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Meta-data in Bioconductor Educational Materials 2004 R. Gentleman 1
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Page 1: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

Meta-data in Bioconductor

Educational Materials©2004 R. Gentleman

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Overview

� Closing the gap between knowledge of sequence and knowledgeof function requires aggressive, integrative use of biologicalresearch databases of many different types.

� In this lecture we focus attention on resources that can help tomake use of meta-data in different analyses.

� We make use of the following packages: annotate, GO, KEGG,hgu133a, GOstats, and cMAP.

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Per chip annotation

� An early design decision was that we should provide meta-dataon a per chip-type basis.> library("hgu133a")

> ls("package:hgu133a")

[1] "hgu133a" "hgu133aACCNUM"

[3] "hgu133aCHR" "hgu133aCHRLENGTHS"

[5] "hgu133aCHRLOC" "hgu133aENZYME"

[7] "hgu133aENZYME2PROBE" "hgu133aGENENAME"

[9] "hgu133aGO" "hgu133aGO2ALLPROBES"

[11] "hgu133aGO2PROBE" "hgu133aGRIF"

[13] "hgu133aLOCUSID" "hgu133aMAP"

[15] "hgu133aOMIM" "hgu133aORGANISM"

[17] "hgu133aPATH" "hgu133aPATH2PROBE"

[19] "hgu133aPMID" "hgu133aPMID2PROBE"

[21] "hgu133aREFSEQ" "hgu133aSUMFUNC"

[23] "hgu133aSYMBOL" "hgu133aUNIGENE"

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A brief description

� These packages contain R environments, which are used ashash tables.

� For each package there is quality control information available,use hgu133a(); which report how many of each of the differentmappings were found.

� You can access the data directly using any of the standardsubsetting or extraction tools for environments; get, mget, $and [[.

> hgu133aSYMBOL$"201473_at"

[1] "JUNB"

> hgu133aLOCUSID[["201476_s_at"]]

[1] 6240

> get("201475_x_at", hgu133aOMIM)

[1] "156560"

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MetaData

LocusLink is a catalog of genetic loci that connects curatedsequence information to official nomenclatur

UniGene defines sequence clusters. UniGene focuses onprotein-coding genes of the nuclear genome (excluding rRNAand mitochondrial sequences).

RefSeq is a non-redundant dataset of transcripts and proteins ofknown genes for a variety of species, including human, mouseand rat.

Enzyme Commission (EC) numbers are assigned to differentenzymes and linked to genes through their association withLocusLink identifiers.

Gene Ontology (GO) is a structured vocabulary of termsdescribing gene products according to relevant molecularfunction, biological process, or cellular component.

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Meta-data

PubMed is a service of the U.S. National Library of Medicine.PubMed provides a very rich resource of data and tools forworking with papers published in journals that are related tomedicine and health. The data source, while large, is notcomprehensive and not all papers have been abstracted.

LITDB The Protein Research Foundation curates LITDB, whichcovers all articles dealing with peptides from scientific journalsaccessible in Japan.

OMIM Online Mendelian Inheritance in Man is a catalog ofhuman genes and genetic disorders.

NetAffx The NetAffx Analysis Center provides tools thatcorrelate experimental data assayed using the AffymetrixGeneChip technology.

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Meta-data

KEGG Kyoto Encyclopedia of Genes and Genomes; a collection ofdata resources including a rich collection of pathway data.

cMAP Pathway data from both KEGG and BioCarta, in acomputable form.

Chromosomal Location Genes are identified with chromosomes,and where appropriate with strand.

Data Archives The NCBI coordinates the Gene ExpressionOmnibus (GEO); TIGR provides the Resourcerer database,and the EBI supports ArrayExpress.

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Working with Meta-data

� Suppose for example, we are interested in the gene BAD.> gsyms <- unlist(as.list(hgu95av2SYMBOL))

> whBAD <- grep("^BAD$", gsyms)

> gsyms[whBAD]

1861_at

"BAD"

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BAD Pathways

� Now find the pathways that BAD is associated with.> BADpath <- hgu95av2PATH$"1861_at"

> mget(BADpath, KEGGPATHID2NAME)

$"04210"

[1] "Apoptosis"

$"05030"

[1] "Amyotrophic lateral sclerosis (ALS)"

> allProbes <- mget(BADpath, hgu95av2PATH2PROBE)

> sapply(allProbes, length)

04210 05030

149 28

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Annotating a Genome

� Bioconductor also provides some comprehensive annotationsfor whole genomes (e.g. S. cerevisae).

