[TIP] biomaRt

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http://biomart2010.wikispaces.com/

Installing biomaRt

• source( "http://www.bioconductor.org/biocLite.R")
  biocLite(’biomaRt’)

Check Available BioMarts

• library(biomaRt)
  listMarts()

Select the Ensembl BioMart

• ensembl = useMart("ensembl")
   datasets = listDatasets(ensembl)
   ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
   attributes=listAttributes(ensembl)
   filters=listFilters(ensembl)

Task 1a

• affyids = c("211550_at","202431_s_at","206044_s_at")
  annotation = getBM(c("affy_hg_u133_plus_2","ensembl_gene_id","hgnc_symbol","chromosome_name","start_position","end_position","band","strand"), filters="affy_hg_u133_plus_2", values=affyids,mart = ensembl)
  print(annotation)

Task 1aa

library(biomaRt)
mart = useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
refseq = c("NM_006945", "NM_152486", "NM_198317", "XM_001125684" )
#getBM(filters=c( "refseq_mrna", "refseq_mrna_predicted"), attributes="external_gene_id", values=refseq, mart=mart)
getBM(filters="refseq_mrna", attributes=c("refseq_mrna", "hgnc_symbol"), values=refseq, mart=mart)
listAttributes( mart)[grep( "refseq", listAttributes( mart)[,1]), ]
# coding
NM = getBM(filters="refseq_mrna", attributes=c("refseq_mrna", "hgnc_symbol"), values=refseq, mart=mart)
# coding - predict
XM = getBM(filters="refseq_mrna_predicted", attributes=c("refseq_mrna_predicted", "hgnc_symbol"), values=refseq, mart=mart )
# non-coding
NR = getBM(filters="refseq_ncrna" , attributes=c("refseq_ncrna", "hgnc_symbol"), values=refseq, mart=mart )
# non-coding-predicted
XR = getBM(filters="refseq_ncrna_predicted", attributes=c("refseq_ncrna_predicted", "hgnc_symbol"), values=refseq, mart=mart )

colnames( NM)  = c("refseq", "hgnc")
colnames( XM)  = c("refseq", "hgnc")
colnames( NR)  = c("refseq", "hgnc")
colnames( XR)  = c("refseq", "hgnc")
refseq2hgnc = rbind( NM, XM, NR, XR )

Task 1b

• illuminaIDs = c("ILMN_1728071","ILMN_1662668")
  goAnnot = getBM(c("illumina_humanwg_6_v2", "go_biological_process_id","go_biological_process_linkage_type"), filters="illumina_humanwg_6_v2", values=illuminaIDs, mart = ensembl)
  print(goAnnot[1:5,])

Task 2

• diab=getBM(c("ensembl_gene_id","hgnc_symbol"),filters=c("mim_morbid_accession","go"), values=list(c("125853","222100"),"GO:0003700"),mart=ensembl)
  print(diab)

Task3

• miRNA = getBM(c("mirbase_id","ensembl_gene_id","start_position","chromosome_name"), filters=c("chromosome_name","with_mirbase"), values=list(13,TRUE), mart=ensembl)
  miRNA[1:5,]

Task4

• filterOptions("snptype_filters",ensembl)
  entrez = getBM("entrezgene",filters=c("chromosome_name","snptype_filters"), values=list(22,"NON_SYNONYMOUS_CODING"),mart=ensembl)
  entrez[1:5,]

Task5

• seq = getSequence(id="CDH1", type="hgnc_symbol",seqType="gene_exon", mart = ensembl)
  seq[1,]

Task6

• promoter=getSequence(id=c("APC","CUL1"), type="hgnc_symbol",seqType="coding_gene_flank",upstream =2000, mart=ensembl)

