| Title: | Predicting Targets for Drosophila Intragenic miRNAs |
|---|---|
| Description: | Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR. |
| Authors: | Surajit Bhattacharya and Daniel Cox |
| Maintainer: | Surajit Bhattacharya <[email protected]> |
| License: | GPL-2 |
| Version: | 1.27.0 |
| Built: | 2024-09-28 02:57:36 UTC |
| Source: | https://github.com/bioc/IntramiRExploreR |
A precomputed dataset containing the targets, scores and other attributes of 83 intragenic microRNAs using Distance Correlation for plaform Affymetrix 1.
Affy1_Distance_FinalAffy1_Distance_Final
A data frame with 53399 rows and 8 variables:
miRNA name, miRNA symbol
Gene name, in Gene Symbol
Gene name, in FlybaseID
Gene name, in CGID
Computed Score, in float
Gene Functions, from Flybase
Experiments, from ArrayExpress
Target Database Name, from TargetDatabases
A precomputed dataset containing the targets, scores and other attributes of 83 intragenic microRNAs using Pearson Correlation for plaform Affymetrix 1.
Affy1_Pearson_FinalAffy1_Pearson_Final
A data frame with 41845 rows and 8 variables:
miRNA name, miRNA symbol
Gene name, in Gene Symbol
Gene name, in FlybaseID
Gene name, in CGID
Computed Score, in float
Gene Functions, from Flybase
Experiments, from ArrayExpress
Target Database Name, from TargetDatabases
A precomputed dataset containing the targets, scores and other attributes of 83 intragenic microRNAs using Distance Correlation for plaform Affymetrix 1.
Affy2_Distance_FinalAffy2_Distance_Final
A data frame with 73374 rows and 8 variables:
miRNA name, miRNA symbol
Gene name, in Gene Symbol
Gene name, in FlybaseID
Gene name, in CGID
Computed Score, in float
Gene Functions, from Flybase
Experiments, from ArrayExpress
Target Database Name, from TargetDatabases
A precomputed dataset containing the targets, scores and other attributes of 83 intragenic microRNAs using Pearson Correlation for plaform Affymetrix 1.
Affy2_Pearson_FinalAffy2_Pearson_Final
A data frame with 52913 rows and 8 variables:
miRNA name, miRNA symbol
Gene name, in Gene Symbol
Gene name, in FlybaseID
Gene name, in CGID
Computed Score, in float
Gene Functions, from Flybase
Experiments, from ArrayExpress
Target Database Name, from TargetDatabases
Extract Host Gene for a given Intragenic miRNA.
extract_HostGene(miRNA)extract_HostGene(miRNA)
miRNA |
A String containing the miRNA name. |
genf, a character string or vector containing Host gene for the Intragenic miRNA.
miRNA="dme-miR-12" extract_HostGene(miRNA)miRNA="dme-miR-12" extract_HostGene(miRNA)
Extract Intragenic miRNA for a given Host gene.
extract_intragenic_miR(gene)extract_intragenic_miR(gene)
gene |
character. Gene Symbol. |
miRf, a character string or vector containing Intragenic miRNA for the Host Gene.
gene="Gmap" extract_intragenic_miR(gene)gene="Gmap" extract_intragenic_miR(gene)
Visualises the targetGene:miRNA network using Cytoscape and igraph .
Gene_Visualisation( mRNA, mRNA_type = c("GeneSymbol", "FBGN", "CGID"), method = c("Pearson", "Distance", "Both"), platform = c("Affy1", "Affy2"), visualisation = c("igraph", "Cytoscape", "text", "console"), path = tempdir(), layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive") )Gene_Visualisation( mRNA, mRNA_type = c("GeneSymbol", "FBGN", "CGID"), method = c("Pearson", "Distance", "Both"), platform = c("Affy1", "Affy2"), visualisation = c("igraph", "Cytoscape", "text", "console"), path = tempdir(), layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive") )
mRNA |
character. gene Identifier. |
mRNA_type |
character. mRNA id type. The choices are 'GeneSymbol','FBID' and 'CGID'. |
method |
character. Statistical Methods. Choices are 'Pearson','Distance','Both' |
platform |
character. Affymetrix Platforms. Choices are 'Affy1','Affy2'. |
visualisation |
character.Visualisation type. Choices are 'igraph','Cytoscape','text'and "console" |
path |
character. Path where data.frame is saved when visualisation is text. Default is tempdir(). |
layout |
character. Network choices. Choices are 'kamadakawai','reingold.tilford','fruchterman.reingold' and 'interactive'. |
Depending upon the ouput choice network image or dataframe containg miRNAs that target the query gene are ouput.
