motifbreakR: an Introduction
Introduction
This document offers an introduction and overview of motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation is a good match to known transcription factor binding sites, and how much information is gained or lost in one allele of the polymorphism relative to another or mutation vs. wildtype. motifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum, 2) log-probabilities, and 3) relative entropy. motifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.
As of version 2.0 motifbreakR is also able to perform it’s analysis on indels, small insertions or deletions.
motifbreakR works with position probability matrices (PPM). PPM are derived as the fractional occurrence of nucleotides A,C,G, and T at each position of a position frequency matrix (PFM). PFM are simply the tally of each nucleotide at each position across a set of aligned sequences. With a PPM, one can generate probabilities based on the genome, or more practically, create any number of position specific scoring matrices (PSSM) based on the principle that the PPM contains information about the likelihood of observing a particular nucleotide at a particular position of a true transcription factor binding site.
This guide includes a brief overview of the processing flow, an example focusing more in depth on the practical aspect of using motifbreakR, and finally a detailed section on the scoring methods employed by the package.
Processing overview
motifbreakR may be used to interrogate SNPs or SNVs for their potential effect on transcription factor binding by examining how the two alleles of the variant effect the binding score of a motif. The basic process is outlined in the figure below.
Outline of process
motifbreakR workflow: How inputs (trapezoids) are generated from R functions (rectangles). Diamonds represent decisions of the user.
This straightforward process allows the interrogation of SNPs and
SNVs in the context of the different species represented by BSgenome
packages (at least 22 different species) and allows the use of the full
MotifDb
data set that includes over 4200 motifs across 8 studies and 22
organisms that we have supplemented with over 2800 additional motifs
across four additional studies in Humans see
data(encodemotif)1, data(factorbook)2,
data(hocomoco)3 and data(homer)4 for the additional
studies that we have included.
Practically motifbreakR has involves three phases.
- Read in Single Nucleotide Variants or Indels: The first step is to read in the list of variants. Variants can be a list of rsIDs if your SNPs are represented in one of the SNPlocs packages, may be included as a .bed file with a specifically formatted name field, or may be provided as a .vcf file. We then transform these input such that it may be read my motifbreakR.
- Find Broken Motifs: Next we present motifbreakR
with the input generated in the previous step, along with a set of
motifs formatted as class
MotifList, and your preferred scoring method. - Visualize SNPs and motifs: Finally we can visualize which motifs are broken by any individual SNP using our plotting function.
How To Use motifbreakR: A Practical Example
This section offers an example of how to use motifbreakR to identify potentially disrupted transcription factor binding sites due to 701 SNPs output from a FunciSNP analysis of Prostate Cancer (PCa) genome wide association studies (GWAS) risk loci. The SNPs are included in this package here:
library(motifbreakR)
pca.snps.file <- system.file("extdata", "pca.enhancer.snps", package = "motifbreakR")
pca.snps <- as.character(read.table(pca.snps.file)[,1])The simplest form of a motifbreakR analysis is summarized as follows:
variants <- snps.from.rsid(rsid = pca.snps,
dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37,
search.genome = BSgenome.Hsapiens.UCSC.hg19)
motifbreakr.results <- motifbreakR(snpList = variants, pwmList = MotifDb, threshold = 0.9)
plotMB(results = motifbreakr.results, rsid = "rs7837328", effect = "strong")Lets look at these steps more closely and see how we can customize our analysis.
Step 1 | Read in Single Nucleotide Variants
Variants can be input either as a list of rsIDs or as a .bed
file. The main factor determining which you will use is if your variants
have rsIDs that are included in one of the Bioconductor
SNPlocs packages. The present selection is seen here:
## [1] "SNPlocs.Hsapiens.dbSNP144.GRCh37" "SNPlocs.Hsapiens.dbSNP144.GRCh38"
## [3] "SNPlocs.Hsapiens.dbSNP149.GRCh38" "SNPlocs.Hsapiens.dbSNP150.GRCh38"
## [5] "SNPlocs.Hsapiens.dbSNP155.GRCh37" "SNPlocs.Hsapiens.dbSNP155.GRCh38"
## [7] "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38"For cases where your rsIDs are not available in a SNPlocs package, or you have novel variants that are not cataloged at all, variants may be entered in BED format as seen below:
snps.file <- system.file("extdata", "snps.bed", package = "motifbreakR")
read.delim(snps.file, header = FALSE)## V1 V2 V3 V4 V5 V6
## 1 chr2 12581137 12581138 rs10170896 0 +
## 2 chr2 12594017 12594018 chr2:12594018:G:A 0 +
## 3 chr3 192388677 192388678 rs13068005 0 +
## 4 chr4 122361479 122361480 rs12644995 0 +
## 5 chr6 44503245 44503246 chr6:44503246:A:T 0 +
## 6 chr6 44503247 44503248 chr6:44503248:G:C 0 +
## 7 chr6 85232897 85232898 rs4510639 0 +
## 8 chr6 44501872 44501873 rs932680 0 +Our requirements for the BED file are that it must include
chromosome, start, end,
name, score and strand fields –
where the name field is required to be in one of two formats, either an
rsID that is present in a SNPlocs package, or in the form
chromosome:position:referenceAllele:alternateAllele e.g.,
chr2:12594018:G:A. It is also essential that the fields are
TAB separated, not a mixture of tabs and spaces.
More to the point here are the two methods for reading in the variants.
SNPs from rsID:
We use the SNPlocs.Hsapiens.dbSNP155.GRCh37 which is the SNP locations and alleles defined in dbSNP155 as a source for looking up our rsIDs and BSgenome.Hsapiens.UCSC.hg19 which holds the reference sequence for UCSC genome build hg19. Additional SNPlocs packages are availble from Bioconductor.
## Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading
## 'SNPlocs.Hsapiens.dbSNP155.GRCh37'## [1] "rs1551515" "rs1551513" "rs17762938" "rs4473999" "rs7823297" "rs9656964"snps.mb <- snps.from.rsid(rsid = pca.snps,
dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37,
search.genome = BSgenome.Hsapiens.UCSC.hg19)## Warning in rowids2rowidx(user_rowids, ids, x_rowids_env, ifnotfound): SNP ids not found: rs78914317, rs75425437, rs114099824, rs79509278, rs74738513, rs137898974
##
## They were dropped.## GRanges object with 1173 ranges and 3 metadata columns:
## seqnames ranges strand | SNP_id REF ALT
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet>
## rs10007915:A chr4 106065308 * | rs10007915 C A
## rs10007915:G chr4 106065308 * | rs10007915 C G
## rs10007915:T chr4 106065308 * | rs10007915 C T
## rs10015716 chr4 95548550 * | rs10015716 G A
## rs10034824:A chr4 95524838 * | rs10034824 G A
## ... ... ... ... . ... ... ...
## rs991429:T chr17 69109773 * | rs991429 G T
## rs9973650 chr2 238380266 * | rs9973650 G A
## rs998071:A chr4 95591976 * | rs998071 C A
## rs998071:G chr4 95591976 * | rs998071 C G
## rs998071:T chr4 95591976 * | rs998071 C T
## -------
## seqinfo: 25 sequences (1 circular) from hg19 genomeA far greater variety of variants may be read into motifbreakR
via the snps.from.file function. In fact motifbreakR
will work with any organism present as a Bioconductor BSgenome
package. This includes 76 genomes representing 22 species.