Task7

• human=useMart("ensembl", dataset="hsapiens_gene_ensembl")
  chicken=useMart("ensembl", dataset="ggallus_gene_ensembl")
  mapping = getLDS(attributes=c("affy_hg_u95av2","hgnc_symbol"), filters="affy_hg_u95av2", values=c("1888_s_at","1434_at"),mart=human,attributesL="affy_chicken", martL=chicken)

Accessing Archived Ensembl versions

• listMarts(host="may2009.archive.ensembl.org/biomart/martservice/")
  ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org/biomart/martservice/")
  listDatasets(ensembl54)
  ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org/biomart/martservice/", dataset='hsapiens_gene_ensembl')

Task8

• snp=useMart("snp", dataset="hsapiens_snp")
  out=getBM(attributes=c("refsnp_id","allele","chrom_start"), filters=c("chr_name","chrom_start","chrom_end"), values=list(8,148350,158612), mart=snp)
  out[1:5,]

Task9

• hapmap = useMart("HapMap_rel27", dataset="hm27_variation_yri")
  yri = getBM(c("chrom","start","alleles","ref_allele","ref_allele_freq","other_allele_freq"),filters=c("chrom","coding_nonsynon"),values=list("chr19",TRUE),mart=hapmap)
  head(yri)

Task10

• cosmic=useMart("CosmicMart",dataset="COSMIC47")
  mut = getBM(c("sample_name","gene_name","aa_mut_syntax","mut_type_cds","zygosity"),filters="sample_name",values=c("MCF7","BT474"),mart=cosmic)
  head(mut)

Task11

• reactome = useMart("REACTOME", dataset="pathway")
  ids = getBM(c("referencedatabase_uniprot","_displayname"),filters=c("_displayname","species_selection"),value=list(c("DNA Repair","Signaling by WNT","Muscle contraction"),"Homo sapiens"), mart=reactome)

Task12

• gramene = useMart("ENSEMBL_MART_ENSEMBL", dataset="athaliana_eg_gene")
  getBM(c("ensembl_gene_id","external_gene_id","description","start_position","end_position"), filters=c("chromosome_name","start","end"), values=list("1", "30000","41000"), mart=gramene)

Task13

• worm = useMart("wormbase195", dataset="wormbase_rnai")
  pheno = getBM(c("rnai","phenotype_primary_name"), filters="gene", values="WBGene00006763", mart=worm)
  head(pheno)

Task14 : get gene infos

• gene.list = c( "MBNL3", "WNT5A", "NFIA" ) 
• gs = getBM(attributes=c("hgnc_symbol", "ensembl_gene_id", "chromosome_name", 'strand', "start_position", "end_position", "band"), filter=c("hgnc_symbol"), values=gene.list, mart=ensmart)

archive:
http://useast.ensembl.org/info/website/archives/index.html

## biomart = "ENSEMBL_MART_ENSEMBL"           # use archive to get ensembl 65
## biomaRt_dataset = "mmusculus_gene_ensembl" # mouse dataset id name 
## host = "dec2011.archive.ensembl.org"       # use ensembl 65 for annotation for mm9
## goAnno = "org.Mm.eg.db"                    # GO annotation database

## mm10
mart = useMart('ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl',host="may2012.archive.ensembl.org")

to get customized seqs

library(biomaRt) 

ensmart=useMart("ensembl",dataset="hsapiens_gene_ensembl" ) #, mysql=TRUE) 

gene = getGene(id='PITX2', type='hgnc_symbol', mart=ensmart) 

seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart)
show(seq)

seq = getSequence(id="1939_at", type="affy_hg_u95av2", seqType="gene_flank",upstream = 20, mart = mart)
show(seq)

##
## entrez
##
entrez=c("673","7157","837")
getSequence(id = entrez, type="entrezgene",seqType="coding_gene_flank",upstream=10, mart=ensmart)


OR

library(BSgenome.Hsapiens.UCSC.hg19)
toString(subseq(Hsapiens$chr17, 1000000,1000005))

OR
http://useast.ensembl.org/das/Homo_sapiens.GRCh37.reference/sequence?segment=1:100000,110000

