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": "2021-12-01T20:12", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/chapter/chapter_57.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 N013f4a4d3b8c467c863b4c3b202bb94f
2 N09c9817a5627443a8927504313bba746
3 N2b6c592dd6a44f7c8c4d6b6f123f545e
4 N2f48592da1084b13bbc40727a02129ed
5 N37ded9cb70f9456cbe3475b03b8f7574
6 N5d2d134ccb2c43abba985240d69824a3
7 N67660f7b9c6e4c4d9607c290e916be9d
8 N6b97192456b548d6aa50b29ca8f0198b
9 N8227410155414a849b698654a147e66f
10 Na5696246fe73408fb9dbb750c15b0ce0
11 Nc75cb7f85ff4400895fa785fbff2584f
12 Nd25ac83ab0a342d59fea504751683ad7
13 Ne618a9226ac9444097c684800fc6e10a
14 anzsrc-for:06
15 anzsrc-for:0604
16 schema:author Na7889418443a46d29602556cede7adfd
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 Ne535a7ef1e554a65b5752610351dd43b
21 schema:genre chapter
22 schema:inLanguage en
23 schema:isAccessibleForFree false
24 schema:isPartOf N3ab37a552a404001b41e94fae64f7575
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 N62e641540118422eac0d74d30a27b26c
87 N9f491ba7e2b742f8bc8bb08dd1e8efed
88 Nbb19c50242cd4b8ca685852cb6dbff69
89 schema:publisher N358cbf3be59f4db1b1e5f8e865bab9fd
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 2021-12-01T20:12
93 schema:sdLicense https://scigraph.springernature.com/explorer/license/
94 schema:sdPublisher N66609b5371c04c4eb9c1eee414877232
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 N013f4a4d3b8c467c863b4c3b202bb94f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Animals
101 rdf:type schema:DefinedTerm
102 N01e5598ccd984921a90e3703f7eeaf09 rdf:first sg:person.01361770421.50
103 rdf:rest rdf:nil
104 N09c9817a5627443a8927504313bba746 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Software
106 rdf:type schema:DefinedTerm
107 N2b6c592dd6a44f7c8c4d6b6f123f545e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name RNA, Messenger
109 rdf:type schema:DefinedTerm
110 N2f48592da1084b13bbc40727a02129ed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Mice
112 rdf:type schema:DefinedTerm
113 N358cbf3be59f4db1b1e5f8e865bab9fd schema:name Springer Nature
114 rdf:type schema:Organisation
115 N37ded9cb70f9456cbe3475b03b8f7574 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Internet
117 rdf:type schema:DefinedTerm
118 N3ab37a552a404001b41e94fae64f7575 schema:isbn 978-1-4939-6864-0
119 978-1-4939-6866-4
120 schema:name MicroRNA Detection and Target Identification
121 rdf:type schema:Book
122 N5d2d134ccb2c43abba985240d69824a3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
123 schema:name MicroRNAs
124 rdf:type schema:DefinedTerm
125 N62e641540118422eac0d74d30a27b26c schema:name dimensions_id
126 schema:value pub.1085056296
127 rdf:type schema:PropertyValue
128 N66609b5371c04c4eb9c1eee414877232 schema:name Springer Nature - SN SciGraph project
129 rdf:type schema:Organization
130 N67660f7b9c6e4c4d9607c290e916be9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Rats
132 rdf:type schema:DefinedTerm
133 N6b97192456b548d6aa50b29ca8f0198b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name Algorithms
135 rdf:type schema:DefinedTerm
136 N8227410155414a849b698654a147e66f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
137 schema:name 3' Untranslated Regions
138 rdf:type schema:DefinedTerm
139 N9f491ba7e2b742f8bc8bb08dd1e8efed schema:name pubmed_id
140 schema:value 28439836
141 rdf:type schema:PropertyValue
142 Na5696246fe73408fb9dbb750c15b0ce0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Databases, Genetic
144 rdf:type schema:DefinedTerm
145 Na7889418443a46d29602556cede7adfd rdf:first sg:person.01345025713.05
146 rdf:rest Nc81b4ccdbde84a5ab9cce5949f3d9659
147 Nae53e2906e7f4b9eb009c010ab5d4584 schema:familyName Dalmay
148 schema:givenName Tamas
149 rdf:type schema:Person
150 Nbb19c50242cd4b8ca685852cb6dbff69 schema:name doi
151 schema:value 10.1007/978-1-4939-6866-4_15
152 rdf:type schema:PropertyValue
153 Nc75cb7f85ff4400895fa785fbff2584f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
154 schema:name Genomics
155 rdf:type schema:DefinedTerm
156 Nc81b4ccdbde84a5ab9cce5949f3d9659 rdf:first sg:person.0700636421.39
157 rdf:rest N01e5598ccd984921a90e3703f7eeaf09
158 Nd25ac83ab0a342d59fea504751683ad7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
159 schema:name Gene Expression Regulation
160 rdf:type schema:DefinedTerm
161 Ne535a7ef1e554a65b5752610351dd43b rdf:first Nae53e2906e7f4b9eb009c010ab5d4584
162 rdf:rest rdf:nil
163 Ne618a9226ac9444097c684800fc6e10a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
164 schema:name Humans
165 rdf:type schema:DefinedTerm
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)


...