## [1] 113## [1] "BSgenome.Alyrata.JGI.v1"
## [2] "BSgenome.Amellifera.BeeBase.assembly4"
## [3] "BSgenome.Amellifera.NCBI.AmelHAv3.1"
## [4] "BSgenome.Amellifera.UCSC.apiMel2"
## [5] "BSgenome.Amellifera.UCSC.apiMel2.masked"
## [6] "BSgenome.Aofficinalis.NCBI.V1"
## [7] "BSgenome.Athaliana.TAIR.04232008"
## [8] "BSgenome.Athaliana.TAIR.TAIR9"
## [9] "BSgenome.Btaurus.UCSC.bosTau3"
## [10] "BSgenome.Btaurus.UCSC.bosTau3.masked"
## [11] "BSgenome.Btaurus.UCSC.bosTau4"
## [12] "BSgenome.Btaurus.UCSC.bosTau4.masked"
## [13] "BSgenome.Btaurus.UCSC.bosTau6"
## [14] "BSgenome.Btaurus.UCSC.bosTau6.masked"
## [15] "BSgenome.Btaurus.UCSC.bosTau8"
## [16] "BSgenome.Btaurus.UCSC.bosTau9"
## [17] "BSgenome.Btaurus.UCSC.bosTau9.masked"
## [18] "BSgenome.Carietinum.NCBI.v1"
## [19] "BSgenome.Celegans.UCSC.ce10"
## [20] "BSgenome.Celegans.UCSC.ce11"
## [21] "BSgenome.Celegans.UCSC.ce2"
## [22] "BSgenome.Celegans.UCSC.ce6"
## [23] "BSgenome.Cfamiliaris.UCSC.canFam2"
## [24] "BSgenome.Cfamiliaris.UCSC.canFam2.masked"
## [25] "BSgenome.Cfamiliaris.UCSC.canFam3"
## [26] "BSgenome.Cfamiliaris.UCSC.canFam3.masked"
## [27] "BSgenome.Cjacchus.UCSC.calJac3"
## [28] "BSgenome.Cjacchus.UCSC.calJac4"
## [29] "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1"
## [30] "BSgenome.Creinhardtii.JGI.v5.6"
## [31] "BSgenome.Dmelanogaster.UCSC.dm2"
## [32] "BSgenome.Dmelanogaster.UCSC.dm2.masked"
## [33] "BSgenome.Dmelanogaster.UCSC.dm3"
## [34] "BSgenome.Dmelanogaster.UCSC.dm3.masked"
## [35] "BSgenome.Dmelanogaster.UCSC.dm6"
## [36] "BSgenome.Drerio.UCSC.danRer10"
## [37] "BSgenome.Drerio.UCSC.danRer11"
## [38] "BSgenome.Drerio.UCSC.danRer5"
## [39] "BSgenome.Drerio.UCSC.danRer5.masked"
## [40] "BSgenome.Drerio.UCSC.danRer6"
## [41] "BSgenome.Drerio.UCSC.danRer6.masked"
## [42] "BSgenome.Drerio.UCSC.danRer7"
## [43] "BSgenome.Drerio.UCSC.danRer7.masked"
## [44] "BSgenome.Dvirilis.Ensembl.dvircaf1"
## [45] "BSgenome.Ecoli.NCBI.20080805"
## [46] "BSgenome.Gaculeatus.UCSC.gasAcu1"
## [47] "BSgenome.Gaculeatus.UCSC.gasAcu1.masked"
## [48] "BSgenome.Ggallus.UCSC.galGal3"
## [49] "BSgenome.Ggallus.UCSC.galGal3.masked"
## [50] "BSgenome.Ggallus.UCSC.galGal4"
## [51] "BSgenome.Ggallus.UCSC.galGal4.masked"
## [52] "BSgenome.Ggallus.UCSC.galGal5"
## [53] "BSgenome.Ggallus.UCSC.galGal6"
## [54] "BSgenome.Gmax.NCBI.Gmv40"
## [55] "BSgenome.Hsapiens.1000genomes.hs37d5"
## [56] "BSgenome.Hsapiens.NCBI.GRCh38"
## [57] "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0"
## [58] "BSgenome.Hsapiens.UCSC.hg17"
## [59] "BSgenome.Hsapiens.UCSC.hg17.masked"
## [60] "BSgenome.Hsapiens.UCSC.hg18"
## [61] "BSgenome.Hsapiens.UCSC.hg18.masked"
## [62] "BSgenome.Hsapiens.UCSC.hg19"
## [63] "BSgenome.Hsapiens.UCSC.hg19.masked"
## [64] "BSgenome.Hsapiens.UCSC.hg38"
## [65] "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major"
## [66] "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor"
## [67] "BSgenome.Hsapiens.UCSC.hg38.masked"
## [68] "BSgenome.Hsapiens.UCSC.hs1"
## [69] "BSgenome.Mdomestica.UCSC.monDom5"
## [70] "BSgenome.Mfascicularis.NCBI.5.0"
## [71] "BSgenome.Mfascicularis.NCBI.6.0"
## [72] "BSgenome.Mfuro.UCSC.musFur1"
## [73] "BSgenome.Mmulatta.UCSC.rheMac10"
## [74] "BSgenome.Mmulatta.UCSC.rheMac2"
## [75] "BSgenome.Mmulatta.UCSC.rheMac2.masked"
## [76] "BSgenome.Mmulatta.UCSC.rheMac3"
## [77] "BSgenome.Mmulatta.UCSC.rheMac3.masked"
## [78] "BSgenome.Mmulatta.UCSC.rheMac8"
## [79] "BSgenome.Mmusculus.UCSC.mm10"
## [80] "BSgenome.Mmusculus.UCSC.mm10.masked"
## [81] "BSgenome.Mmusculus.UCSC.mm39"
## [82] "BSgenome.Mmusculus.UCSC.mm8"
## [83] "BSgenome.Mmusculus.UCSC.mm8.masked"
## [84] "BSgenome.Mmusculus.UCSC.mm9"
## [85] "BSgenome.Mmusculus.UCSC.mm9.masked"
## [86] "BSgenome.Osativa.MSU.MSU7"
## [87] "BSgenome.Ppaniscus.UCSC.panPan1"
## [88] "BSgenome.Ppaniscus.UCSC.panPan2"
## [89] "BSgenome.Ptroglodytes.UCSC.panTro2"
## [90] "BSgenome.Ptroglodytes.UCSC.panTro2.masked"
## [91] "BSgenome.Ptroglodytes.UCSC.panTro3"
## [92] "BSgenome.Ptroglodytes.UCSC.panTro3.masked"
## [93] "BSgenome.Ptroglodytes.UCSC.panTro5"
## [94] "BSgenome.Ptroglodytes.UCSC.panTro6"
## [95] "BSgenome.Rnorvegicus.UCSC.rn4"
## [96] "BSgenome.Rnorvegicus.UCSC.rn4.masked"
## [97] "BSgenome.Rnorvegicus.UCSC.rn5"
## [98] "BSgenome.Rnorvegicus.UCSC.rn5.masked"
## [99] "BSgenome.Rnorvegicus.UCSC.rn6"
## [100] "BSgenome.Rnorvegicus.UCSC.rn7"
## [101] "BSgenome.Scerevisiae.UCSC.sacCer1"
## [102] "BSgenome.Scerevisiae.UCSC.sacCer2"
## [103] "BSgenome.Scerevisiae.UCSC.sacCer3"
## [104] "BSgenome.Sscrofa.UCSC.susScr11"
## [105] "BSgenome.Sscrofa.UCSC.susScr3"
## [106] "BSgenome.Sscrofa.UCSC.susScr3.masked"
## [107] "BSgenome.Tgondii.ToxoDB.7.0"
## [108] "BSgenome.Tguttata.UCSC.taeGut1"
## [109] "BSgenome.Tguttata.UCSC.taeGut1.masked"
## [110] "BSgenome.Tguttata.UCSC.taeGut2"
## [111] "BSgenome.Vvinifera.URGI.IGGP12Xv0"
## [112] "BSgenome.Vvinifera.URGI.IGGP12Xv2"
## [113] "BSgenome.Vvinifera.URGI.IGGP8X"SNPs from BED formatted file:
Here we examine two possibilities. In one case we have a mixture of
rsIDs and our naming scheme that allows for arbitrary variants. Second
we have a list of variants for the zebrafish Danio rerio that
does not have a SNPlocs package, but does have it’s genome
present among the availible.genomes().