� These packages are like the chip annotation packages, except adifferent set of primary keys is used (e.g. for yeast we use thesystematic names such as YBL088C)> library("YEAST")

> ls("package:YEAST")

[1] "YEAST" "YEASTALIAS"

[3] "YEASTCHR" "YEASTCHRLENGTHS"

[5] "YEASTCHRLOC" "YEASTDESCRIPTION"

[7] "YEASTENZYME" "YEASTENZYME2PROBE"

[9] "YEASTGENENAME" "YEASTGO"

[11] "YEASTGO2ALLPROBES" "YEASTGO2PROBE"

[13] "YEASTORGANISM" "YEASTPATH"

[15] "YEASTPATH2PROBE" "YEASTPMID"

[17] "YEASTPMID2PROBE"

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The annotate package

� Functions for harvesting of curated persistent data sources

� functions for simple HTTP queries to web service providers

� interface code that provides common calling sequences for theassay based meta-data packages such as getGI and getSEQ

perform web queries to NCBI to extract the GI or nucleotidesequence corresponding to a GenBank accession number.> ggi <- getGI("M22490")

> ggi

[1] "179503"

> gsq <- getSEQ("M22490")

> substring(gsq, 1, 40)

[1] "GGCAGAGGAGGAGGGAGGGAGGGAAGGAGCGCGGAGCCCG"

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The annotate package

� other interface functions include getGO, getSYMBOL, getPMID,and getLL

� functions whose names start with pm work with lists of PubMedidentifiers for journal articles.> hoxa9 <- "37809_at"

> absts <- pm.getabst(hoxa9, "hgu95av2")

> substring(abstText(absts[[1]][[1]]), 1, 60)

[1] "In primary cells from acute leukemia patients, expression of"

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Working with GO

� An ontology is a structured vocabulary that characterizes someconceptual domain.

� The Gene Ontology (GO) Consortium defines three ontologiescharacterizing aspects of knowledge about genes and geneproducts.

� These ontologies are

– molecular function (MF),

– biological process (BP)

– cellular component (CC).

� for explicit descriptions of these categories you should consultthe GO web page.

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GO

� molecular function of a gene product is what it does at thebiochemical level. This describes what the gene product cando, but without reference to where or when this activityactually occurs. Examples of functional terms include“enzyme,”“transporter,” or “ligand.”

� biological process is a biological objective to which the geneproduct contributes. There is often a temporal aspect to abiological process. Biological processes usually involve thetransformation of a physical thing. The terms “DNAreplication” or “signal transduction” describe general biologicalprocesses.

� cellular component is a part of a cell that is a component ofsome larger object or structure. Examples of cellularcomponents include “chromosome”, “nucleus” and “ribosome”.

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GO Characteristics

Number of Terms

BP 8578

CC 1335

MF 6891

Table 1: Number of GO terms per ontology.

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Working with GO For precision and conciseness, all indexing of GOresources employs the 7 digit tags with prefix GO:. Three very basictasks that are commonly performed in conjunction with GO are

� navigating the hierarchy, determining parents and children ofselected terms, and deriving subgraphs of the overall DAGconstituting GO;

� resolving the mapping from GO tag to natural languagecharacterizations of function, location, or process;

� resolving the mapping between GO tags or terms and elementsof catalogs of genes or gene products.

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Navigating the hierarchy

� Finding parents and children of different terms is handled byusing the PARENT and CHILDREN mappings.

� To find the children of "GO:0008094" we use:> get("GO:0008094", GOMFCHILDREN)

[1] "GO:0004003" "GO:0008722" "GO:0015616" "GO:0043142"

� We use the term offspring to refer to all descendants (children,grandchildren, and so on) of a node.

