RPISeq protocols

View RPISeq computational protocol

RPISeq statistics

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RPISeq specifications

Information


Unique identifier OMICS_08899
Name RPISeq
Interface Web user interface
Restrictions to use None
Input data Protein sequence, RNA sequence
Input format Raw
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Usha K. Muppirala <>

Publication for RPISeq

RPISeq in pipeline

2017
PMCID: 5647044
PMID: 28849135
DOI: 10.3892/mmr.2017.7304

[…] cytoscape software (version 3.0; http://www.cytoscape.org/download.php)., in order to investigate the association between clinical pathological features and lncrnas, computer analysis based on the rpiseq rna-protein interaction prediction program (pridb.gdcb.iastate.edu/rpiseq), which uses random forest (rf) and support vector machine (svm) classifiers to predict the association […]


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RPISeq in publications

 (27)
PMCID: 5896100
PMID: 29642935
DOI: 10.1186/s13046-018-0747-x

[…] and post-transcriptional levels. afterwards, the binding probabilities between spry4-it1 and rna binding proteins were analyzed by rna-protein interaction prediction (http://pridb.gdcb.iastate.edu/rpiseq/). the data showed that spry4-it1 potentially binds ezh2, suz12, lsd1, dnmt1, corest, sirt1, stau1 and tdp43 (with rf and svm scores > 0.5, additional file : figure s2a). rip assays […]

PMCID: 5843596
PMID: 29520069
DOI: 10.1038/s41467-018-03394-7

[…] (fig. ). conversely, both brg1 and hdac9 are captured in vsmc lysates through the use of malat1 antisense probes, but not with a control (lacz) probe (fig. ). rna-protein interactions prediction (rpiseq) confirmed hdac9 and brg1 as highest scoring proteins interacting with malat1 within hdac9 gene association network identified above (supplementary fig. , supplementary data ).fig. 3, we next […]

PMCID: 5822613
PMID: 29466992
DOI: 10.1186/s12943-018-0813-1

[…] not alter the levels of shp-1 in human hcc cells (additional file : figure s6b and c), suggesting that hnf1α or hnf1a-as1 could not regulate the expression of shp-1., interestingly, the prediction by rpiseq [] (http://pridb.gdcb.iastate.edu/rpiseq/), a database of rna-protein interactions, suggested a potential interaction of hnf1a-as1 with the shp-1 protein with high binding affinity (rf = 0.7/sv […]

PMCID: 5833400
PMID: 29445134
DOI: 10.1038/s41419-018-0275-9

[…] levels. relative expression was calculated using the formula of log 10 (2−δδct). the primer sequences are listed in the supplementary file (table )., the rna-protein interaction prediction (rpiseq) methodology established by the dobbs and honavar laboratories, iowa state university, was used to predict the rnabinding protein that could bind to foxd2-as1. the website […]

PMCID: 5787324
PMID: 29374493
DOI: 10.1186/s13046-018-0684-8

[…] in nucleus is more higher (fig. ). furthermore, we predicted the interaction probabilities of duxap10 and rna binding protein via rna-protein interaction prediction (http://pridb.gdcb.iastate.edu/rpiseq/), and the results showed that duxap10 may potentially bind with prc2, lsd1, wdr, dnmt1, hur, ago2 and stau1 (as the rf or svm score > 0.5, fig. ). additionally, rip assays determined […]


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RPISeq institution(s)
Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Department of Computer Science, Iowa State University, Ames, IA, USA

RPISeq review

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shradha suyal's avatar image No country

shradha suyal

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Web
I had used this server http://pridb.gdcb.iastate.edu/RPISeq/ for my study. but it is no longer available.