snps.bed.file <- system.file("extdata", "snps.bed", package = "motifbreakR")
# see the contents
read.table(snps.bed.file, header = FALSE)## V1 V2 V3 V4 V5 V6
## 1 chr2 12581137 12581138 rs10170896 0 +
## 2 chr2 12594017 12594018 chr2:12594018:G:A 0 +
## 3 chr3 192388677 192388678 rs13068005 0 +
## 4 chr4 122361479 122361480 rs12644995 0 +
## 5 chr6 44503245 44503246 chr6:44503246:A:T 0 +
## 6 chr6 44503247 44503248 chr6:44503248:G:C 0 +
## 7 chr6 85232897 85232898 rs4510639 0 +
## 8 chr6 44501872 44501873 rs932680 0 +Seeing as we have some SNPs listed by their rsIDs we can query those
by including a SNPlocs object as an argument to
snps.from.file
library(SNPlocs.Hsapiens.dbSNP155.GRCh37)
#import the BED file
snps.mb.frombed <- snps.from.file(file = snps.bed.file,
dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37,
search.genome = BSgenome.Hsapiens.UCSC.hg19,
format = "bed", check.unnamed.for.rsid = TRUE)
snps.mb.frombed## Warning in snps.from.file(file = snps.bed.file, dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37, :
## rs7601289 was found as a match for chr2:12594018:G:A; using entry from dbSNP
## rs11753604 was found as a match for chr6:44503246:A:T; using entry from dbSNP## GRanges object with 13 ranges and 3 metadata columns:
## seqnames ranges strand | SNP_id REF ALT
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet>
## rs10170896 chr2 12581138 * | rs10170896 G A
## rs10170896 chr2 12581138 * | rs10170896 G C
## rs12644995 chr4 122361480 * | rs12644995 C A
## rs13068005 chr3 192388678 * | rs13068005 G A
## rs13068005 chr3 192388678 * | rs13068005 G C
## ... ... ... ... . ... ... ...
## rs932680 chr6 44501873 * | rs932680 G C
## rs932680 chr6 44501873 * | rs932680 G T
## rs7601289 chr2 12594018 * | rs7601289 G A
## rs11753604 chr6 44503246 * | rs11753604 A T
## chr6:44503248:G:C chr6 44503248 * | chr6:44503248:G:C G C
## -------
## seqinfo: 4 sequences from hg19 genomeWe see also that two of our custom variants
chr2:12594018:G:A and chr6:44503246:A:T were
actually already included in dbSNP155, and were therefor annotated in
the output as rs7601289 and rs11753604
respectively.
If our BED file includes no rsIDs, then we may omit the
dbSNP argument from the function. This example uses
variants from Danio rerio
library(BSgenome.Drerio.UCSC.danRer7)
snps.bedfile.nors <- system.file("extdata", "danRer.bed", package = "motifbreakR")
read.table(snps.bedfile.nors, header = FALSE)## V1 V2 V3 V4 V5 V6
## 1 chr18 13030932 13030933 chr18:13030933:G:A 0 +
## 2 chr18 30445455 30445456 chr18:30445456:T:A 0 +
## 3 chr5 22065023 22065024 chr5:22065024:A:T 0 +
## 4 chr14 36140941 36140942 chr14:36140942:T:A 0 +
## 5 chr3 16701576 16701577 chr3:16701577:T:A 0 +
## 6 chr14 20887995 20887996 chr14:20887996:G:A 0 +
## 7 chr7 25195449 25195450 chr7:25195450:G:T 0 +
## 8 chr2 59181852 59181853 chr2:59181853:A:G 0 +
## 9 chr3 58162674 58162675 chr3:58162675:C:T 0 +
## 10 chr22 18708824 18708825 chr22:18708825:T:A 0 +snps.mb.frombed <- snps.from.file(file = snps.bedfile.nors,
search.genome = BSgenome.Drerio.UCSC.danRer7,
format = "bed")
snps.mb.frombed## GRanges object with 10 ranges and 3 metadata columns:
## seqnames ranges strand | SNP_id REF ALT
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet>
## chr2:59181853:A:G chr2 59181853 * | chr2:59181853:A:G A G
## chr3:16701577:T:A chr3 16701577 * | chr3:16701577:T:A T A
## chr3:58162675:C:T chr3 58162675 * | chr3:58162675:C:T C T
## chr5:22065024:A:T chr5 22065024 * | chr5:22065024:A:T A T
## chr7:25195450:G:T chr7 25195450 * | chr7:25195450:G:T G T
## chr14:20887996:G:A chr14 20887996 * | chr14:20887996:G:A G A
## chr14:36140942:T:A chr14 36140942 * | chr14:36140942:T:A T A
## chr18:13030933:G:A chr18 13030933 * | chr18:13030933:G:A G A
## chr18:30445456:T:A chr18 30445456 * | chr18:30445456:T:A T A
## chr22:18708825:T:A chr22 18708825 * | chr22:18708825:T:A T A
## -------
## seqinfo: 26 sequences (1 circular) from danRer7 genomesnps.from.file also can take as input a vcf file with
SNVs, by using format = "vcf".
