micrornas are small endogenous rna molecules that affect many biological processes by regulating gene expression in a post - transcriptional way .
they are 2122  nt in length whose primary role is to regulate gene expression through translational repression and/or mrna degradation ( 1 ) . the first mirna molecules and mirna targets were identified in 1993 via classical genetic techniques in caenorhabditis elegans ( 2 ) . since then , there has been a dramatic increase in the number of mirnas registered in mirbase ( 3 ) . in parallel , the development of the first computational target prediction programs ( 47 ) led to the experimental identification of dozens of mirna targets ( 8) , and emphasized the need to provide mirna target predictions in an efficient way to assist biologists in experimental design .
the previous version of the diana - microt web server ( 9 ) presented extensive information for predicted mirna target gene interactions in a user - friendly interface .
it offers links to nomenclature , sequence and protein databases , information for experimentally verified targets through tarbase ( 8) and targets predicted by pictar ( 6 ) or targetscan ( 10 ) .
also , users are facilitated by being able to search for targeted genes using different names or functional features .
here , we describe an extensive update of this web server with several important improvements : ( i ) an advanced bibliographic analysis which correlates mirnas to diseases , ( ii ) support for two additional species , ( iii ) a graphical display with all relevant functional information from the ucsc genome browser , ( iv ) tracking of changes in mirna nomenclature and ( v ) user personalized sessions allowing personal query history and bookmarks .
diana microt web server provides functional analysis of mirnas that reaches beyond a simple listing of mirna targets through integration of knowledge extracted from bibliography and known biological pathways . in the previous version of the web server ,
bibliographic integration considered automated searches in pubmed providing publications related to a mirna , each target gene or combination of the two .
related diseases has been added that directly associates a mirna to publications connected to one or several diseases .
this feature is based on information included in the title or the abstract of publications found in pubmed .
all abstracts associated with a mirna are retrieved from pubmed , based on the presence of the name of the mirna or a member of its family , as defined by mirbase , in the title or abstract of the publication .
the retrieved publications are associated with medical subject headings ( mesh ) , the national library of medicine 's controlled vocabulary thesaurus , through their metadata .
all disease associated mesh terms for a mirna are counted and visualized through a tag cloud ( figure 1 ) , where mesh terms appear in a size proportional to the number of publications reporting this mirna - disease association .
the mesh terms of the tag cloud also serve as hyperlinks to the relevant publications .
for example , in figure 2 mir-455-star ( mir-455 * ) has been associated with a publication indicating that lower expression of this mirna correlates with poor overall survival in endometrial serous adenocarcinoma ( 11 ) . 

figure 1.an example of a tag cloud for hsa - mir-1 showing relevant disease associated mesh terms . 
 figure 2.example of a diana - microt web server results page .
related diseases tag cloud contains links to pubmed and specifies all papers which associate the particular disease with the corresponding mirna .
pubmed links provides automated bibliography searches based only on the name of mirnas , protein coding genes or the combination of both .
ucsc graphic link presents the predicted binding sites in a ucsc genome browser window along with tracks such as snps and repeat elements .
the left side of the page is devoted to the administration of the user personal space and reports their latest searches and bookmarks .
an example of a tag cloud for hsa - mir-1 showing relevant disease associated mesh terms .
related diseases tag cloud contains links to pubmed and specifies all papers which associate the particular disease with the corresponding mirna .
pubmed links provides automated bibliography searches based only on the name of mirnas , protein coding genes or the combination of both .
ucsc graphic link presents the predicted binding sites in a ucsc genome browser window along with tracks such as snps and repeat elements .
the left side of the page is devoted to the administration of the user personal space and reports their latest searches and bookmarks .
the feature that allowed the user to filter the targets of a mirna based on kegg pathways ( 12 ) is now integrated in the initial input query form .
the user has now the option to enter a mirna together with names of pathways of interest and provided immediately with only the mirna target genes found in the pathways of interest .
for example , a query for hsa - mir-221 would return 113 predicted targets at a score threshold of 0.5 while the combined search of the mirna with the term  mapk - signaling - pathway would filter the results to 21 relevant targets .