(my gene_list is in gene symbol)
 >my_mart = useMart("ensembl",dataset="hsapiens_gene_ensembl")
 >seq_3utr = getSequence(id = unique(gene.symbol),  
type="hgnc_symbol",seqType="3utr",mart = my_mart)
 >seq_3utr = seq_3utr[seq_3utr[,"3utr"] != "Sequence unavailable",]
 >here: extract longest 3'UTR for each unique gene symbol
 >exportFASTA(seq_3utr, file=paste("s3utr.fa",sep=""))

As my project goes, I now need 3'UTR genomic coordinates to get  
phastcons conservation for some regions in 3'UTR.
To do that, I first convert hgnc_symbol back to ensembl_gene_id, then  
get 3'UTR coordinates using getBM like this:

 >s3utr = read.DNAStringSet(paste("s3utr.fa",sep=""),format="fasta")
 >gene_names = names(s3utr)
 >hgnc2ensembl  = getBM(attributes=c("hgnc_symbol","ensembl_gene_id"),  
filters="hgnc_symbol", values=gene_names, mart=my_mart)
 >s3utr_pos  = getBM(attributes=c("ensembl_gene_id",  
"chromosome_name","strand","3_utr_start", "3_utr_end"),
  filters="ensembl_gene_id", values=as.character(hgnc2ensembl 
$ensembl_gene_id), mart=my_mart)
 >s3utr_pos = s3utr_pos[complete.cases(s3utr_pos),]

By doing that, now I can only get about 5000 gene symbols with 3'UTR  
coordinates (converting from hgnc_symbol back to ensembl_gene_id  
looses about 250 genes). I was thinking it might be version  
difference? So I tried to use ensembl archive but it gives me error as  
below:

 > my_mart =  
useMart("ensembl_mart_50",dataset="hsapiens_gene_ensembl",archive=T)
Error in value[[3L]](cond) :
   Request to BioMart web service failed. Verify if you are still  
connected to the internet.  Alternatively the BioMart web service is  
temporarily down.
In addition: Warning message:
In file(file, "r") : cannot open: HTTP status was '404 Not Found'

Retrieve genomic positions

#R --slave \< ../get-genomic-coordinate-using-biomaRt.R genelist output


args = commandArgs()
gene.list.file = args[3]
output = args[4]


#gene.list.file = "a"
gene.list = read.table( file=gene.list.file, header=F, sep="\t" )
gene.list = as.vector( gene.list$V1 )   # V1 == hgnc_symbol


#library(GenomeGraphs)
library(biomaRt)
#mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
#----------------
# match to hg19 / NCBI build 37
#----------------
#mart = useMart( biomart="ensembl", dataset = "hsapiens_gene_ensembl")

###----------------
### match to hg18 / NCBI build 36
###----------------
mart = useMart( biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "may2009.archive.ensembl.org", path = "/biomart/martservice", archive = FALSE) # to use
 the hg18, NCBI build 36

gs = getBM(attributes=c("hgnc_symbol", "ensembl_gene_id", "chromosome_name", 'strand', "start_position", "end_position", "band"), filter=c("hgnc_symbol"), values=gene.list, mart
=mart)

#gs = getBM(attributes=c("hgnc_symbol", "ensembl_gene_id", "chromosome_name", "start_position", "end_position", "band"), filter=c("hgnc_symbol"), values=gene_symbol, mart=mart)

  
#att1 = c("ensembl_gene_id", "hgnc_symbol", "chromosome_name", "strand", "start_position", "end_position", "transcript_start", "transcript_end", "band")  


#att2 = c("ensembl_gene_id", "5_utr_start",  "5_utr_end","3_utr_start", "3_utr_end", "exon_chrom_start", "exon_chrom_end")