mRNA='Syb' Gene_Visualisation(mRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'), platform=c('Affy1'), visualisation = "console")mRNA='Syb' Gene_Visualisation(mRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'), platform=c('Affy1'), visualisation = "console")
Extracting miRNAs that target a query gene.
genes_Stat( gene, geneIDType = c("GeneSymbol", "FBGN", "CGID"), method = c("Pearson", "Distance", "Both", "BothIntersect"), Platform = c("Affy1", "Affy2"), Text = FALSE, outpath = tempdir() )genes_Stat( gene, geneIDType = c("GeneSymbol", "FBGN", "CGID"), method = c("Pearson", "Distance", "Both", "BothIntersect"), Platform = c("Affy1", "Affy2"), Text = FALSE, outpath = tempdir() )
gene |
character. gene Identifier. |
geneIDType |
character. GeneIDtype choices are 'GeneSymbol', 'FBGN', 'CGID' |
method |
character. Choices are 'Pearson','Distance','Both' and 'BothIntersected' |
Platform |
character. Choices are 'Affy1','Affy2'. |
Text |
logical . To choose between storing the data as text file. Default is FALSE. |
outpath |
character. The path where the data is stored if TEXT=TRUE. Default is |
Outputs the miRNA information, Target Prediction Score, miRNA miRNA function and Target Database that predicts the interaction in a dataframe. Depending upon the ouput choice data is stored in the path specified. Default option prints output to the console.
gene="Syb" genes_Stat(gene,geneIDType="GeneSymbol",method=c("Pearson"), Platform=c("Affy1"),Text=FALSE)gene="Syb" genes_Stat(gene,geneIDType="GeneSymbol",method=c("Pearson"), Platform=c("Affy1"),Text=FALSE)
Gene ontology for Target Genes.
GetGOS_ALL( gene, GO = c("topGO"), term = c("GOTERM_BP_ALL", "GOTERM_MF_ALL", "GOTERM_CC_ALL"), geneIdType = "ALIAS", path = tempdir(), ontology = c("GO_BP", "GO_MF", "GO_CC"), filename )GetGOS_ALL( gene, GO = c("topGO"), term = c("GOTERM_BP_ALL", "GOTERM_MF_ALL", "GOTERM_CC_ALL"), geneIdType = "ALIAS", path = tempdir(), ontology = c("GO_BP", "GO_MF", "GO_CC"), filename )
gene |
List A String or vector containing the Gene names. |
GO |
A String depicting the chosen GO tool. Choice is "topGO" |
term |
A String depicting the chosen term. Choices are "GOTERM_BP_ALL","GOTERM_MF_ALL", "GOTERM_CC_ALL". |
geneIdType |
Type of gene Id given as input. Default "ALIAS" |
path |
String. The path where the data is stored if TEXT=TRUE. |
ontology |
Ontology selection for topGO. Choices are "GO_BP","GO_MF","GO_CC". |
filename |
Name of the file to store Gene Ontology. |
Depending upon the ouput choice data is stored in the path specified. Default option prints output to the console.
## Not run: miR="dme-miR-12" a<-Visualisation(miR,mRNA_type=c("GeneSymbol"),method=c("Both"), platform=c("Affy1"),thresh=100) genes<-a$Target_GeneSymbol GetGOS_ALL(genes,GO=c("topGO"),term=c("GO_BP"),path=tempdir(), filename="test") ## End(Not run)## Not run: miR="dme-miR-12" a<-Visualisation(miR,mRNA_type=c("GeneSymbol"),method=c("Both"), platform=c("Affy1"),thresh=100) genes<-a$Target_GeneSymbol GetGOS_ALL(genes,GO=c("topGO"),term=c("GO_BP"),path=tempdir(), filename="test") ## End(Not run)
Prediction of targets for Drosophila Intragenic microRNAs and Integrated approach using Gene Ontology and Networking tools.