in addition , the positions of the binding sites on the mrna of the target gene are graphically presented through the ucsc genome browser .
this automatic upload can be used to provide information in comparison to other tracks of interest such as single nucleotide polymorphisms ( snps ) , repeat elements and alternative 3-utr splice forms .
the relation of mirnas to function and diseases described above is based on mirna nomenclature . since mirna biology is still a field in flux , it can occur that a mirna may change name between two successive versions of mirbase .
due to such changes , researchers may lose track of a mirna full history and related literature searches will remain incomplete . to address this issue , an extended analysis on 13 versions of mirbase ( versions 7.1 . to 14 ) is performed , and the nomenclature history of each mirna is extracted .
this version includes 1884 mature mirnas for the four species supported in the web server .
mimat id and one associated mirna specific name . among versions , changes are found in 77 mimat ids ( 38 in human , 37 in mouse and 2 in drosophila ) and 151 mirna names ( 76 in human , 71 in mouse and 4 in drosophila ) .
this indicates that name changes are more frequent than changes in mimat ids . to keep track of these changes ,
its name was later changed to mmu - mir-455 - 5  p in version 8.2 and later appeared as mmu - mir-455 * in version 10.0 ( figure 3 ) .
this information can be retrieved from the mirna history , but is also used to extend the association of mmu - mir-455 * with endometrial serous adenocarcinoma in the publication where it is referred to as mir-455 - 5  p ( figure 2 ) . 

figure 3.graphic presentation of the changes involved in the history of mirna mmu - mir-455 .
initially , mimat0003485 was presented in version 8.1 as mmu - mir-455 but its name changed consecutively to mmu - mir-455 - 5  p in version 8.2 and mmu - mir-455-star ( mmu - mir-455 * ) in version 10.0 .
similarly , mimat0003742 was first presented in version 8.2 as mmu - mir-455 - 3  p , while in version 10.0 , its sequence changed and it was renamed to mmu - mir-455 .
initially , mimat0003485 was presented in version 8.1 as mmu - mir-455 but its name changed consecutively to mmu - mir-455 - 5  p in version 8.2 and mmu - mir-455-star ( mmu - mir-455 * ) in version 10.0 .
similarly , mimat0003742 was first presented in version 8.2 as mmu - mir-455 - 3  p , while in version 10.0 , its sequence changed and it was renamed to mmu - mir-455 . the first version of diana - microt web server was designed to support the functional analysis of human and mouse mirnas .
now the server has been updated with predictions for two additional species and newer versions of mirbase ( mirbase 13 ) and ensembl ( ensembl 54 ) ( 13 ) . in total predictions for 723 new mirnas
have been added , out of which 147 correspond to drosophila melanogaster , 154 to c. elegans and the rest being new homo sapiens and mus musculus mirnas .
this results in an approximately doubled number of predicted targets in comparison to the previous version , totaling to more than six million predicted target genes .
the web server can support different prediction algorithms and currently provides the targets of an updated version of the previously used algorithm ( 14 ) . while microt - v3.0 is based on features separating real and mock ( shuffled ) mirnas the current version , microt - v4.0 , uses high throughput experimental data for the same purpose ( 15 ) . to allow users to take full advantage of the web server 's functions ,
the most important is an integrated personal user space in which users can easily save important searches and results that they wish to keep for future analysis . in particular
, the system keeps the most recent user searches , giving the opportunity to repeat searches . a bookmarking mechanism provides the opportunity to save interesting results along with user comments .
the personal space provides usage statistics regarding the most recent searches , thus , enabling them to keep track of their latest findings .
it is noted that researchers may use any feature of the web server irrespectively of the personal user space feature .
finally , special attention has been given to the web server documentation introducing hovering help notes for important fields .
diana microt web server provides functional analysis of mirnas that reaches beyond a simple listing of mirna targets through integration of knowledge extracted from bibliography and known biological pathways . in the previous version of the web server ,
bibliographic integration considered automated searches in pubmed providing publications related to a mirna , each target gene or combination of the two .