Indels
As of version 2.0 motifbreakR
is able to parse and analyse indels as well as SNVs. The function
variants.from.file() allows the import of indels and SNVs
simultaneously.
snps.indel.vcf <- system.file("extdata", "chek2.vcf.gz", package = "motifbreakR")
snps.indel <- variants.from.file(file = snps.indel.vcf,
search.genome = BSgenome.Hsapiens.UCSC.hg19,
format = "vcf")
snps.indel## GRanges object with 1456 ranges and 3 metadata columns:
## seqnames ranges strand | SNP_id REF ALT
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet>
## rs541513166 chr22 29083808 * | rs541513166 T TA
## rs540410451 chr22 29083826 * | rs540410451 G A
## rs562206743 chr22 29083843 * | rs562206743 A G
## rs529320954 chr22 29083856 * | rs529320954 A G
## rs544216926 chr22 29083913 * | rs544216926 C T
## ... ... ... ... . ... ... ...
## rs539227672 chr22 29137758 * | rs539227672 G A
## rs554107994 chr22 29137761 * | rs554107994 T G
## rs566344661 chr22 29137770 * | rs566344661 C G
## rs536566373 chr22 29137782 * | rs536566373 A G
## rs142541707 chr22 29137790 * | rs142541707 C A
## -------
## seqinfo: 25 sequences (1 circular) from hg19 genomeWe can filter to specifically see the indels like this:
## GRanges object with 66 ranges and 3 metadata columns:
## seqnames ranges strand | SNP_id REF ALT
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet>
## rs541513166 chr22 29083808 * | rs541513166 T TA
## rs552933761 chr22 29086616-29086617 * | rs552933761 CA C
## rs61611714 chr22 29086940-29086941 * | rs61611714 TG T
## rs541631272 chr22 29087474-29087478 * | rs541631272 GAAAT G
## rs537685613 chr22 29089333 * | rs537685613 A AT
## ... ... ... ... . ... ... ...
## rs543703620 chr22 29133462-29133463 * | rs543703620 CT C
## rs113960351 chr22 29135358 * | rs113960351 C CT
## rs17882761 chr22 29136187 * | rs17882761 C CA
## rs547061967 chr22 29136972-29136973 * | rs547061967 CG C
## rs199585274 chr22 29137694-29137695 * | rs199585274 CA C
## -------
## seqinfo: 25 sequences (1 circular) from hg19 genomeStep 2 | Find Broken Motifs
Now that we have our data in the required format, we may continue to the task at hand, and determine which variants modify potential transcription factor binding. An important element of this task is identifying a set of transcription factor binding motifs that we wish to query. Fortunately MotifDb includes a large selection of motifs across multiple species that we can see here:
## MotifDb object of length 12657
## | Created from downloaded public sources, last update: 2022-Mar-04
## | 12657 position frequency matrices from 22 sources:
## | FlyFactorSurvey: 614
## | HOCOMOCOv10: 1066
## | HOCOMOCOv11-core-A: 181
## | HOCOMOCOv11-core-B: 84
## | HOCOMOCOv11-core-C: 135
## | HOCOMOCOv11-secondary-A: 46
## | HOCOMOCOv11-secondary-B: 19
## | HOCOMOCOv11-secondary-C: 13
## | HOCOMOCOv11-secondary-D: 290
## | HOMER: 332
## | JASPAR_2014: 592
## | JASPAR_CORE: 459
## | ScerTF: 196
## | SwissRegulon: 684
## | UniPROBE: 380
## | cisbp_1.02: 874
## | hPDI: 437
## | jaspar2016: 1209
## | jaspar2018: 1564
## | jaspar2022: 1956
## | jolma2013: 843
## | stamlab: 683
## | 62 organism/s
## | Hsapiens: 6075
## | Mmusculus: 1554
## | Dmelanogaster: 1437
## | Athaliana: 1371
## | Scerevisiae: 1221
## | NA: 184
## | other: 815
## Scerevisiae-ScerTF-ABF2-badis
## Scerevisiae-ScerTF-CAT8-badis
## Scerevisiae-ScerTF-CST6-badis
## Scerevisiae-ScerTF-ECM23-badis
## Scerevisiae-ScerTF-EDS1-badis
## ...
## Mmusculus-UniPROBE-Zfp740.UP00022
## Mmusculus-UniPROBE-Zic1.UP00102
## Mmusculus-UniPROBE-Zic2.UP00057
## Mmusculus-UniPROBE-Zic3.UP00006
## Mmusculus-UniPROBE-Zscan4.UP00026### Here we can see which organisms are availible under which sources
### in MotifDb
table(mcols(MotifDb)$organism, mcols(MotifDb)$dataSource)| FlyFactorSurvey | HOCOMOCOv10 | HOCOMOCOv11-core-A | HOCOMOCOv11-core-B | HOCOMOCOv11-core-C | HOCOMOCOv11-secondary-A | HOCOMOCOv11-secondary-B | HOCOMOCOv11-secondary-C | HOCOMOCOv11-secondary-D | HOMER | JASPAR_2014 | JASPAR_CORE | ScerTF | SwissRegulon | UniPROBE | cisbp_1.02 | hPDI | jaspar2016 | jaspar2018 | jaspar2022 | jolma2013 | stamlab | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Acarolinensis | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Amajus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 3 | 0 | 0 |
| Anidulans | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | 0 |
| Apisum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Aterreus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Athaliana | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 48 | 5 | 0 | 0 | 0 | 107 | 0 | 191 | 452 | 568 | 0 | 0 |
| Bdistachyon | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
| Celegans | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 15 | 5 | 0 | 0 | 2 | 22 | 0 | 23 | 23 | 34 | 0 | 0 |
| Cparvum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Csativa | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ddiscoideum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 0 | 0 | 0 | 0 | 0 | 0 |
| Dmelanogaster | 614 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 131 | 125 | 0 | 0 | 0 | 138 | 0 | 139 | 140 | 150 | 0 | 0 |
| Drerio | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 |
| Gaculeatus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Gallus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ggallus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 4 | 1 | 0 | 0 |
| Hcapsulatum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Hroretzi | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| Hsapiens | 0 | 640 | 181 | 84 | 135 | 46 | 19 | 13 | 290 | 0 | 117 | 66 | 0 | 684 | 2 | 313 | 437 | 442 | 522 | 691 | 710 | 683 |
| Hsapiens;Ocuniculus;Mmusculus;Rrattus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Hvulgare | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| Mdomestica | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mgallopavo | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mmurinus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Mmusculus | 0 | 426 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 66 | 47 | 0 | 0 | 282 | 132 | 0 | 165 | 160 | 143 | 133 | 0 |
| Mmusculus;Hsapiens | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 |
| Mmusculus;Rnorvegicus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| Mmusculus;Rnorvegicus;Hsapiens | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 0 |
| Mmusculus;Rnorvegicus;Hsapiens;Ocuniculus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Mmusculus;Rnorvegicus;Omykiss;Ggallus;Hsapiens | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Mmusculus;Rnorvegicus;Xlaevis;Stropicalis;Ggallus;Hsapiens;Btaurus;Ocuniculus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| Mmusculus;Rrattus;Hsapiens;Ocuniculus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Mtruncatula | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 40 | 144 | 0 | 0 |
| Ncrassa | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 15 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ngruberi | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Nhaematococca | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Nsp. | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| Nsylvestris | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Nvectensis | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ocuniculus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 |
| Osativa | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 |
| Otauri | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
| Pcapensis | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Pfalciparum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 26 | 0 | 0 | 0 | 0 | 0 | 0 |
| Phybrida | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| Ppatens | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ppygmaeus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Psativum | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 0 | 0 | 0 | 1 | 0 | 3 | 3 | 1 | 0 | 0 |
| Ptetraurelia | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Rnorvegicus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 8 | 0 | 0 | 0 | 2 | 0 | 12 | 7 | 3 | 0 | 0 |
| Rnorvegicus;Hsapiens | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Rrattus | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 |
| Scerevisiae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 177 | 177 | 196 | 0 | 91 | 60 | 0 | 175 | 175 | 170 | 0 | 0 |
| Taestivam | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| Tthermophila | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Vertebrata | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 4 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 |
| Vvinifera | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Xlaevis | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 2 | 1 | 0 | 0 |
| Xtropicalis | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Zmays | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 6 | 0 | 0 | 0 | 1 | 0 | 6 | 8 | 41 | 0 | 0 |
We have leveraged the MotifList introduced by MotifDb
to include an additional set of motifs that have been gathered to this
package:
