Prediction of miRNA–mRNA Interactions Using miRGate View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2017-04-25

AUTHORS

Eduardo Andrés-León , Gonzalo Gómez-López , David G. Pisano

ABSTRACT

miRGate (http://mirgate.bioinfo.cnio.es/) is a freely available database that contains predicted and experimentally validated microRNA–messenger RNA (miRNA–mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3′-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus.The approach intends to circumvent one of the main drawbacks in this area, as diverse sequences and gene database versions cause poor overlap among different target prediction methods even with experimentally confirmed targets. As a result, miRGate predictions have been successfully validated using functional assays in several laboratories.This chapter describes how a user can access target information via miRGate’s web interface. It also shows how automatically access the database through the programmatic interface based on representational state transfer services (REST), using the application programming interface (API) available at http://mirgate.bioinfo.cnio.es/API. More... »

PAGES

225-237

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-6866-4_15

DOI

http://dx.doi.org/10.1007/978-1-4939-6866-4_15

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1085056296

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28439836


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "3' Untranslated Regions", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Internet", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "MicroRNAs", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Messenger", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Rats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Bioinformatics Unit, Instituto de Parasitolog\u00eda y Biomedicina \u201cL\u00f3pez Neyra\u201d, Consejo Superior de Investigaciones Cient\u00edficas (IPBLN-CSIC), PTS Granada, 18016, Granada, Spain", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Bioinformatics Unit, Instituto de Parasitolog\u00eda y Biomedicina \u201cL\u00f3pez Neyra\u201d, Consejo Superior de Investigaciones Cient\u00edficas (IPBLN-CSIC), PTS Granada, 18016, Granada, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Andr\u00e9s-Le\u00f3n", 
        "givenName": "Eduardo", 
        "id": "sg:person.01345025713.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345025713.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain", 
          "id": "http://www.grid.ac/institutes/grid.7719.8", 
          "name": [
            "Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "G\u00f3mez-L\u00f3pez", 
        "givenName": "Gonzalo", 
        "id": "sg:person.0700636421.39", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700636421.39"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain", 
          "id": "http://www.grid.ac/institutes/grid.7719.8", 
          "name": [
            "Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pisano", 
        "givenName": "David G.", 
        "id": "sg:person.01361770421.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361770421.50"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2017-04-25", 
    "datePublishedReg": "2017-04-25", 
    "description": "AbstractmiRGate (http://mirgate.bioinfo.cnio.es/) is a freely available database that contains predicted and experimentally validated microRNA\u2013messenger RNA (miRNA\u2013mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3\u2032-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus.The approach intends to circumvent one of the main drawbacks in this area, as diverse sequences and gene database versions cause poor overlap among different target prediction methods even with experimentally confirmed targets. As a result, miRGate predictions have been successfully validated using functional assays in several laboratories.This chapter describes how a user can access target information via miRGate\u2019s web interface. It also shows how automatically access the database through the programmatic interface based on representational state transfer services (REST), using the application programming interface (API) available at http://mirgate.bioinfo.cnio.es/API.", 
    "editor": [
      {
        "familyName": "Dalmay", 
        "givenName": "Tamas", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-4939-6866-4_15", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-4939-6864-0", 
        "978-1-4939-6866-4"
      ], 
      "name": "MicroRNA Detection and Target Identification", 
      "type": "Book"
    }, 
    "keywords": [
      "application programming interface", 
      "Representational State Transfer (REST) services", 
      "web interface", 
      "programming interface", 
      "programmatic interface", 
      "transfer service", 
      "database version", 
      "target prediction methods", 
      "target information", 
      "available databases", 
      "sequence datasets", 
      "main drawback", 
      "prediction method", 
      "interface", 
      "database", 
      "users", 
      "algorithm", 
      "datasets", 
      "miRNA-mRNA interactions", 
      "services", 
      "drawbacks", 
      "information", 
      "prediction", 
      "resources", 
      "miRNA sequences", 
      "Kaposi's sarcoma-associated herpes virus", 
      "diverse sequences", 
      "version", 
      "sequence", 
      "genome", 
      "functional assays", 
      "genes", 
      "target pairs", 
      "novel predictions", 
      "method", 
      "virus", 
      "results", 
      "chapter", 
      "pairs", 
      "area", 
      "assays", 
      "humans", 
      "herpes virus", 
      "target", 
      "interaction", 
      "Epstein-Barr", 
      "laboratory", 
      "approach", 
      "AbstractmiRGate", 
      "microRNA\u2013messenger RNA (miRNA\u2013mRNA) target pairs", 
      "RNA (miRNA\u2013mRNA) target pairs", 
      "comprehensive sequence dataset", 
      "miRNA viruses", 
      "sarcoma-associated herpes virus", 
      "gene database versions", 
      "different target prediction methods", 
      "miRGate predictions", 
      "miRGate\u2019s web interface", 
      "state transfer services"
    ], 
    "name": "Prediction of miRNA\u2013mRNA Interactions Using miRGate", 
    "pagination": "225-237", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1085056296"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-4939-6866-4_15"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "28439836"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-4939-6866-4_15", 
      "https://app.dimensions.ai/details/publication/pub.1085056296"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2022-01-01T19:18", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/chapter/chapter_326.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/978-1-4939-6866-4_15"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-6866-4_15'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-6866-4_15'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-6866-4_15'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-6866-4_15'


 

This table displays all metadata directly associated to this object as RDF triples.