related diseases has been added that directly associates a mirna to publications connected to one or several diseases .
this feature is based on information included in the title or the abstract of publications found in pubmed .
all abstracts associated with a mirna are retrieved from pubmed , based on the presence of the name of the mirna or a member of its family , as defined by mirbase , in the title or abstract of the publication .
the retrieved publications are associated with medical subject headings ( mesh ) , the national library of medicine 's controlled vocabulary thesaurus , through their metadata .
all disease associated mesh terms for a mirna are counted and visualized through a tag cloud ( figure 1 ) , where mesh terms appear in a size proportional to the number of publications reporting this mirna - disease association .
the mesh terms of the tag cloud also serve as hyperlinks to the relevant publications .
for example , in figure 2 mir-455-star ( mir-455 * ) has been associated with a publication indicating that lower expression of this mirna correlates with poor overall survival in endometrial serous adenocarcinoma ( 11 ) . 

figure 1.an example of a tag cloud for hsa - mir-1 showing relevant disease associated mesh terms . 
 figure 2.example of a diana - microt web server results page .
related diseases tag cloud contains links to pubmed and specifies all papers which associate the particular disease with the corresponding mirna .
pubmed links provides automated bibliography searches based only on the name of mirnas , protein coding genes or the combination of both .
ucsc graphic link presents the predicted binding sites in a ucsc genome browser window along with tracks such as snps and repeat elements .
the left side of the page is devoted to the administration of the user personal space and reports their latest searches and bookmarks .
an example of a tag cloud for hsa - mir-1 showing relevant disease associated mesh terms .
related diseases tag cloud contains links to pubmed and specifies all papers which associate the particular disease with the corresponding mirna .
pubmed links provides automated bibliography searches based only on the name of mirnas , protein coding genes or the combination of both .
ucsc graphic link presents the predicted binding sites in a ucsc genome browser window along with tracks such as snps and repeat elements .
the left side of the page is devoted to the administration of the user personal space and reports their latest searches and bookmarks .
the feature that allowed the user to filter the targets of a mirna based on kegg pathways ( 12 ) is now integrated in the initial input query form .
the user has now the option to enter a mirna together with names of pathways of interest and provided immediately with only the mirna target genes found in the pathways of interest .
for example , a query for hsa - mir-221 would return 113 predicted targets at a score threshold of 0.5 while the combined search of the mirna with the term  mapk - signaling - pathway would filter the results to 21 relevant targets .
in addition , the positions of the binding sites on the mrna of the target gene are graphically presented through the ucsc genome browser .
this automatic upload can be used to provide information in comparison to other tracks of interest such as single nucleotide polymorphisms ( snps ) , repeat elements and alternative 3-utr splice forms .
the relation of mirnas to function and diseases described above is based on mirna nomenclature . since mirna biology is still a field in flux , it can occur that a mirna may change name between two successive versions of mirbase .
due to such changes , researchers may lose track of a mirna full history and related literature searches will remain incomplete . to address this issue , an extended analysis on 13 versions of mirbase ( versions 7.1 . to 14 )
this version includes 1884 mature mirnas for the four species supported in the web server .
mimat id and one associated mirna specific name . among versions , changes are found in 77 mimat ids ( 38 in human , 37 in mouse and 2 in drosophila ) and 151 mirna names ( 76 in human , 71 in mouse and 4 in drosophila ) .
this indicates that name changes are more frequent than changes in mimat ids . to keep track of these changes ,
its name was later changed to mmu - mir-455 - 5  p in version 8.2 and later appeared as mmu - mir-455 * in version 10.0 ( figure 3 ) .
this information can be retrieved from the mirna history , but is also used to extend the association of mmu - mir-455 * with endometrial serous adenocarcinoma in the publication where it is referred to as mir-455 - 5  p ( figure 2 ) . 