## MotifDb object of length 2817
## | Created from downloaded public sources, last update: 2022-Mar-04
## | 2817 position frequency matrices from 4 sources:
## | ENCODE-motif: 2065
## | FactorBook: 79
## | HOCOMOCO: 426
## | HOMER: 247
## | 1 organism/s
## | Hsapiens: 2817
## Hsapiens-ENCODE-motifs-SIX5_disc1
## Hsapiens-ENCODE-motifs-MYC_disc1
## Hsapiens-ENCODE-motifs-SRF_disc1
## Hsapiens-ENCODE-motifs-AP1_disc1
## Hsapiens-ENCODE-motifs-SIX5_disc2
## ...
## Hsapiens-HOMER-yy1.motif
## Hsapiens-HOMER-zbtb33.motif
## Hsapiens-HOMER-zfx.motif
## Hsapiens-HOMER-znf263.motif
## Hsapiens-HOMER-znf711.motifThe different studies included in this data set may be called individually; for example:
## MotifDb object of length 426
## | Created from downloaded public sources, last update: 2022-Mar-04
## | 426 position frequency matrices from 1 source:
## | HOCOMOCO: 426
## | 1 organism/s
## | Hsapiens: 426
## Hsapiens-HOCOMOCO-AHR_si
## Hsapiens-HOCOMOCO-AIRE_f2
## Hsapiens-HOCOMOCO-ALX1_si
## Hsapiens-HOCOMOCO-ANDR_do
## Hsapiens-HOCOMOCO-AP2A_f2
## ...
## Hsapiens-HOCOMOCO-ZN333_f1
## Hsapiens-HOCOMOCO-ZN350_f1
## Hsapiens-HOCOMOCO-ZN384_f1
## Hsapiens-HOCOMOCO-ZN423_f1
## Hsapiens-HOCOMOCO-ZN589_f1See ?motifbreakR_motif for more information and
citations.
Some of our data sets include a sequenceCount. These include
FlyFactorSurvey, hPDI,
JASPAR_2014, JASPAR_CORE, and
jolma2013 from MotifDb
and HOCOMOCO from the set of
motifbreakR_motif. Using these we calculate a pseudocount
to allow us to calculate the logarithms in the case where we have a
0 in a pwm. The calculation for incorporating pseudocounts
is
ppm <- (ppm * sequenceCount + 0.25)/(sequenceCount + 1).
If the sequenceCount for a particular ppm is NA we use 20
as a default sequenceCount.
Now that we have the three necessary components to run motifbreakR:
- A
BSgenomeobject for our organism, in this caseBSgenome.Hsapiens.UCSC.hg19 - A
MotifListobject containing our motifs, in this casehocomoco, - And our input
GRangesobject generated bysnps.from.rsid, in this casesnps.mb
We get to the task of actually running the function
motifbreakR().
We have several options that we may pass to the function, the main
ones that will dictate how long the function will run with a given set
of variants and motifs are the threshold we pass and the
method we use to score.
Here we specify the snpList, pwmList,
threshold that we declare as the cutoff for reporting
results, filterp set to true declares that we are filtering
by p-value, the method, and bkg the relative
nucleotide frequency of A, C, G, and T.
For the purposes of this small example, we use the
SerialParam back end. However, for larger variant lists,
MulticoreParam or one of the other BiocParallel
back-ends could speed up completion.
results <- motifbreakR(snpList = snps.mb[1:12], filterp = TRUE,
pwmList = subset(MotifDb,
dataSource %in% c("HOCOMOCOv11-core-A", "HOCOMOCOv11-core-B", "HOCOMOCOv11-core-C")),
threshold = 1e-4,
method = "ic",
bkg = c(A=0.25, C=0.25, G=0.25, T=0.25),
BPPARAM = BiocParallel::SerialParam())The results reveal which variants disrupt which motifs, and to which degree. If we want to examine a single variant, we can select one like this:
## GRanges object with 27 ranges and 20 metadata columns:
## seqnames ranges strand | SNP_id REF ALT varType
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet> <character>
## rs1006140:C chr19 38778915 - | rs1006140 A C SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## ... ... ... ... . ... ... ... ...
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:C chr19 38778915 - | rs1006140 A C SNV
## rs1006140:C chr19 38778915 - | rs1006140 A C SNV
## rs1006140:T chr19 38778915 - | rs1006140 A T SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## motifPos geneSymbol dataSource providerName providerId