192 TRIPLES      23 PREDICATES      97 URIs      90 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-4939-6866-4_15 schema:about N041e4f832de64d8f9d45dea41bb7e826
2 N07445fc10f6a4d6ea5dcac91e62b38f9
3 N57e65ba30ae3416db457ff0c9761c34b
4 N5f85015ce6224f1fb37e33286a3e8c77
5 N624dbe1d44ea42f5a96c6f32a24549bd
6 N68dbd69359924de9a901e5a31c9deb83
7 N71bc9601911c4c048149db1dd7c485ff
8 N7cda1ff4be634611b8e3ad98a6e75185
9 Na4ab4e0183634b1f949a785ab59bffde
10 Nbb900b0b52a247e299b9e57c1eab1dc5
11 Ndc85e4442d9044bdb537bb684188e74d
12 Ne44b70765e574a10ad2acd8816b7a1b6
13 Ne526fe0a4b8a494bb361f1d4d2e7ec84
14 anzsrc-for:06
15 anzsrc-for:0604
16 schema:author Ne9402b5afd404712a3e5869d3bfa790f
17 schema:datePublished 2017-04-25
18 schema:datePublishedReg 2017-04-25
19 schema:description AbstractmiRGate (http://mirgate.bioinfo.cnio.es/) is a freely available database that contains predicted and experimentally validated microRNA–messenger RNA (miRNA–mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3′-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus.The approach intends to circumvent one of the main drawbacks in this area, as diverse sequences and gene database versions cause poor overlap among different target prediction methods even with experimentally confirmed targets. As a result, miRGate predictions have been successfully validated using functional assays in several laboratories.This chapter describes how a user can access target information via miRGate’s web interface. It also shows how automatically access the database through the programmatic interface based on representational state transfer services (REST), using the application programming interface (API) available at http://mirgate.bioinfo.cnio.es/API.
20 schema:editor N76011b542c4f48789925fa432f0b0bed
21 schema:genre chapter
22 schema:inLanguage en
23 schema:isAccessibleForFree false
24 schema:isPartOf N94bf121be2c64259b1c3c192c3d4ac69
25 schema:keywords AbstractmiRGate
26 Epstein-Barr
27 Kaposi's sarcoma-associated herpes virus
28 RNA (miRNA–mRNA) target pairs
29 Representational State Transfer (REST) services
30 algorithm
31 application programming interface
32 approach
33 area
34 assays
35 available databases
36 chapter
37 comprehensive sequence dataset
38 database
39 database version
40 datasets
41 different target prediction methods
42 diverse sequences
43 drawbacks
44 functional assays
45 gene database versions
46 genes
47 genome
48 herpes virus
49 humans
50 information
51 interaction
52 interface
53 laboratory
54 main drawback
55 method
56 miRGate predictions
57 miRGate’s web interface
58 miRNA sequences
59 miRNA viruses
60 miRNA-mRNA interactions
61 microRNA–messenger RNA (miRNA–mRNA) target pairs
62 novel predictions
63 pairs
64 prediction
65 prediction method
66 programmatic interface
67 programming interface
68 resources
69 results
70 sarcoma-associated herpes virus
71 sequence
72 sequence datasets
73 services
74 state transfer services
75 target
76 target information
77 target pairs
78 target prediction methods
79 transfer service
80 users
81 version
82 virus
83 web interface
84 schema:name Prediction of miRNA–mRNA Interactions Using miRGate
85 schema:pagination 225-237
86 schema:productId N3d7485a545674814be177c35e326f250
87 N5bb07554220f4c25bac03a37752e0ec6
88 Nb070d7f87bc24963b9ddec24976a1a4d
89 schema:publisher N90b49dcdaae94651a7feee70f8d74cb0
90 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085056296
91 https://doi.org/10.1007/978-1-4939-6866-4_15
92 schema:sdDatePublished 2022-01-01T19:18
93 schema:sdLicense https://scigraph.springernature.com/explorer/license/
94 schema:sdPublisher N400a77d9c317465e97248a42c89c81f6
95 schema:url https://doi.org/10.1007/978-1-4939-6866-4_15
96 sgo:license sg:explorer/license/
97 sgo:sdDataset chapters
98 rdf:type schema:Chapter
99 N041e4f832de64d8f9d45dea41bb7e826 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name RNA, Messenger
101 rdf:type schema:DefinedTerm
102 N07445fc10f6a4d6ea5dcac91e62b38f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
103 schema:name Mice
104 rdf:type schema:DefinedTerm
105 N29adad87048140b6ab547fabb4d912de schema:familyName Dalmay
106 schema:givenName Tamas
107 rdf:type schema:Person