� Similarly we use the term ancestor to refer to the parents,grandparents, and so on, of a node.> get("GO:0008094", GOMFOFFSPRING)

[1] "GO:0004003" "GO:0008722" "GO:0015616" "GO:0043142"

[5] "GO:0017116" "GO:0043140" "GO:0043141"

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Searching for terms

� All GO terms are provided in the GOTERM environment. It isrelatively easy to search for a term with the word chromosomein it using eapply and grep or agrep.> hasChr <- eapply(GOTERM, function(x) x[grep("chromosome",

+ Term(x))])

> lens <- sapply(hasChr, length)

> hasChr <- hasChr[lens > 0]

> length(hasChr)

[1] 64

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Searching for terms

� We can write a function:> GOTerm2Tag <- function(term) {

+ GTL <- eapply(GOTERM, function(x) {

+ grep(term, x@Term, value = TRUE)

+ })

+ Gl <- sapply(GTL, length)

+ names(GTL[Gl > 0])

+ }

� and then apply to find all terms with a specific phrase, forexample, “transcription factor binding”:> hasTFA <- GOTerm2Tag("transcription factor binding")

> hasTFA

[1] "GO:0003719" "GO:0008134"

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Evidence Codes

� The mapping of genes to GO terms is carried out separately byGOA

� Four environments in the GO package address the associationbetween LocusLink sequence entries and GO terms: GOLOCUSID,GOALLOCUSID, GOLOCUSID2GO, and GOLOCUSID2ALLGO

Term Definition

IMP inferred from mutant phenotype

ISS inferred from sequence similarity

IEA inferred from electronic annotation

TAS traceable author statement

Table 2: Some GO Evidence Codes.

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GO Evidence Codes

� find the GO identifier for “transcription factor binding” and usethat to get all LocusLink identifiers that have that annotation.> gg1 <- get(GOTerm2Tag("^transcription factor binding$"),

+ GOLOCUSID)

> table(names(gg1))

IDA IMP IPI ISS NAS TAS

9 1 8 16 4 28

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LocusLink ID

� consider the gene with LocusLink ID 7355, SLC35A2> ll1 <- GOLOCUSID2GO[["7355"]]

> length(ll1)

[1] 9

> sapply(ll1, function(x) x$Ontology)

GO:0000139 GO:0015785 GO:0005459 GO:0008643 GO:0006012

"CC" "BP" "MF" "BP" "BP"

GO:0016021 GO:0015780 GO:0005338 GO:0005351

"CC" "BP" "MF" "MF"

� there are 9 different GO terms.

� We get those from the BP ontology by using getOntology.> getOntology(ll1, "BP")

[1] "GO:0015785" "GO:0008643" "GO:0006012" "GO:0015780"

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Evidence Codes

� then get the evidence codes using getEvidence

� we can drop codes using dropEcode

> getEvidence(ll1)

GO:0000139 GO:0015785 GO:0005459 GO:0008643 GO:0006012

"IEA" "TAS" "TAS" "IEA" "TAS"

GO:0016021 GO:0015780 GO:0005338 GO:0005351

"IEA" "IEA" "IEA" "IEA"

> zz <- dropECode(ll1, code = "IEA")

> getEvidence(zz)

GO:0015785 GO:0005459 GO:0006012

"TAS" "TAS" "TAS"

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GO graphs

� For any set of selected genes, and any of the three GOontologies the induced GO graph is the set of GO terms that thegenes are associated with, together with all less specific terms

� the term “transcription factor activity” is in the molecularfunction (MF) ontology and has the GO label GO:0003700

> library("GO")

> library("GOstats")

> GOTERM$"GO:0003700"

GOID = GO:0003700

Term = transcription factor activity

Definition = Any protein required to initiate or

regulate transcription; includes both gene

regulatory proteins as well as the general

transcription factors.

Ontology = MF

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� The induced graph, based on the MF hierarchy, can beproduced using the GOGraph function of the package GOstats

> tfG <- GOGraph("GO:0003700", GOMFPARENTS)

� we can plot the induced GO graph using Rgraphviz and thecode below.> plot(tfG, nodeAttrs = nattr)

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transcription factor activity

DNA binding

transcription regulator activity

molecular_function

nucleic acid binding

binding

GO

Figure 1: Graph of GO relationships for the term “transcriptionfactor activity”.