#gs1 = getBM(mart=mart, attributes=att1, value=c("hgnc_symbol") ) #, values=gene_symbol) 
#gs2 = getBM(mart=mart, attributes=att2 ) #, values=gene_symbol) 
#gs= merge(gs1,gs2)
#gs = unique( gs )



#gene.list = c( "EIF4ENIF1" )
out = NULL
notMatch = NULL
for( symbol in gene.list ) {
 ## this can be multi-lines
 info = gs[gs$hgnc_symbol == symbol,][,c(1,3:6)]  
 if( length(info) == 0 ) {
  notMatch = c( notMatch, symbol )
 } else {
  chr = as.vector( info$chromosome_name ) 
  out = rbind( out, info[grep( "^[0-9XY]", chr ),]  )
 }
}
print( out )
#out[ out$chromosome_name == "X",]$chromosome_name = "23"
#out[ out$chromosome_name == "Y",]$chromosome_name = "24"
write.table( out, file=output, row.names=F, col.names=F, sep="\t", quot=F )

to get the attributes from multiple pages of the same mart.

library("biomaRt")
mart = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl", mart = mart)

p = c("200641_s_at" , "229411_at" , "223376_s_at")

Q1 = getBM(attributes =
              c("affy_hg_u133_plus_2","entrezgene","ensembl_gene_id"),
            filters = "affy_hg_u133_plus_2", mart=ensembl, values=p)

Q2 = getBM(attributes=c("validated","ensembl_gene_id"),
            filters="affy_hg_u133_plus_2", mart=ensembl, values=p)

## clean up:
## Q1 = subset(Q1, !is.na(entrezgene))

Q = merge(Q1,Q2)

SNPs

library("biomaRt")

snp = useMart("snp", dataset="hsapiens_snp")

ensemblids = c("ENSG00000204296")

out = getBM(attributes=c("refsnp_id","chr_name","chrom_start",

                          "ensembl_gene_stable_id","validated",

                          "consequence_type_tv"),

             filters=c("ensembl_gene"), values=c(ensemblids), mart=snp)

head(out)

  refsnp_id chr_name chrom_start ensembl_gene_stable_id               validated

1  rs517922        6    32258836        ENSG00000204296                  hapmap

2 rs3117133        6    32313653        ENSG00000204296 cluster,freq,1000Genome

3 rs6621681        6    32292217        ENSG00000204296                        

4 rs6621681        6    32292217        ENSG00000204296                        

5 rs6621682        6    32292221        ENSG00000204296                        

6 rs6621682        6    32292221        ENSG00000204296                        

    consequence_type_tv

1            DOWNSTREAM

2              INTRONIC

3              INTRONIC

4 NON_SYNONYMOUS_CODING

5              INTRONIC

6     SYNONYMOUS_CODING

Search TFBS agains promoter regions (~up/dn2K from TSS)

IUPAC Code   Meaning  Complement
A  A  T
C  C  G
G  G  C
T/U  T  A
M  A or C  K
R  A or G  Y
W  A or T  W
S  C or G  S
Y  C or T  R
K  G or T  M
V  A or C or G  B
H  A or C or T  D
D  A or G or T  H
B  C or G or T  V
N  G or A or T or C  N

[kwangmin@10 MSigDB-v3.0]$ grep PITX2 c3.tft.v3.0.symbols.gmt.morifSeq.txt
V$PITX2_Q2  CTCNANGTGNY
GGATTA_V$PITX2_Q2 YATGNWAAT

[kwangmin@10 MSigDB-v3.0]$ grep SOX9 c3.tft.v3.0.symbols.gmt.morifSeq.txt
V$SOX9_B1 SKYTAAAAATAACYCH
CATTGTYY_V$SOX9_B1 YATGNWAAT
[kwangmin@10 MSigDB-v3.0]$ grep PITX2_Q2 c3.tft.v3.0.symbols.gmt


library( biomaRt )
library(BSgenome.Hsapiens.UCSC.hg19)

