Data Download
The download page allows users to download the various RNA modification data stored in RMBase v3.0. And there are detailed descriptions to help users make better use of the downloaded data.
To download various RNA modification data, users could click the green "Download xxx" button to show the filter fields, then look in the drop-down list for the genomes, modification type, enzyme and other items that you require. The download will begin after you click the navy blue 'Download' button.
RNA Modifications
A tab separated table of various of RNA modification sites of 62 species. The named format of downloaded file is "genome.modType.tar.gz", like "hg38.m6A.tar.gz". The "modID" of 4th column is unique in all files stored in RMBase v3.0. The modID in any file you downloaded from other section can be searched for details in files downloaded from this section.
File Description 
Column Number: Label -> Header Details
[ For all species: ]
1: Chrom -> Chromosome.
2: Start -> The starting coordinate.
3: End -> The end coordinate.
4: modID -> Unique ID identification.
5: Score -> Score.
6: Strand -> The direction of the strand containing this RNA modification site.
7: modType -> The RNA modification type of this site.
8: supportNum -> The number of datasets from which identified this RNA modification site.
9: supportList -> The list of merged-datasets from which identified this RNA modification site.
10: supportListSub -> The list of datasets from which identified this RNA modification site.
11: pubList -> The list of pubmeds coorespond to above-mentioned datasets.
12: cellList -> The list of cells or tissues in which this RNA modification is identified.
13: seqTypeList -> The list of type of sequencing data of datasets.
14: geneID -> The list of gene that the RNA modification site reside in.
15: transcriptID -> The list of transcript that the RNA modification site reside in.
16: geneName -> Gene name corresponding to the gene ID.
17: geneType -> Gene biotype on which the RNA modification site distribute.
18: Region -> Gene feature on which the RNA modification site distribute.
19: Seq -> The sequence is 41-nt long that was extended by an additional 20 nt in both the 5′- and 3′-directions for the modification site.
[ For Homo sapiens, Mus musculus, Rattus norvegicus, Pan Troglodytes, Macaca Mulatta, Sus Scrofa, Saccharomyces cerevisiae, Danio Rerio, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster: ]
20: motifScore -> The 'Motif score' is alignment score to evaluate the accuracy of identified motif regions of m6A. The higher of motif score means a more accurate motif and a more reliable modification site. The range is from 0 to 5.
21: conservedSitesList -> The list of sites that are conserved with this RNA modification site in other species.
22: snoRNA_detailInfo -> Details of snoRNA that guide RNA modifications, eg. "U2:25|G|SCARNA2|C/D|snOPY" represents "snoRNA_guideSite", the base of this site, snoRNA name, snoRNA type and source of snoRNA.
23: snoRNA_guideSite -> The position of the RNA modification site guided by snoRNAs on RNA, eg. "U2:25" means that this RNA modification site is in he 25th position of U2.
24: snoRNA_nameList -> The list of snoRNAs that guide this RNA modification site.
25: snoRNA_dataBase -> The source of information of this modification site guided by snoRNAs.
[ For Homo sapiens: ]
26: writerLoc -> The genome coordinate of writer binding site. There may be multiple semicolon-separated values that correpond to the informations separated by semicolon in the 27-29 columns.
27: writerID -> The list of writer ID that is unique ID.
28: writerNameList -> The name of writers that catalyze this RNA modification site.
29: source -> The source ID (sample) of writer.
Mechanisms
A tab separated table of mechanism data that list various of RNA modification sites that guided by snoRNAs and/or enzyme of 7 species, that are Homo sapiens, Mus musculus, Danio rerio, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Saccharomyces cerevisiae. The compressed file contains a summary file wirh 8 column and a detailed list file in the same format as the RNA Modifications file. The named format of files about snoRNAs is "genome.modSite.guideBySnoRNA.tar.gz", and the files about enzyme if "genome.enzyme.guide.modSite.tar.gz". The modID (eg. m6A_site_66 of m6aList) in the downloaded file corresponds the "modID" (4th column) of the RNA Modifications file. If you are interested in details of the specific modification site (eg. m6A_site_66), it is necessary to download coresponding file in RNA Modifications module and query this site in the downloaded file.
File Description
Column Number: Label -> Header Details
[ 1. For RNA Modifications guided by Enzymes: ]
1: Enzyme -> Enzyme name.