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Induced GO graphs

> tfch <- GOMFCHILDREN$"GO:0003700"

[1] "GO:0003705"

> tfchild <- mget(tfch, GOTERM)

$"GO:0003705"

GOID = GO:0003705

Term = RNA polymerase II transcription factor

activity, enhancer binding

Definition = Functions to initiate or regulate RNA

polymerase II transcription by binding a

promoter or enhancer region of DNA.

Ontology = MF

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KEGG

� KEGG provides on set of mappings from genes to pathways.

� For each package we provide mappings, you can also query thesite directly using KEGGSOAP or any other software.

� One problem with the KEGG is that the data is not in a formthat is amenable to computation. The cMAP project providesdata that is somewhat more useful for constructing networks.

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KEGG

Data available in the KEGG package includes:

KEGGEXTID2PATHID which provides mappings from eitherLocusLink (for human, mouse and rat) or Open Reading Frame(yeast) to KEGG pathways, a second environment,KEGGPATHID2EXTID contains the mappings in the otherdirection.

KEGGPATHID2NAME which provides mappings from theKEGG path ID to a name (textual description of the pathway).Only the numeric part of the KEGG pathway identifiers is used(and not the three letter species codes).

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Counts per species

ath dme hsa mmu rno sce

Counts 105 105 133 123 115 98

Table 3: Pathway Counts Per Species

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Exploring KEGG

� Consider the pathway 00140

� species specific mappings, from a pathway to the genes itcontains, are indicated by gluing together a three letter speciescode, such as hsa for homo sapiens, to the numeric pathwaycode.> KEGGPATHID2NAME$"00140"

[1] "C21-Steroid hormone metabolism"

> KEGGPATHID2EXTID$hsa00140

[1] "1109" "1583" "1584" "1585" "1586" "1589" "3283" "3284"

[9] "3290" "3291" "6718"

> KEGGPATHID2EXTID$sce00140

[1] "YGL001C"

� We look up PAK1, which has LocusLink ID 5058 in humans,and find that it is involved in two pathways, hsa04010 andhsa04510.

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� For mice, the LocusLink ID for PAK1 is 18479.> KEGGEXTID2PATHID$"5058"

[1] "hsa04010" "hsa04510"

> KEGGEXTID2PATHID$"18479"

[1] "mmu04010"

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cMAP

� The cancer Molecular Analysis Project (cMAP) is a projectthat provides software and data for the comprehensiveexploration of data relevant to cancer.

� cMAP provides pathway data in a format that is amenable tocomputational manipulation.> keggproc <- eapply(cMAPKEGGINTERACTION, function(x) x$process)

> table(unlist(keggproc))

character(0)

> cartaproc <- eapply(cMAPCARTAINTERACTION, function(x) x$process)

> length(table(unlist(cartaproc)))

[1] 0

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cMAP

� We study the pathway labeled hsa00020 as an example.> cMK <- ls(cMAPKEGGPATHWAY)

> spec <- substr(cMK, 1, 3)

> table(spec)

spec

hsa map

81 4

> cMK[[2]]

[1] "hsa00020"

> pw2 <- cMAPKEGGPATHWAY[[cMK[2]]]

> names(pw2)

[1] "id" "organism" "source" "name"

[5] "component"

> pw2$name

[1] "citrate cycle (tca cycle)"

> pw2$component

[1] 63 71 3473 80 68 78 79 77 72 65 55

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[12] 82 74 84 75 64 83 61 58 59 69 81

[23] 60 56 73 66 76 1367 62 54

� We select the first element of the pw2$component; it is aninteraction so we first extract it, and then explore itscomponents.> getI1 <- get("63", cMAPKEGGINTERACTION)

> unlist(getI1[1:4])

source process reversible condition

"KEGG" NA "TRUE" NA

> unlist(getI1[[5]][[2]])

id edge role location activity

2 NA NA NA NA

� We find that ATP is an input to the citrate cycle:> get("2", cMAPKEGGMOLECULE)[[2]][7:8]

AS AS

"adenosine 5'-triphosphate" "ATP"

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Homology

� Two genes are said to be homologous if they have descendedfrom a common ancestral DNA sequence.