## <list> <character> <character> <character> <character>
## rs1006140:C -13, 8 ZN467 HOCOMOCOv11-core-C ZN467_HUMAN.H11MO.0.C ZN467_HUMAN.H11MO.0.C
## rs1006140:G -8, 4 E2F7 HOCOMOCOv11-core-B E2F7_HUMAN.H11MO.0.B E2F7_HUMAN.H11MO.0.B
## rs1006140:G -15, 6 SP1 HOCOMOCOv11-core-A SP1_HUMAN.H11MO.0.A SP1_HUMAN.H11MO.0.A
## rs1006140:G -5, 5 KLF12 HOCOMOCOv11-core-C KLF12_HUMAN.H11MO.0.C KLF12_HUMAN.H11MO.0.C
## rs1006140:G -6, 8 KLF9 HOCOMOCOv11-core-C KLF9_HUMAN.H11MO.0.C KLF9_HUMAN.H11MO.0.C
## ... ... ... ... ... ...
## rs1006140:G -14, 7 ZN143 HOCOMOCOv11-core-A ZN143_HUMAN.H11MO.0.A ZN143_HUMAN.H11MO.0.A
## rs1006140:C -14, 7 ZN143 HOCOMOCOv11-core-A ZN143_HUMAN.H11MO.0.A ZN143_HUMAN.H11MO.0.A
## rs1006140:C -11, 3 KLF9 HOCOMOCOv11-core-C KLF9_HUMAN.H11MO.0.C KLF9_HUMAN.H11MO.0.C
## rs1006140:T -5, 4 KLF4 HOCOMOCOv11-core-A KLF4_HUMAN.H11MO.0.A KLF4_HUMAN.H11MO.0.A
## rs1006140:G -11, 10 SP2 HOCOMOCOv11-core-A SP2_HUMAN.H11MO.0.A SP2_HUMAN.H11MO.0.A
## seqMatch pctRef pctAlt scoreRef scoreAlt Refpvalue Altpvalue
## <character> <numeric> <numeric> <numeric> <numeric> <logical> <logical>
## rs1006140:C ctctgctgaccccactcccc.. 0.775627 0.806966 10.66759 11.08109 <NA> <NA>
## rs1006140:G accccactcccc.. 0.803434 0.923907 6.68298 7.65925 <NA> <NA>
## rs1006140:G ctctgctgaccccactcccc.. 0.758168 0.845123 14.10174 15.67334 <NA> <NA>
## rs1006140:G cccactcccc.. 0.840058 0.928011 10.99304 12.13449 <NA> <NA>
## rs1006140:G tgaccccactcccc.. 0.806264 0.847777 11.52649 12.10930 <NA> <NA>
## ... ... ... ... ... ... ... ...
## rs1006140:G ctctgctgaccccactcccc.. 0.747658 0.695443 12.66301 11.8163 <NA> <NA>
## rs1006140:C ctctgctgaccccactcccc.. 0.747658 0.685454 12.66301 11.6544 <NA> <NA>
## rs1006140:C tgaccccactcccc.. 0.806264 0.862410 11.52649 12.3147 <NA> <NA>
## rs1006140:T ccactcccc.. 0.957953 0.921141 10.72543 10.3171 <NA> <NA>
## rs1006140:G ctctgctgaccccactcccc.. 0.812640 0.918401 9.06648 10.1848 <NA> <NA>
## altPos alleleDiff alleleEffectSize effect
## <integer> <numeric> <numeric> <character>
## rs1006140:C 1 0.413503 0.0303419 weak
## rs1006140:G 1 0.976264 0.1179651 strong
## rs1006140:G 1 1.571597 0.0850776 strong
## rs1006140:G 1 1.141453 0.0873421 strong
## rs1006140:G 1 0.582811 0.0409094 weak
## ... ... ... ... ...
## rs1006140:G 1 -0.846669 -0.0505330 strong
## rs1006140:C 1 -1.008640 -0.0602002 strong
## rs1006140:C 1 0.788242 0.0553293 strong
## rs1006140:T 1 -0.408366 -0.0364878 weak
## rs1006140:G 1 1.118277 0.1012240 strong
## -------
## seqinfo: 25 sequences (1 circular) from hg19 genomeHere we can see that SNP rs1006140 disrupts multiple motifs. We can
then check what the pvalue for each allele is with regard to each motif,
using calculatePvalue.
## GRanges object with 16 ranges and 23 metadata columns:
## seqnames ranges strand | SNP_id REF ALT varType
## <Rle> <IRanges> <Rle> | <character> <DNAStringSet> <DNAStringSet> <character>
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:T chr19 38778915 - | rs1006140 A T SNV
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:T chr19 38778915 - | rs1006140 A T SNV
## ... ... ... ... . ... ... ... ...
## rs1006140:G chr19 38778915 - | rs1006140 A G SNV
## rs1006140:T chr19 38778915 - | rs1006140 A T SNV
## rs1006140:C chr19 38778915 - | rs1006140 A C SNV
## rs1006140:C chr19 38778915 - | rs1006140 A C SNV
## rs1006140:T chr19 38778915 - | rs1006140 A T SNV
## motifPos geneSymbol dataSource providerName providerId seqMatch
## <list> <character> <character> <character> <character> <character>
## rs1006140:G -5, 5 KLF1 HOCOMOCO KLF1_f1 KLF1_HUMAN cccactc..
## rs1006140:G -2, 8 EGR1 HOCOMOCO EGR1_f2 EGR1_HUMAN cccactc..
## rs1006140:T -5, 5 KLF1 HOCOMOCO KLF1_f1 KLF1_HUMAN cccactc..
## rs1006140:G -10, 11 RREB1 HOCOMOCO RREB1_si RREB1_HUMAN gctctgctgaccccactc..
## rs1006140:T -3,13 ZBTB4 HOCOMOCO ZBTB4_si ZBTB4_HUMAN gctgaccccactc..
## ... ... ... ... ... ... ...
## rs1006140:G -3, 9 EPAS1 HOCOMOCO EPAS1_si EPAS1_HUMAN accccactc..
## rs1006140:T -3, 9 EPAS1 HOCOMOCO EPAS1_si EPAS1_HUMAN accccactc..
## rs1006140:C -6, 8 ZNF148 HOCOMOCO ZN148_si ZN148_HUMAN tgaccccactc..
## rs1006140:C -3, 9 EPAS1 HOCOMOCO EPAS1_si EPAS1_HUMAN accccactc..
## rs1006140:T -2, 5 IKZF1 HOCOMOCO IKZF1_f1 IKZF1_HUMAN actc..
## pctRef pctAlt scoreRef scoreAlt Refpvalue Altpvalue snpPos alleleRef
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <integer> <numeric>
## rs1006140:G 0.960844 0.871972 8.99202 8.18880 3.24249e-05 2.63691e-04 <NA> NA
## rs1006140:G 0.871144 0.918955 9.92843 10.46639 1.41621e-04 3.98159e-05 <NA> NA
## rs1006140:T 0.960844 0.860781 8.99202 8.08766 3.24249e-05 3.42369e-04 <NA> NA
## rs1006140:G 0.821312 0.749228 10.06841 9.21044 1.83542e-05 2.63112e-04 <NA> NA
## rs1006140:T 0.797832 0.744510 12.74424 11.91989 1.21765e-05 8.17876e-05 <NA> NA
## ... ... ... ... ... ... ... ... ...
## rs1006140:G 0.915901 0.792753 7.09686 6.17249 1.02818e-05 7.11918e-04 <NA> NA
## rs1006140:T 0.915901 0.811224 7.09686 6.31114 1.02818e-05 4.33713e-04 <NA> NA
## rs1006140:C 0.880142 0.935234 9.89863 10.50089 4.94868e-05 6.27805e-06 <NA> NA
## rs1006140:C 0.915901 0.836589 7.09686 6.50153 1.02818e-05 2.00659e-04 <NA> NA
## rs1006140:T 0.852780 0.991006 6.25307 7.25513 1.83105e-03 7.62939e-05 <NA> NA
## alleleAlt effect altPos alleleDiff alleleEffectSize
## <numeric> <character> <integer> <numeric> <numeric>
## rs1006140:G NA strong 1 -0.803230 -0.0859444
## rs1006140:G NA weak 1 0.537962 0.0472796
## rs1006140:T NA strong 1 -0.904368 -0.0967661
## rs1006140:G NA strong 1 -0.857970 -0.0703529
## rs1006140:T NA strong 1 -0.824348 -0.0519448
## ... ... ... ... ... ...
## rs1006140:G NA strong 1 -0.924373 -0.1196115
## rs1006140:T NA strong 1 -0.785724 -0.1016707
## rs1006140:C NA weak 1 0.602262 0.0537307
## rs1006140:C NA weak 1 -0.595327 -0.0770338
## rs1006140:T NA strong 1 1.002061 0.1368875
## -------
## seqinfo: 16 sequences from hg19 genomeAnd here we see that for each SNP we have at least one allele
achieving a p-value below 1e-4 threshold that we required. The
seqMatch column shows what the reference genome sequence is
at that location, with the variant position appearing in an uppercase
letter. pctRef and pctAlt display the the score for the motif in the
sequence as a percentage of the best score that motif could achieve on
an ideal sequence. In other words (scoreVariant − minscorePWM)/(maxscorePWM − minscorePWM).