2: EnzymeLoc -> The genome coordinate of enzyme binding site.
3: EnzymeID -> Unique ID identification.
4: Source -> The source ID of Enzyme.
5: modType -> The type of RNA modification guided by this enzyme, like m6A, 2'-O-Me.
6: modType-Sub -> The sub-type of RNA modification guided by this enzyme, like Am and Gm that are subsets of 2'-O-Me.
7: modSiteNum -> The number of RNA modification sites guided by this enzyme.
8: modSiteList -> The list of RNA modification sites guided by this enzyme.
[ 2. For RNA Modifications guided by snoRNAs: ]
1: snoName -> snoRNA name.
2: snoSite -> The RNA type and site guided by snoRNA.
3: snoBase -> The base of site guided by snoRNA.
4: snoBox/snoType -> The type of snoRNA, like C/D box, H/ACA box.
5: snoSource -> The source of information of the site guided by the snoRNA.
6: modType -> The type of RNA modification site guided by the snoRNA.
7: modNum -> The number of RNA modification sites guided by the snoRNA.
8: modList -> The ID list of RNA modification sites guided by the snoRNA. The ID is unique and corresponds to the "modID" in the RNA Modifications Data.
modGene
A tab separated table of various of RNA modification sites on each gene of 62 species. "Gene Case" presents all RNA modifications distributed on each gene, while "Transcript Case" presents all RNA modifications on each transcript. The named format of file is "genes/trans.genome.tar.gz". The "modID" (eg. m6A_site_23) of modList (eg. m6aList) in the file downloaded form modGene corresponds the "modID" (4th column) of the RNA Modifications file. If you are interested in details of the specific modification site (eg. m6A_site_23), it is necessary to download coresponding file in RNA Modifications module and query this site in the downloaded file.
File Description
Column Number: Label -> Header Details
[ 1. For RNA Modifications on Genes: ]
[ For file about Gene Case (1-3th): ]
1: geneID -> Gene ID.
2: geneName -> Gene name.
3: transID -> Transcript ID.
[ For file about Transcript Case (1-3th): ]
1: transID -> Transcript ID.
2: geneID -> Gene ID.
3: geneName -> Gene name.
[ For files about both Gene Case and Transcript Case: ]
4: geneType -> Gene biotype.
5: region -> Gene feature.
6: m6aNum -> The number of m6A sites located in this gene.
7: m6aList -> The list of m6A sites located in this gene.
8: m1aNum -> The number of m1A sites located in this gene.
9: m1aList -> The list of m1A sites located in this gene.
10: m5cNum -> The number of m5C sites located in this gene.
11: m5cList -> The list of m5C sites located in this gene.
12: m7gNum -> The number of m7G sites located in this gene.
13: m7gList -> The list of m7G sites located in this gene.
14: pseudoNum -> The number of Pseudo sites located in this gene.
15: pseudoList -> The list of Pseudo sites located in this gene.
16: nmNum -> The number of Nm sites located in this gene.
17: nmList -> The list of Nm sites located in this gene.
18: editingNum -> The number of RNA-editing sites located in this gene.
19: editingList -> The list of RNA-editing sites located in this gene.
20: otherNum -> The number of other type of RNA modification sites located in this gene.
21: otherList -> The list of other type of RNA modification sites located in this gene.
22: totalNum -> The total of all RNA modifications sites located in this gene.
[ 2. For RNA Modifications on Clusters Derived from Genes: ]
[ For Human and Mouse: ]
1: geneID -> The ID of gene in which the cluster locate.
1: geneName -> The name of gene in which the cluster locate.
1: geneType -> The type of gene in which the cluster locate.
1: geneClass -> The class of gene in which the cluster locate.
1: clusterChr -> Chromosome of the cluster.
1: clusterStart -> Start of genomic coordinate of the cluster.
1: clusterEnd -> End of genomic coordinate of the cluster.
1: clusterStrand -> Strand of the cluster.
1: Distance -> The region of the cluster, that is the distance from the start to the end.
1: NumberOfModSite -> The Number of RNA modification sites within the cluster.
1: Density -> Average distance between RNA modification sites within the cluster.
[ For Human (12-20th): ]
12: NumberOfWriter -> Number of writers related to the cluster.
13: ListOfWriter -> List of writers related to the cluster.