� there is some interest in using homologous genes when studyingrelated phenomena across species

� there is one homology package for each species; a three letterspecies name (for homo sapiens hsa) and a suffix of homology

� the mappings provided are between HomoloGene’s identifiersand a variety of other commonly used identifiers, namelyLocusLink and UniGene.> library("hsahomology")

> ls("package:hsahomology")

[1] "hsahomology" "hsahomologyACC2HGID"

[3] "hsahomologyDATA" "hsahomologyHGID"

[5] "hsahomologyHGID2ACC" "hsahomologyHGID2LL"

[7] "hsahomologyLL2HGID" "hsahomologyORGCODE"

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Homology

� the data linking genes is provided in hsahomologyDATA

� each element in the list represents a gene that is homologous tothe key

� there are three different types of homology that are recordedand represented in the data.

� a single letter is used; the type can be:

– B (reciprocal best best between three or more organisms),

– b (reciprocal best match between two organisms), or

– c (curated homology relationship between two organisms)

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Homology Example

� the code for homo sapiens is 9606

� the Homologene project uses its own set of gene identifiers,

� to find the homologs for estrogen receptor 1 (ESR1) we use itsLocusLink ID (2099) and find the corresponding HomoloGeneID.> esrHG <- hsahomologyLL2HGID$"2099"

> hesr <- get(as.character(esrHG), hsahomologyDATA)

> sapply(hesr, function(x) x$homoOrg)

10090 10090 10116 10090 10116 8022 8355 8364 9823 7955

"mmu" "mmu" "rno" "mmu" "rno" "omy" "xla" "xtr" "ssc" "dre"

9913

"bta"

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Homology Cross Species

� to find all potential homologs in one species, starting with thegenes in a different species.

� to find all Xenopus Laevis homologs for human genes we usethe following code> hXp <- eapply(hsahomologyDATA, function(x) {

+ gd <- sapply(x, function(x) if (!is.na(x$homoOrg) &&

+ x$homoOrg == "xla")

+ TRUE

+ else FALSE)

+ x[gd]

+ })

> lh <- sapply(hXp, length)

> hXp2 <- hXp[lh > 0]

� we find 7021 human genes that have a potential homolog inXenopus Laevis.

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Visualizing Genomic Data

� High-density scatterplots using hexbin and

� Heatmap: rectangular false-color displays.

� Visualizing distances

� Special plots: genomic coordinates

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Visualization

� visualization is more than simply plotting data

� visualization is the process of plotting data so that the contentsare easily and accurately perceived by the user

� irrelevant details should be suppressed, and importantcomparisons enhanced and put on an appropriate scale, orencoded using color etc.

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Use of Color

� color can greatly enhance perception

� the RColorBrewer package provides a number of differentpalettes to choose from

� There are 3 types of palettes, sequential, diverging, andqualitative.

� see the manual page for brewer.pal for more details

� the R function hcl provides another set of colors (which maybe more appropriate for statistical graphics).

� both colorRamp and colorRampPalette provide tools forcreating palettes of colors that map between two chosen colors.

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> csphd(c("blue", "green", "yellow", "orange"))

> csphd(hcl(h = c(30, 120, 210, 300)))

> csphd(hcl(h = c(30, 120, 210, 300), c = 20, l = 90,

+ fixup = FALSE))

> csphd(hcl(h = seq(60, 240, by = 60)))

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Computer Science PhD Graduates

Year

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dent

s

0

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a) b)

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FallSummerSpringWinter

Computer Science PhD Graduates

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72 74 76 78 80 82 84

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Computer Science PhD Graduates

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c) d)

Figure 2: Four different color schemes - the lower right is suitablefor color-blind viewers.

45

Page 46: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

High-density scatterplots

> library("affydata")

> data("Dilution")

> x <- log2(exprs(Dilution)[, 1:2])

> x <- x %*% cbind(A = c(1, 1), M = c(-1, 1))

> plot(x, pch = ".")