We can also see the absolute scores for our method in scoreRef and
scoreAlt and thier respective p-values.
Parallel Evaluation (an aside)
Important to note, is that motifbreakR uses the BiocParallel
parallel back-end, and one may modify what type of parallel evaluation
it uses (or if it runs in parallel at all). Here we can see the versions
available on the machine this vignette was compiled on.
## $MulticoreParam
## class: MulticoreParam
## bpisup: FALSE; bpnworkers: 2; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: TRUE; bpexportvariables: FALSE; bpforceGC: FALSE
## bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: FORK
##
## $SnowParam
## class: SnowParam
## bpisup: FALSE; bpnworkers: 2; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: TRUE; bpexportvariables: TRUE; bpforceGC: FALSE
## bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: SOCK
##
## $SerialParam
## class: SerialParam
## bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
## bpfallback: FALSE
## bplogdir: NA
## bpresultdir: NA## class: MulticoreParam
## bpisup: FALSE; bpnworkers: 2; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: TRUE; bpexportvariables: FALSE; bpforceGC: FALSE
## bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: FORKBy default motifbreakR uses bpparam() as an
argument to BPPARAM and will use all available cores on the
machine on which it is running. However on Windows machines this reverts
to using a serial evaluation model, so if you wish to run in parallel on
a Windows machine consider using a different parameter shown in
BiocParallel::registered() such as SnowParam
passing BPPARAM = SnowParam().
Step 3 | Visualize
Now that we have our results, we can visualize them with the function
plotMB. Lets take a look at rs1006140.
## Loading required namespace: Cairo## Warning in checkValidSVG(doc, warn = warn): This picture may not have been generated by Cairo
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## graphics; errors may result## Loading required namespace: Cairo## Warning in checkValidSVG(doc, warn = warn): This picture may not have been generated by Cairo
## graphics; errors may result## Loading required namespace: Cairo## Warning in checkValidSVG(doc, warn = warn): This picture may not have been generated by Cairo
## graphics; errors may result
Shiny version
In addition to the existing interface, we have implemented an R/Shiny graphical user interface to simplify and enhance access to researchers with different skill sets. This is focused on human variants.
In order to launch the shiny version, one executes the following two lines:
Added functionality | Query Remap 2022 Peaks
While computational prediction of differential transcription factor binding potential based on sequence preference is the core of motifbreakR, grounding the analysis in observed transcription factor binding can improve the prioritization of results. ReMap[^remap2022] provides manually curated, high quality catalogs of regulatory regions based on DNA binding experiments in Human, Mouse, Fly and Arabidopsis thaliana
We can annotate results with the ReMap sourced TF peaks corresponding to to motif/transcription factor relationships provided by the constituent public MotifDb sources. The user may optionally query an expanded motif/transcription factor relationship encompassing the entire potential transcription factor family as implemented by MotifDb based on TFClass[^TFclass].
[^remap2022] Website: Remap Paper: ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
[^TFclass] Website: Classification of Transcription Factors in Mammalia Paper: TFClass: expanding the classification of human transcription factors to their mammalian orthologs
Export Results
There are two exports that motifbreakR can generate in addition to the figures. We can export a table of results resembling the results object, either as CSV or TSV files.
Alternatively, we can export a BED file of results. The BED file
represents the variants that interact with motifs. They are named by the
variant name, reference and alternate alleles, and the name of the motif
disrupted. The intervals may be colored with diverging color scale for
effect_size (blue representing stronger binding in
REF}, red representing stronger binding inALT), or a sequential color scale otherwise (low values as purple, high values as yellow). The score column is either theeffect_size(alleleDiffcolumn), the -log10(p-value) (capped at 10), corresponding toRefpvalue,Altpvalue, or the best match of the two, or thescorepctRef,pctAlt`,
or the highest match of the two.
Methods
motifbreakR
works with position probability matrices (PPM). PPM are derived as the
fractional occurrence of nucleotides A,C,G, and T at each position of a
position frequency matrix (PFM). PFM are simply the tally of each
nucleotide at each position across a set of aligned sequences. With a
PPM, one can generate probabilities based on the genome, or more
practically, create any number of position specific scoring matrices
(PSSM) based on the principle that the PPM contains information about
the likelihood of observing a particular nucleotide at a particular
position of a true transcription factor binding site. What follows is a
discussion of the three different algorithms that may be employed in
calls to the motifbreakR
function via the method argument.
Suppose we have a frequency matrix M of width n (i.e. a PPM as described above). Furthermore, we have a sequence s also of length n, such that si ∈ {A, T, C, G}, i = 1, …n. Each column of M contains the frequencies of each letter in each position.
Commonly in the literature sequences are scored as the sum of log probabilities:
Sum of Log Probabilities
$$F( s,M ) = \sum_{i = 1}^{n}{\log( \frac{M_{s_{i},i}}{b_{s_{i}}} )}$$
where bsi
is the background frequency of letter si in the genome
of interest. This method can be specified by the user as
method='log'.
As an alternative to this method, we introduced a scoring method to
directly weight the score by the importance of the position within the
match sequence. This method of weighting is accessed by specifying
method='default' (weighted sum). A general representation
of this scoring method is given by:
Weighted Sum
F(s, M) = p(s) ⋅ ωM
where ps is the scoring vector derived from sequence s and matrix M, and wM is a weight vector derived from M. First, we compute the scoring vector of position scores p:
Calculating Scoring Vector p
$$p( s ) = ( M_{s_{i},i} ) \textrm{ where } \frac{i = 1,\ldots n}{s_{i} \in \{ A,C,G,T \}}$$
and second, for each M a constant vector of weights ωM = (ω1, ω2, …, ωn).
There are two methods for producing ωM. The first, which we call weighted sum, is the difference in the probabilities for the two letters of the polymorphism (or variant), i.e. Δpsi, or the difference of the maximum and minimum values for each column of M:
Calculating ω For Weighted Sum
ωi = max {Mi} − min {Mi} where i = 1, …n
The second variation of this theme is to weight by relative entropy. Thus the relative entropy weight for each column i of the matrix is given by:
Calculating ω For Relative Entropy
$$\omega_{i} = \sum_{j \in \{ A,C,G,T \}}^{}{M_{j,i}\log_2( \frac{M_{j,i}}{b_{i}} )}\textrm{ where }i = 1,\ldots n$$
where bi is again the background frequency of the letter i.