14: NumberOfPeak -> Number of writer peaks overlapped with the cluster.
15: NumberOfReader -> Number of readers related to the cluster.
16: ListOfReader -> List of readers related to the cluster.
17: NumberOfBindingSite -> Number of binding sites of readers overlapped with the cluster.
18: Gene_Description -> The description of gene.
19: GO -> Gene Ontology of the gene.
20: Protein_Function -> The biological function of gene.
[ For Mouse (12-14th): ]
12: Gene_Description -> The description of gene.
13: GO -> Gene Ontology of the gene.
14: Protein_Function -> The biological function of gene.
RNA Modifications related to RBPs
A tab separated table of various of RNA modification sites related to RBP (the RNA modification site is located in RBP binding site) of 6 species, that are Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. The named format of file is "genome.rbpType.tar.gz". The modID (like "m6A_site_586230") of the column named "RNAmodID" in the mod-RBP file corresponds the "modID" (4th column) of the RNA Modifications file. If you are interested in details of the specific modification site (eg. m6A_site_586230), it is necessary to download coresponding file in RNA Modifications module and query this site in the downloaded file.
File Description
Column Number: Label -> Header Details
[ For all species: ]
1: rbpSiteID -> Unique ID identification of modRBP.
2: rbpName -> RBP (RNA Binding Protein) name.
3: narrowPeak -> Narrow peak of RBP binding site.
4: broadPeak -> Broad peak of RBP binding site.
5: rbpRand -> Unique ID identification of RBP.
6: clipExpNum -> The number of supporting CLIP experiments or studies of the RBP binding region that the modification site reside in.
7: dataSetIdList -> The list of supporting CLIP experiments or studies of the RBP binding region that the modification site reside in.
8: RNAmodID -> The unique ID of RNA modification site related to RBP.
9: RNAmodLoc -> The genome coordinate of RNA modifications corresponds to ID list in 8th column.
10: RNAmodType -> The type of RNA modification site related to RBP.
11: geneID -> The list of gene that the RNA modification site reside in.
12: transcriptID -> The list of transcript that the RNA modification site reside in.
13: geneName -> Gene name corresponding to the gene ID.
14: geneType -> Gene biotype on which the RNA modification site distribute.
15: Region -> Gene feature on which the RNA modification site distribute.
16: Conservation -> The list of sites that are conserved with the RNA modification site related to RBP in other species.
17: rbpType -> RBP type like "writer", "reader", "eraser" and/or other type.
RNA Modifications related to miRNA Targets
A tab separated table of various of RNA modification sites related to miRNA target (the RNA modification site is located in miRNA target) among Homo sapiens and Mus musculus. The named format of file is "genome.mirTarget.tar.gz". The compressed file contains two files, that are mod-mirTar file and miRNA-target align file respectively. The modID (like "m6A_site_185574") of the column named "RNAmodList" in the mod-mirTar file corresponds the "modID" (4th column) of the RNA Modifications file. If you are interested in details of the specific modification site (eg. m6A_site_185574), it is necessary to download coresponding file in RNA Modifications module and query this site in the downloaded file.
File Description
Column Number: Label -> Header Details
[ For mod-mirTar file: It present the information about miRNA and its targets prediceted by several softwares, as well as RNA modifications related it. ]
1: mirTarRand -> The clusterID, a unique ID to identification, that corresponds to the first column of miRNA-target align file.
2: miRNAID -> miRNA ID.
3: mirRNAName -> miRNA name.
4: mirTarChr -> The chromosome of miRNA target.
5: mirTarStart -> The start of miRNA target.
6: mirTarEnd -> The end of miRNA target.
7: mirTarStrand -> The strand the miRNA target.
8: predictIdNum -> The number of software that predicted target RNA of the miRNAs.
9: PITAID -> The unique ID of target RNA predicted by PITAID.
10: PicTarID -> The unique ID of target RNA predicted by PicTarID.
11: RNA22ID -> The unique ID of target RNA predicted by RNA22ID.
12: TargetScanID -> The unique ID of target RNA predicted by TargetScanID.
13: miRandaID -> The unique ID of target RNA predicted by miRandaID.
14: miRmapID -> The unique ID of target RNA predicted by miRmapID.
15: microTID -> The unique ID of target RNA predicted by microTID.