#ensmart = useMart( biomart="E", dataset = "hsapiens_gene_ensembl" ) 
ensmart = useMart( biomart="ensembl", dataset="hsapiens_gene_ensembl")

system( "awk -F\"\t\" '{ if($4 > 2.5 && $5 > 2.5) print $2}'  ~/Desktop/shSOX9_shPITX2-vs-shControl-BH5pct-FC1.csv  | sort | uniq > up" )

system( "awk -F\"\t\" '{ if($4 < 0.5 && $5 < 0.5) print $2}'  ~/Desktop/shSOX9_shPITX2-vs-shControl-BH5pct-FC1.csv  | sort | uniq > dn" )


#gene.list = c( "SOX9", "PITX2", "RORA" )
#gene.list = as.vector( read.table( file="up")$V1 )
gene.list = as.vector( read.table( file="dn")$V1 )

#gs = getBM(attributes=c("hgnc_symbol", "ensembl_gene_id", "chromosome_name", 'strand', "start_position", "end_position", "band"), filter=c("hgnc_symbol"), values=gene.list, mart=ensmart) 

## ---> not gene start/end, but transcript_start/end for TSS.

## use only complete chromosome
##
gs = gs[ grep( "^[0-9|X|Y]", gs$chromosome_name, perl=T), ]
g.sym = gs$hgnc_symbol
g.str = gs$strand
g.start = gs$start_position
g.end = gs$end_position
g.chr = paste( "chr", gs$chromosome, sep="")

##
## getSequence is cool for get up2k, but not dn2k.
##
## getSequence(id=gene.list, type="hgnc_symbol", seqType="coding_gene_flank", upstream = 20, mart = ensmart)


##
## up-stream from TSS
##
promoter = 2000

g.seq.up = NULL
g.seqs.up = NULL
for( i in 1:length(g.sym) ) {
 if( g.str[i] == 1 ) {
  g.seq.up = toString(subseq(Hsapiens[[g.chr[i]]], g.start[i]-promoter, g.start[i] ))
  g.seqs.up = c( g.seqs.up, g.seq.up )
 } else if( g.str[i] == -1 ) {
  g.seq.up = toString( reverseComplement( subseq(Hsapiens[[g.chr[i]]], g.end[i], g.end[i]+promoter)) )
  g.seqs.up = c( g.seqs.up, g.seq.up ) 
 }
}

##
## down-stream from TSS
##
g.seq.dn = NULL
g.seqs.dn = NULL
for( i in 1:length(g.sym) ) {
 if( g.str[i] == 1 ) {
  g.seq.dn = toString(subseq(Hsapiens[[g.chr[i]]], g.start[i], g.start[i]+promoter ))
  g.seqs.dn = c( g.seqs.dn, g.seq.dn )
 } else if( g.str[i] == -1 ) {
  g.seq.dn = toString( reverseComplement( subseq(Hsapiens[[g.chr[i]]], g.end[i]-promoter, g.end[i])) )
  g.seqs.dn = c( g.seqs.dn, g.seq.dn ) 
 }
}


search.table = as.data.frame( cbind( g.sym, g.chr, g.str, g.seqs.up, g.seqs.dn ) )


#patterns = c( 'AAAAAA' )
#matchPattern( DNAString("G[:upper:]G"), DNAString( search.table$g.seqs.up[1]) , fixed=FALSE)  # 3 hits on strand +

#[kwangmin@10 MSigDB-v3.0]$ grep PITX2 c3.tft.v3.0.symbols.gmt.morifSeq.txt
#V$PITX2_Q2  CTCNANGTGNY
#GGATTA_V$PITX2_Q2 YATGNWAAT

#[kwangmin@10 MSigDB-v3.0]$ grep SOX9 c3.tft.v3.0.symbols.gmt.morifSeq.txt
#V$SOX9_B1 SKYTAAAAATAACYCH
#CATTGTYY_V$SOX9_B1 YATGNWAAT


