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Protocols

TransmiR specifications

Information


Unique identifier OMICS_04417
Name TransmiR
Restrictions to use Academic or non-commercial use
Database management system SQLite
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Maintainers


  • person_outline Yuan Zhou
  • person_outline Juan Wang

Publications for TransmiR

TransmiR citations

 (17)
call_split

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma

2018
PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158
call_split See protocol

[…] ribution) and Spearman correlation coefficient was used as correlations measure (threshold <0.05). In addition, prediction of miRNA-transcription factor was also performed based on mirGen v2.0 () and TransmiR () databases. […]

library_books

Unraveling a tumor type specific regulatory core underlying E2F1 mediated epithelial mesenchymal transition to predict receptor protein signatures

2017
Nat Commun
PMCID: 5543083
PMID: 28775339
DOI: 10.1038/s41467-017-00268-2

[…] levant literature. Moreover, we included microRNA-target interactions, which were extracted from the miRTarBase database (release 4.5). Transcription factors of microRNAs have been extracted from the TransmiR database (v1.2). In addition, we searched PubMed for publications about validated E2F transcription factors, their post-translational modifications, molecular interactions, and connections to […]

library_books

Identification of miRNA mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering

2017
Sci Rep
PMCID: 5318911
PMID: 28220871
DOI: 10.1038/srep42809

[…] d 4 miRNAs and 29 mRNAs of the most significant module 3 selected by the RH-SAC algorithm. This initial module/network was further extended by querying the databases miRTarBase, HTRIdb, TRANSFAC, and TransmiR. Following are the main steps of the network extension:Interactions between 33 seeds or the 4 miRNAs or 29 mRNAs were identified using the above mentioned databases. This forms the primary ne […]

library_books

Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms

2016
Sci Rep
PMCID: 5046091
PMID: 27694855
DOI: 10.1038/srep34512

[…] Validated TF-miRNA interactions and their regulation (activation or repression) were exported from the TransmiR database (release 1.2). Predicted TF-miRNA and TF-gene interactions were on the other hand determined by first retrieving the promoter sequences of all previously identified miRNAs and genes. […]

library_books

TGF β1 promotes colorectal cancer immune escape by elevating B7 H3 and B7 H4 via the miR 155/miR 143 axis

2016
Oncotarget
PMCID: 5341868
PMID: 27626488
DOI: 10.18632/oncotarget.11950

[…] sterProfiler package (http://www.bioconductor.org/) with the deregulated miRNAs and their verified targets (obtained from miRTarBase; http://mirtarbase.mbc.nctu.edu.tw/; ) or transcriptional factors (TransmiR; http://cmbi.bjmu.edu.cn/transmir; ). P < 0.05 was set as the threshold. MiRNAs which had the same target genes were considered to be synergistic miRNAs. A miRNA-miRNA functional synergistic […]

library_books

Systematic dissection of dysregulated transcription factor–miRNA feed forward loops across tumor types

2015
Brief Bioinform
PMCID: 5142013
PMID: 26655252
DOI: 10.1093/bib/bbv107

[…] We obtained the experimentally validated TF and miRNA regulations from TRANSFAC [], TarBase [] and TransmiR [] databases. After eliminating all self-loops, we obtained 10 046 regulations of 597 TFs and 498 miRNAs (Supplementary Table S2). The curated TF and miRNA regulatory network was visualized i […]

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TransmiR institution(s)
Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
TransmiR funding source(s)
Supported by the National Natural Science Foundation of China [81473236]; the Special Project on Precision Medicine under the National Key R&D Program [2016YFC0903000]; and the Fundamental Research Funds for Central Universities of China [BMU2017YJ004].

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