtronDB details.

#STATISTICS: Users can view the statistics information about the
mirtron data available.
Click in an organism
name and access
mirtron data.

#DOWNLOAD: Users can download all the relevant data freely.
The data are available in FASTA, GFF and TSV format.
Download specific
mirtron FASTA file by
organism.
Download specific
mirtron GFF file by
organism.
Download specific
mirtron tabular file by
organism.
To access JBrowse
data by Organism

#JBROWSE: Users can visualize mirtrons in his genome context.
Link to mirtronDB
details page.

#JBROWSE: Users can visualize mirtrons in his genome context.
You can visualize mirtron details if you right-click it and
choose "Open mirtronDB details"

#SUBMIT: Users can access the guidelines for contribute
with mirtronDB.

How to Use mirtronDB

More Related Content

What's hot (15)

Similar to How to Use mirtronDB (20)

Recently uploaded (20)

How to Use mirtronDB