## Not run: gene='Gmap' extract_intragenic_miR(gene) ## End(Not run)## Not run: gene='Gmap' extract_intragenic_miR(gene) ## End(Not run)
A dataset containing the function for the intragenic miRNA.
miRNA_ID_to_FunctionmiRNA_ID_to_Function
A data frame with 66 rows and 4 variables:
miRNA name, miRNA symbol
target gene name, gene symbol
miRNA function, from Flybase
A dataset containing the summary for the intragenic miRNA.
miRNA_summary_DBmiRNA_summary_DB
A data frame with 257 rows and 6 variables:
miRNA name, miRNA symbol
Responsee, in boolean
Responsee, in boolean
miRNA name, miRNA symbol
Type of Hostgene
Comments about the miRNA
Extracting miRNAs that target a query gene.
miRTargets_Stat( miR, method = c("Pearson", "Distance", "Both", "BothIntersect"), Platform = c("Affy1", "Affy2"), outpath = tempdir(), Text = FALSE )miRTargets_Stat( miR, method = c("Pearson", "Distance", "Both", "BothIntersect"), Platform = c("Affy1", "Affy2"), outpath = tempdir(), Text = FALSE )
miR |
character. miRNA symbol. |
method |
character. Choices are "Pearson", "Distance","Both" and "BothIntersected" |
Platform |
character. Choices are "Affy1","Affy2". |
outpath |
character. The path where the data is stored if TEXT=TRUE. Default is tempdir(). |
Text |
logical . To choose between storing the data as text file. Default is FALSE. |
Outputs the target information, Target Prediction Score, miRNA target function and Target Database that predicts the interaction in a dataframe. Depending upon the ouput choice data is stored in the path specified. Default option prints output to the console.
miRNA="dme-miR-12" miRTargets_Stat (miRNA,method=c ("Pearson"),Platform=c ("Affy1"),Text=FALSE)miRNA="dme-miR-12" miRTargets_Stat (miRNA,method=c ("Pearson"),Platform=c ("Affy1"),Text=FALSE)
Visualises the targetGene:miRNA network using Cytoscape and igraph .
Visualisation( miRNA, mRNA_type = c("GeneSymbol", "FBID", "CGID"), method = c("Pearson", "Distance", "Both"), platform = c("Affy1", "Affy2"), thresh = 50, visualisation = c("igraph", "Cytoscape", "Text", "console"), path = tempdir(), layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive") )Visualisation( miRNA, mRNA_type = c("GeneSymbol", "FBID", "CGID"), method = c("Pearson", "Distance", "Both"), platform = c("Affy1", "Affy2"), thresh = 50, visualisation = c("igraph", "Cytoscape", "Text", "console"), path = tempdir(), layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive") )
miRNA |
character. miRNA Identifier. |
mRNA_type |
character. mRNA id type. The choices are 'GeneSymbol','FBID' and 'CGID'. |
method |
character. Statistical Methods. Choices are 'Pearson','Distance','Both' |
platform |
character. Affymetrix Platforms. Choices are 'Affy1','Affy2'. |
thresh |
integar. Threshold depicting number of rows to show. |
visualisation |
character.Visualisation type. Choices are 'igraph','Cytoscape','text' and 'console'. |
path |
character. Path where data.frame is saved when visualisation is text. Default is tempdir(). |
layout |
character. Network choices. Choices are 'kamadakawai','reingold.tilford','fruchterman.reingold' and 'interactive'. |
Depending upon the ouput choice network image or dataframe containg miRNAs that target the query gene are ouput.
miRNA='dme-miR-12' Visualisation(miRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'), platform=c('Affy1'),visualisation=c('igraph'),layout=c('kamadakawai'), path=tempdir())miRNA='dme-miR-12' Visualisation(miRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'), platform=c('Affy1'),visualisation=c('igraph'),layout=c('kamadakawai'), path=tempdir())