##
## for detailed match position, use matchPattern()
##
# matchPattern( DNAString("AAAMCT"), DNAString( search.table$g.seqs.up[1]) , fixed=F)  # IUPAC 3 hits on strand 

##
## IUPAC ambiguity codes
##
pattern = c( "[A|T][A|T]CAA[A|T]G", "CTCANGTGNY", "YATGNWAAT", "SKYTAAAAATAACYCH" )

##
## converted into regular expression for grep( perl=T)
##
pattern = c( "[A|T][A|T]CAA[A|T]G", "CTCA[G|A|T|C]GTG[G|A|T|C][C|T]", "[C|T]ATG[G|A|T|C][A|T]AAT", "[C|G][G|T][C|T]TAAAAATAAC[C|T]C[A|C]" )

up = NULL
dn = NULL
upPromPatt = NULL
dnPromPatt = NULL
upProm = NULL
dnProm = NULL

for( i in 1:length(pattern)) {
  promoter.up = grep( pattern[i], search.table$g.seqs.up, perl=T)
  if( length(promoter.up) > 0) {
    for( j in promoter.up) {
      upPromPatt = c( upPromPatt, pattern[i])
      upProm = c( upProm, as.vector(search.table$g.sym[j]) )  
      #print( upProm )
    }  
    up = rbind( up, cbind( upPromPatt, upProm ) )
    upPromPatt = NULL
    upProm = NULL
  }

  promoter.dn = grep( pattern[i], search.table$g.seqs.dn, perl=T)
  if( length(promoter.dn) > 0 ) {
    for( k in promoter.dn) {
      dnPromPatt = c( dnPromPatt, pattern[i])
      #print( dnPromPatt)
      dnProm = c( dnProm, as.vector(search.table$g.sym[k]) )
    }
    dn = rbind( dn, cbind( dnPromPatt, dnProm ) )
    dnPromPatt = NULL
    dnProm = NULL
  }
}

#write.table( up, file="shSOX9-and-shPITX2-both-2.5xUP-up2K-search.xls", sep="\t", row.names=F, quote=F)
#write.table( dn, file="shSOX9-and-shPITX2-both-2.5xUP-dn2K-search.xls", sep="\t", row.names=F, quote=F)

write.table( up, file="shSOX9-and-shPITX2-both-0.5xDN-up2K-search.xls", sep="\t", row.names=F, quote=F)
write.table( dn, file="shSOX9-and-shPITX2-both-0.5xDN-dn2K-search.xls", sep="\t", row.names=F, quote=F)

q()

bsgenome.Hsapiens.UCSC package

Examples
http://svitsrv25.epfl.ch/R-doc/library/Biostrings/html/reverse.html

Get Exon seq from ID

t = read.csv( file=file, sep="\t", header=T)
exon.id = as.character(t[,28] )


#exon.id = exon.id[1:4]
#exon.id[5] = "jlkfljs"
exon.id.all = unlist( strsplit( exon.id, "[|]", perl=T) )

# listDatabasets( e65 )
# listFilters( e65 )
# listAttributes( e65 )

myMart = getBM( attributes=c("ensembl_exon_id","gene_exon"), mart=e65, filter=c("ensembl_exon_id"), value=exon.id.all )

exon.seqs = NULL
for( exon in exon.id ) {
    array = unlist( strsplit( exon, "[|]", perl=T) ) 
 if( length(array) == 0 ) {
  exon.seqs = c( exon.seqs, " | -" )
 } else {
  concat = NULL
  for( id in array ) {
   seq = myMart[ grep( paste("^",id,"$",sep=""), myMart$ensembl_exon_id), ]$gene_exon 
   if( length(seq) == 0 ) {
    seq = "-"
   }
   concat = paste( concat, seq, sep=" | " )
  } 
  exon.seqs = c( exon.seqs, concat )
 }
}

t$exon.seqs = exon.seqs

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