16: RNAmodSiteNum -> The number of RNA modification sites reside in the target RNA of the miRNA.
17: RNAmodList -> The list of unique ID of RNA modification sites reside in the target RNA of the miRNAs. The ID corresponds to "modID" of RNA Modifications Data.
18: RNAmodLoc -> The genome coordinate of RNA modifications corresponds to ID list in column 17.
[ For miRNA-target align file: It presents alignment information about miRNA and its targets. ]
1: bindID -> The clusterID, a unique ID to identification, that corresponds to the first column of mod-mirTar file.
2: miRNAseq -> The sequence of miRNA.
3: align -> The alignment information between miRNA and its targets.
4: targetSeq -> The sequence of target RNA of miRNA.
RNA Modifications related to Var
A tab separated table of various of RNA modification sites related to SNP and SNV of Homo sapiens. You can directly click the targeted button to download the corrsponding file. The named format of file is "genome.varType.tar.gz". The modID (like "m1A_site_124") of the column named "modID" in the mod-snp file corresponds the "modID" (4th column) of the RNA Modifications file. If you are interested in details of the specific modification site (eg. m1A_site_124), it is necessary to download coresponding file in RNA Modifications module and query this site in the downloaded file.
File Description
Column Number: Label -> Header Details
[ 1. For SNP file: ]
1: snpID -> The unique ID of modSNP to identificate.
2: snpChr -> The chromosome of SNP site.
3: snpStart -> The start of SNP site.
4: snpEnd -> The end of SNP site.
5: rsID -> The SNP ID (rsID).
6: snpScore -> Score.
7: snpStrand -> The strand of SNP.
8: refBase -> The reference base on the pre-mutant transcript.
9: altBase -> The mutant base.
10: snpSource -> The source of the SNP site.
11: snpShift -> The offset of SNP loci relative to the modification site. The range is from -10 to 10, the positive number means the SNP site appears in the downstream of RNA modification site and the negative means upstream.
12: modID -> The unique ID of RNA modification site related SNP.
13: RNAmodLoc -> The genome coordinate of RNA modifications corresponds to ID list in 12th column.
14: modType -> The type of RNA modification site related SNP.
15: geneID -> The list of gene that the RNA modification site related to SNP reside in.
16: transcriptID -> The list of transcript that the RNA modification site related to SNP reside in.
17: geneName -> Gene name corresponding to the gene ID.
18: geneType -> Gene biotype on which the RNA modification site distribute.
19: region -> Gene feature on which the RNA modification site distribute.
20: Source -> The Source of SNP, the value is "GWASdb" or "LD_derived".
21: derived_from -> It means that the SNP is derived from linkage disequilibrium(LD) analysis to extract SNPs that had high LD relationship with disease-related SNPs using a threshold of r2 > 0.5.
22: GWAS_disease/trait -> Details of disease about SNP.
23: pValue -> P Value.
24: pubmedID -> The pubmed of SNP information.
[ 2. For SNV file: ]
1: modSNVID -> The unique ID of modSNV to identificate.
2: snvChr -> The chromosome of SNV site.
3: snvStart -> The starrt of SNV site.
4: snvEnd -> The end of SNV site.
5: snvID -> The SNV ID.
6: snvScore -> Score.
7: snvStrand -> Strand.
8: geneName -> Gene that SNV reside in.
9: Cancer -> Cancer about SNV.
10: pubmed -> The pubmed of SNV information.
11: snvSource -> The source of SNV information.
12: cancerInfoList -> The format is "Cancer__Mutation__MutSub1__MutSub2__RefBase__AltBase".
13: shiftPos -> The offset of SNV loci relative to the modification site. The range is from -10 to 10, the positive number means the SNV site appears in the downstream of RNA modification site and the negative means upstream.
14: modID -> The unique ID of RNA modification site related SNV.
15: RNAmodLoc -> The genome coordinate of RNA modifications corresponds to ID list in 14th column.
16: modType -> The type of RNA modification site related SNV.
17: geneID -> The list of gene that the RNA modification site related to SNV reside in.
18: transID -> The list of transcript that the RNA modification site related to SNV reside in.
19: geneName -> Gene name corresponding to the gene ID.
20: geneType -> Gene biotype on which the RNA modification site distribute.
21: region -> Gene feature on which the RNA modification site distribute.