> library("hexbin")

> library("geneplotter")

> hb <- hexbin(x, xbins = 50)

> plot(hb, colramp = colorRampPalette(brewer.pal(9,

+ "YlGnBu")[-1]))

> library("prada")

> smoothScatter(x, nrpoints = 500)

> plot(x, col = densCols(x), pch = 20)

46

Page 47: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

47

Page 48: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

15 20 25

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02

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15 20 25

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Counts

a) b)

15 20 25

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15 20 25

−6

−4

−2

02

A

M

c) d)

Figure 3: Four different visualizations of the same data, the mean-difference plotof the unprocessed probe intensities from a pair of microarrays.

48

Page 49: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

Heatmaps

� A heatmap is a two-dimensional, rectangular, colored grid.

� It displays data that themselves come in the form of arectangular matrix.

� The color of each rectangle is determined by the value of thecorresponding entry in the matrix.

� The rows and columns of the matrix can be rearrangedindependently.

� Usually they are reordered so that similar rows are placed nextto each other, and the same for columns.

49

Page 50: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

Heatmaps

� the function heatmap is an implementation with many options

� users can control the ordering of rows and columnsindependently of each other

� they can use row and column labels of their own choosing orselect their own color scheme

� they can also add a colored bar to annotate either the row orthe column data

50

Page 51: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

Heatmaps

> library("ALL")

> data("ALL")

> selSamples <- ALL$mol.biol %in% c("ALL1/AF4",

+ "E2A/PBX1")

> ALLs <- ALL[, selSamples]

> ALLs$mol.biol <- factor(ALLs$mol.biol)

> colnames(exprs(ALLs)) <- paste(ALLs$mol.biol,

+ colnames(exprs(ALLs)))

> library("genefilter")

> g <- split(1:length(ALLs$mol.biol), ALLs$mol.biol)

> meanThr <- log2(100)

> tThr <- qt(0.9999, df = sum(listLen(g)) - 2)

> s1 <- rowMeans(exprs(ALLs)[, g[[1]]]) > meanThr

> s2 <- rowMeans(exprs(ALLs)[, g[[2]]]) > meanThr

> s3 <- abs(fastT(exprs(ALLs), g[[1]], g[[2]], var.equal = TRUE)$z) >

+ tThr

> selProbes <- (s1 | s2) & s3

> ALLhm <- ALLs[selProbes, ]

51

Page 52: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

> hmcol <- colorRampPalette(brewer.pal(10, "RdBu"))(256)

> spcol <- ifelse(ALLhm$mol.biol == "ALL1/AF4",

+ "goldenrod", "skyblue")

> heatmap(exprs(ALLhm), col = hmcol, ColSideColors = spcol)

52

Page 53: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

53

Page 54: Meta-data in Bioconductor · OMIM Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. NetAffx The NetAffx Analysis Center provides tools that

E2A

/PB

X1

3600

1

E2A

/PB

X1

2401

9

E2A

/PB

X1

0801

8

E2A

/PB

X1

2800

3

E2A

/PB

X1

LAL5

ALL

1/A

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Figure 4: A heatmap comparing the ALL1/AF4 group (brown) to theE2A/PBX1 group (light blue).

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Heatmaps of residuals

� in most cases you can find residuals from any model fit to geneexpression data

� for example, even fitting t-tests to each row (gene) yieldsresiduals

� the residuals are the same size as the original data and aheatmap can reveal structure in them

� often peculiar arrays (those with too many high or low values)can be detected

� as can sets of genes that the model does not fit, in the same way

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> predict.MArrayLM <- function(f, design = f$design) {

+ return(f$coefficients %*% t(design))

+ }

> esFit <- predict(fit)

> res <- exprs(esEset) - esFit

> sel <- order(fit$coefficients[, "ES:T48"], decreasing = TRUE)[1:50]

> four.groups <- as.integer(factor(colnames(exprs(esEset))))

> csc <- brewer.pal(4, "Paired")[four.groups]

> heatmap(exprs(esEset)[sel, ], col = hmcol, ColSideColors = csc)

> heatmap(res[sel, ], col = hmcol, ColSideColors = csc)

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Figure 5: Heatmap of the estrogen data for the 50 probesets withthe highest treatment–time interaction. The horizontal color barcorresponds to the 2× 2 factor levels for treatment and time.

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Figure 6: Heatmap of the residuals of the linear model for the estro-gen data. 59

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Visualizing Distances

� All machine learning involves the use and comparison ofdistances.