108 N3d7485a545674814be177c35e326f250 schema:name dimensions_id
109 schema:value pub.1085056296
110 rdf:type schema:PropertyValue
111 N400a77d9c317465e97248a42c89c81f6 schema:name Springer Nature - SN SciGraph project
112 rdf:type schema:Organization
113 N57e65ba30ae3416db457ff0c9761c34b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name Internet
115 rdf:type schema:DefinedTerm
116 N5bb07554220f4c25bac03a37752e0ec6 schema:name pubmed_id
117 schema:value 28439836
118 rdf:type schema:PropertyValue
119 N5f85015ce6224f1fb37e33286a3e8c77 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Humans
121 rdf:type schema:DefinedTerm
122 N624dbe1d44ea42f5a96c6f32a24549bd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name Gene Expression Regulation
124 rdf:type schema:DefinedTerm
125 N68dbd69359924de9a901e5a31c9deb83 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name Software
127 rdf:type schema:DefinedTerm
128 N71bc9601911c4c048149db1dd7c485ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Genomics
130 rdf:type schema:DefinedTerm
131 N76011b542c4f48789925fa432f0b0bed rdf:first N29adad87048140b6ab547fabb4d912de
132 rdf:rest rdf:nil
133 N76e0400288494e70a0ab3e995d890e35 rdf:first sg:person.0700636421.39
134 rdf:rest N7fb583a623a146ca8bf89b222eb7216d
135 N7cda1ff4be634611b8e3ad98a6e75185 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Algorithms
137 rdf:type schema:DefinedTerm
138 N7fb583a623a146ca8bf89b222eb7216d rdf:first sg:person.01361770421.50
139 rdf:rest rdf:nil
140 N90b49dcdaae94651a7feee70f8d74cb0 schema:name Springer Nature
141 rdf:type schema:Organisation
142 N94bf121be2c64259b1c3c192c3d4ac69 schema:isbn 978-1-4939-6864-0
143 978-1-4939-6866-4
144 schema:name MicroRNA Detection and Target Identification
145 rdf:type schema:Book
146 Na4ab4e0183634b1f949a785ab59bffde schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
147 schema:name MicroRNAs
148 rdf:type schema:DefinedTerm
149 Nb070d7f87bc24963b9ddec24976a1a4d schema:name doi
150 schema:value 10.1007/978-1-4939-6866-4_15
151 rdf:type schema:PropertyValue
152 Nbb900b0b52a247e299b9e57c1eab1dc5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
153 schema:name Databases, Genetic
154 rdf:type schema:DefinedTerm
155 Ndc85e4442d9044bdb537bb684188e74d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
156 schema:name Animals
157 rdf:type schema:DefinedTerm
158 Ne44b70765e574a10ad2acd8816b7a1b6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
159 schema:name Rats
160 rdf:type schema:DefinedTerm
161 Ne526fe0a4b8a494bb361f1d4d2e7ec84 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
162 schema:name 3' Untranslated Regions
163 rdf:type schema:DefinedTerm
164 Ne9402b5afd404712a3e5869d3bfa790f rdf:first sg:person.01345025713.05
165 rdf:rest N76e0400288494e70a0ab3e995d890e35
166 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
167 schema:name Biological Sciences
168 rdf:type schema:DefinedTerm
169 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
170 schema:name Genetics
171 rdf:type schema:DefinedTerm
172 sg:person.01345025713.05 schema:affiliation grid-institutes:None
173 schema:familyName Andrés-León
174 schema:givenName Eduardo
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345025713.05
176 rdf:type schema:Person
177 sg:person.01361770421.50 schema:affiliation grid-institutes:grid.7719.8
178 schema:familyName Pisano
179 schema:givenName David G.
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01361770421.50
181 rdf:type schema:Person
182 sg:person.0700636421.39 schema:affiliation grid-institutes:grid.7719.8
183 schema:familyName Gómez-López
184 schema:givenName Gonzalo
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700636421.39
186 rdf:type schema:Person
187 grid-institutes:None schema:alternateName Bioinformatics Unit, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, 18016, Granada, Spain
188 schema:name Bioinformatics Unit, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS Granada, 18016, Granada, Spain
189 rdf:type schema:Organization
190 grid-institutes:grid.7719.8 schema:alternateName Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
191 schema:name Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
192 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...