Thus, there are 3 possible algorithms to apply via the
method argument. The first is the standard summation of log
probabilities (method='log'). The second and third are the
weighted sum and information content methods
(method='default' and method='ic') specified
by equations for Weighted Sum and Relative Entropy, respectively. motifbreakR
assumes a uniform background nucleotide distribution (b) in equations 4.1 and 4.5 unless otherwise
specified by the user. Since we are primarily interested in the
difference between alleles, background frequency is not a major factor,
although it can change the results. Additionally, inclusion of
background frequency introduces potential bias when collections of
motifs are employed, since motifs are themselves unbalanced with respect
to nucleotide composition. With these cautions in mind, users may
override the uniform distribution if so desired. For all three methods,
motifbreakR
scores and reports the reference and alternate alleles of the sequence
(F(sREF, M)
and F(sALT, M)),
and provides the matrix scores psREF
and psALT
of the SNP (or variant). The scores are scaled as a fraction of scoring
range 0-1 of the motif matrix, M. If either of F(sREF, M)
and F(sALT, M)
is greater than a user-specified threshold (default value of 0.85) the
SNP is reported. By default motifbreakR
does not display neutral effects, (Δpi < 0.4)
but this behavior can be overridden.
Calculate P-values for PWM match
Additionally, now, with the use of TFMPvalue,
we may filter by p-value of the match. This is unfortunately a two step
process. First, by invoking filterp=TRUE and setting a
threshold at a desired p-value e.g 1e-4, we perform a rough filter on
the results by rounding all values in the PWM to two decimal place, and
calculating a scoring threshold based upon that. The second step is to
use the function calculatePvalue() on a selection of
results which will change the Refpvalue and
Altpvalue columns in the output from NA to the
p-value calculated by TFMsc2pv. This can be (although not
always) a very memory and time intensive process if the algorithm
doesn’t converge rapidly.
P-values can also be calculated in parallel, it is highly recommended to round the PWM matrix with the granularity argument. This trades the accuracy of the p-value calculation for speed of convergence. For most purposes a range of 1e-4 to 1e-6 is an acceptable trade off between accuracy and speed.
The granularity in TFMPvalue paper is defined:
“Let M be a matrix of real coefficient values of length m and let ϵ be a positive real number. We denote Mϵ the round matrix deduced from M by rounding each value by ϵ:”
$$M_\epsilon(i,x) = \epsilon \lfloor \frac{M(i,x)}{\epsilon} \rfloor$$
Session Info
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 grid stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BSgenome.Drerio.UCSC.danRer7_1.4.0 BSgenome.Hsapiens.UCSC.hg19_1.4.3
## [3] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24 BSgenome_1.75.0
## [5] rtracklayer_1.67.0 BiocIO_1.17.1
## [7] motifbreakR_2.21.0 MotifDb_1.49.0
## [9] Biostrings_2.75.3 XVector_0.47.0
## [11] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2
## [13] IRanges_2.41.2 S4Vectors_0.45.2
## [15] BiocGenerics_0.53.3 generics_0.1.3
## [17] BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] later_1.4.1 bitops_1.0-9 filelock_1.0.3
## [4] R.oo_1.27.0 tibble_3.2.1 XML_3.99-0.17
## [7] rpart_4.1.23 DirichletMultinomial_1.49.0 lifecycle_1.0.4
## [10] httr2_1.0.7 pwalign_1.3.1 vroom_1.6.5
## [13] lattice_0.22-6 ensembldb_2.31.0 MASS_7.3-61
## [16] backports_1.5.0 magrittr_2.0.3 Hmisc_5.2-1
## [19] sass_0.4.9 rmarkdown_2.29 jquerylib_0.1.4
## [22] yaml_2.3.10 httpuv_1.6.15 grImport2_0.3-3
## [25] Gviz_1.51.0 DBI_1.2.3 buildtools_1.0.0
## [28] CNEr_1.43.0 RColorBrewer_1.1-3 ade4_1.7-22
## [31] abind_1.4-8 zlibbioc_1.52.0 R.utils_2.12.3
## [34] AnnotationFilter_1.31.0 biovizBase_1.55.0 RCurl_1.98-1.16
## [37] nnet_7.3-19 pracma_2.4.4 VariantAnnotation_1.53.0
## [40] rappdirs_0.3.3 GenomeInfoDbData_1.2.13 maketools_1.3.1
## [43] seqLogo_1.73.0 annotate_1.85.0 codetools_0.2-20
## [46] DelayedArray_0.33.3 DT_0.33 xml2_1.3.6
## [49] tidyselect_1.2.1 UCSC.utils_1.3.0 matrixStats_1.4.1
## [52] BiocFileCache_2.15.0 base64enc_0.1-3 GenomicAlignments_1.43.0
## [55] jsonlite_1.8.9 motifStack_1.51.0 Formula_1.2-5
## [58] tools_4.4.2 progress_1.2.3 TFMPvalue_0.0.9
## [61] Rcpp_1.0.13-1 glue_1.8.0 gridExtra_2.3
## [64] SparseArray_1.7.2 xfun_0.49 MatrixGenerics_1.19.0
## [67] dplyr_1.1.4 BiocManager_1.30.25 fastmap_1.2.0
## [70] latticeExtra_0.6-30 fansi_1.0.6 caTools_1.18.3
## [73] digest_0.6.37 R6_2.5.1 mime_0.12
## [76] colorspace_2.1-1 GO.db_3.20.0 gtools_3.9.5
## [79] poweRlaw_0.80.0 jpeg_0.1-10 dichromat_2.0-0.1
## [82] biomaRt_2.63.0 RSQLite_2.3.9 R.methodsS3_1.8.2
## [85] utf8_1.2.4 data.table_1.16.4 prettyunits_1.2.0
## [88] httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.7.1
## [91] TFBSTools_1.45.0 pkgconfig_2.0.3 gtable_0.3.6
## [94] blob_1.2.4 sys_3.4.3 htmltools_0.5.8.1
## [97] ProtGenerics_1.39.0 scales_1.3.0 Biobase_2.67.0
## [100] png_0.1-8 knitr_1.49 rstudioapi_0.17.1
## [103] tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.23
## [106] checkmate_2.3.2 curl_6.0.1 cachem_1.1.0
## [109] stringr_1.5.1 parallel_4.4.2 foreign_0.8-87
## [112] AnnotationDbi_1.69.0 restfulr_0.0.15 pillar_1.9.0
## [115] vctrs_0.6.5 promises_1.3.2 dbplyr_2.5.0
## [118] xtable_1.8-4 cluster_2.1.8 htmlTable_2.4.3
## [121] evaluate_1.0.1 readr_2.1.5 GenomicFeatures_1.59.1
## [124] cli_3.6.3 compiler_4.4.2 Rsamtools_2.23.1
## [127] rlang_1.1.4 crayon_1.5.3 interp_1.1-6
## [130] plyr_1.8.9 stringi_1.8.4 deldir_2.0-4
## [133] BiocParallel_1.41.0 munsell_0.5.1 lazyeval_0.2.2
## [136] Matrix_1.7-1 hms_1.1.3 bit64_4.5.2
## [139] ggplot2_3.5.1 KEGGREST_1.47.0 shiny_1.10.0
## [142] SummarizedExperiment_1.37.0 bsicons_0.1.2 memoise_2.0.1
## [145] bslib_0.8.0 bit_4.5.0.1 splitstackshape_1.4.8Website: encode-motifs Paper: Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments↩︎
Website: Factorbook Paper: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors↩︎
Website: HOCOMOCO Paper: HOCOMOCO: a comprehensive collection of human transcription factor binding sites models↩︎
Website: Homer Paper: http://www.sciencedirect.com/science/article/pii/S1097276510003667↩︎