MiRcode protocols

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MiRcode specifications

Information


Unique identifier OMICS_06681
Name MiRcode
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Erik Larsson <>

Publication for MiRcode

MiRcode in pipelines

 (4)
2017
PMCID: 5565391
PMID: 28860812
DOI: 10.2147/OTT.S141951

[…] hsa-mir-145, hsa-mir-211, and hsa-mir-1297 were also closely related with these target demrnas. moreover, we found that 16 delncrnas were related with the key demirnas, based on retrieving mircode database (). pvt1, as a key delncrna, had interactive associations with mir-145, mir-211, mir-216a, mir-133a, and mir-133b in this network. the delncrna rp11-496d24.2 interacted with mir-145, […]

2017
PMCID: 5731337
PMID: 29276392
DOI: 10.2147/OTT.S149308

[…] lncrna through mres in the cerna network, and thus, we detected whether key mirnas and the above 723 differently expressed lncrnas have the potential mres based on the information retrieved from the mircode database. the predicted results showed that the key mirnas interacted with 14 delncrnas, which could act as key lncrnas. finally, we obtained 22 hub demrnas mediating with 11 demirnas and 14 […]

2016
PMCID: 5349905
PMID: 27863388
DOI: 10.18632/oncotarget.13363

[…] in our study, noncoding rnas which are not included in the annotation were discarded. venn diagram was generated to discover the delncrnas from dernas., lncrna-mirna interactions were predicted by mircode (http://www.mircode.org/) []. mirna targeted mrnas were retrieved from mirtarbase (http://mirtarbase.mbc.nctu.edu.tw/) [], each mirna-mrna pair was experimentally validated by at least two […]

2015
PMCID: 4619599
PMID: 26492393
DOI: 10.1371/journal.pone.0141042

[…] retained. to improve the data reliability, cancer specific lncrnas have not been annotated by gencode (http://www.gencodegenes.org/) were discarded; (ii) lncrna-mirna interactions were predicted by mircode (http://www.mircode.org/) and starbase v2.0 (http://starbase.sysu.edu.cn/); (iii) mrnas targeted by mirnas with experimental support were retrieved from mirtarbase […]


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MiRcode in publications

 (26)
PMCID: 5937496
PMID: 29760555
DOI: 10.2147/OTT.S158309

[…] to as “demrnas”, “delncrnas”, and “demirnas”, respectively) were screened out between 539 crc samples and 11 normal samples. the interactions between delncrnas and demirnas were predicted by mircode. the demrnas targeted by the demirnas were retrieved according to targetscan, mirtar-base, and mirdb. the lncrna–mirna–mrna cerna network was constructed based on the demirna–delncrna […]

PMCID: 5929565
PMID: 29715309
DOI: 10.1371/journal.pone.0196681

[…] in 2015, wang et al. identified functional rna pairs by computing the pearson correlation coefficients and p-values based on expression profiles []. zhang et al. developed a competing network using mircode, starbase and mirtarbase in hcc, with a focus on the hub nodes of the network []. in 2017, guo et al. assessed the joint predictive power of mirnas and lncrnas using mirna and lncrna […]

PMCID: 5834194
PMID: 29499054
DOI: 10.1371/journal.pone.0193898

[…] muscle protein 22-alpha (sm22α). for normalization, the expression level of glyceraldehyde 3-phosphate dehydrogenase (gadph) was used., in the track data hubs of ucsc genome browser [], we utilized mircode, which is a prediction algorithm of human mirna targets based on gencode annotation including lncrnas []. we intersected the mircode track with lncrna track using table browser, to collect […]

PMCID: 5793195
PMID: 29351231
DOI: 10.3390/genes9010044

[…] network-based identification of cerna (mnicerna) to identify cernas in thyroid carcinoma. mnicerna first constructs micro rna (mirna)–messenger rna (mrna)long non-coding rna (lncrna) networks from mircode database and weighted correlation network analysis (wgcna), based on which to identify key drivers of differentially expressed rnas between normal and tumor samples. it then infers cernas […]

PMCID: 5731337
PMID: 29276392
DOI: 10.2147/OTT.S149308

[…] and 11 normal samples. we used the wgcna and protein–protein interaction (ppi) network to identify hub mrnas from the differentially expressed mrnas (demrnas) profile. the databases, mirtarbase and mircode, were used to screen the key differentially expressed lncrnas (delncrnas) and differentially expressed micro rnas (demirnas), as well as demirnas-demrnas interactions. hereafter, […]


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MiRcode institution(s)
Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

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