figure 3.graphic presentation of the changes involved in the history of mirna mmu - mir-455 .
initially , mimat0003485 was presented in version 8.1 as mmu - mir-455 but its name changed consecutively to mmu - mir-455 - 5  p in version 8.2 and mmu - mir-455-star ( mmu - mir-455 * ) in version 10.0 .
similarly , mimat0003742 was first presented in version 8.2 as mmu - mir-455 - 3  p , while in version 10.0 , its sequence changed and it was renamed to mmu - mir-455 .
initially , mimat0003485 was presented in version 8.1 as mmu - mir-455 but its name changed consecutively to mmu - mir-455 - 5  p in version 8.2 and mmu - mir-455-star ( mmu - mir-455 * ) in version 10.0 .
similarly , mimat0003742 was first presented in version 8.2 as mmu - mir-455 - 3  p , while in version 10.0 , its sequence changed and it was renamed to mmu - mir-455 .
the first version of diana - microt web server was designed to support the functional analysis of human and mouse mirnas .
now the server has been updated with predictions for two additional species and newer versions of mirbase ( mirbase 13 ) and ensembl ( ensembl 54 ) ( 13 ) . in total predictions for 723 new mirnas have been added , out of which 147 correspond to drosophila melanogaster , 154 to c. elegans and the rest being new homo sapiens and mus musculus mirnas .
this results in an approximately doubled number of predicted targets in comparison to the previous version , totaling to more than six million predicted target genes .
the web server can support different prediction algorithms and currently provides the targets of an updated version of the previously used algorithm ( 14 ) .
while microt - v3.0 is based on features separating real and mock ( shuffled ) mirnas the current version , microt - v4.0 , uses high throughput experimental data for the same purpose ( 15 ) .
to allow users to take full advantage of the web server 's functions , several functional improvements have been implemented ( figure 2 ) .
the most important is an integrated personal user space in which users can easily save important searches and results that they wish to keep for future analysis . in particular
, the system keeps the most recent user searches , giving the opportunity to repeat searches . a bookmarking mechanism provides the opportunity to save interesting results along with user comments .
the personal space provides usage statistics regarding the most recent searches , thus , enabling them to keep track of their latest findings .
it is noted that researchers may use any feature of the web server irrespectively of the personal user space feature .
finally , special attention has been given to the web server documentation introducing hovering help notes for important fields .
in recent years it has become apparent that web applications are an essential tool for researchers to decipher complex biological processes . as one of these
, the diana microt web server has been updated to integrate different additional resources in order to offer insight for putative mirna involvement in biological processes , and to allow researchers to supplement their knowledge with already published scientific material . performing an extended analysis on the versioning pattern of mirbase
the history of each mirna has been extracted , offering a unique feature in computational mirna analysis .
we believe that the current web server update provides important tools for biological analysis and improves interaction with the complicated interconnections regarding mirna functionality .
the hellenic republic , general secretariat for research and technology ( 09syn-13 - 1055 ) . funding for open access charge : 09syn-13 - 1055 .
 micrornas ( mirnas ) are small endogenous rna molecules that are implicated in many biological processes through post - transcriptional regulation of gene expression . 
 the diana - microt web server provides a user - friendly interface for comprehensive computational analysis of mirna targets in human and mouse . 
 the server has now been extended to support predictions for two widely studied species : drosophila melanogaster and caenorhabditis elegans . in the updated version , 
 the web server enables the association of mirnas to diseases through bibliographic analysis and provides insights for the potential involvement of mirnas in biological processes . 
 the nomenclature used to describe mature mirnas along different mirbase versions has been extensively analyzed , and the naming history of each mirna has been extracted . 
 this enables the identification of mirna publications regardless of possible nomenclature changes . 
 user interaction has been further refined allowing users to save results that they wish to analyze further . 
 a connection to the ucsc genome browser is now provided , enabling users to easily preview predicted binding sites in comparison to a wide array of genomic tracks , such as single nucleotide polymorphisms . 
 the web server is publicly accessible in www.microrna.gr/microt-v4 . 
INTRODUCTION
METHODS AND RESULTS
Relation of miRNAs to functional features, diseases and medical descriptors
Extraction of miRNA history from miRBase
Target prediction and supported miRNAs
Personalized user sessions
CONCLUSION
FUNDING