� the selection of an appropriate distance is important as are thedevelopment and use of methods to visualize distances

� unfortunately one of the most widely used tools (thedendrogram) is the least suited to this objective and should beavoided where possible.

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> standardize <- function(z) {

+ rowmed <- apply(z, 1, median)

+ rowmad <- apply(z, 1, mad)

+ rv <- sweep(z, 1, rowmed)

+ rv <- sweep(rv, 1, rowmad, "/")

+ return(rv)

+ }

> ALLhme <- exprs(ALLhm)

> ALLdist1 <- dist(t(standardize(ALLhme)))

> ALLhc1 <- hclust(ALLdist1)

> plot(ALLhc1, xlab = "", sub = "", main = "ALLhc1")

> ALLsub2 <- exprs(ALLs[(s1 | s2), ])

> rowMads <- apply(ALLsub2, 1, mad)

> ALLsub2 <- ALLsub2[rowMads > 1.4, ]

> ALLdist2 <- dist(t(standardize(ALLsub2)))

> ALLhc2 <- hclust(ALLdist2)

> plot(ALLhc2, xlab = "", sub = "", main = "ALLhc2")

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Figure 7: Dendrograms for the ALL1/AF4 and E2A/PBX1 samples. The clus-tering was obtained a) using the 81 probes in ALLhme that were selected in Sec-tion ?? by the t-statistic, b) using the 58 probes in ALLsub2 that were filteredfor their overall variability.

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Cophentic Distance

� to compute the dendrogram you must have some distancebetween the objects

� the dendrogram induces a second distance between the objects

� the cophenetic correlation is the correlation between these twodistances

� the larger the cophenetic correlation, the more the dendrogramreflects the original distances, and the better the dendrogram isas a visual representation of the data

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> mypal <- brewer.pal(7, "RdBu")

> blue <- mypal[7]

> red <- mypal[1]

> ALLcph1 <- cophenetic(ALLhc1)

> cor(ALLdist1, ALLcph1)

[1] 0.99

> plot(ALLdist1, ALLcph1, pch = "|", col = blue)

> ALLcph2 <- cophenetic(ALLhc2)

> cor(ALLdist2, ALLcph2)

[1] 0.877

> plot(ALLdist2, ALLcph2, pch = "|", col = blue)

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65

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Multidimensional scaling

� MDS starts from a matrix of all pairwise distances ordissimilarities between n objects

� it tries to arrange n points in a k-dimensional Euclidean spacesuch that the distances between the points are as much like thegiven distances as possible

� this can be done in a variety of ways and each leads to slightlydifferent solutions

� R functions for carrying out MDS include: cmdscale in thestats package, and isoMDS and sammon in MASS

� like all dimension reduction methods, it is essential that theuser check to see if the reduction is suitable (you can alwayscompute it, it just does not have to be a good representation ofthe data)

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Goodness of fit

� classical MDS solution, cmdscale returns two statistics.

� one is the sum of the eigenvalues for the components S dividedby the sum of the absolute value of all eigenvalues

� the other is S divided by the sum of all positive eigenvalues

� to decide how many dimensions are necessary to adequatelyrepresent your data, it is useful to look at the scree plot, that isthe plot of the goodness-of-fit statistic as a function of k

� a criterion for the choice of k is to pick a solution for whichadding more dimensions does not significantly improve thegoodness-of-fit.

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Other MDS solutions

� isoMDS provides one form of non-metric MDS. It chooses ak-dimensional configuration to minimize the stress

s2 =

∑i 6=j

(f(pij)− dij)2∑i 6=j

d2ij

, (1)

where pij is the original distance matrix, f is a monotonictransformation, and dij are the distances between the MDSpoints.

� sammon uses a different loss-function

� The different variants of MDS lead to different relativeimportances of large versus small distances to the fitted MDSsolution.

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MDS Example Code

> cm1 <- cmdscale(ALLdist1, eig = TRUE)

> cm1$GOF

[1] 0.908 0.908

> samm1 <- sammon(ALLdist1, trace = FALSE)

> cm2 <- cmdscale(ALLdist2, eig = TRUE)

> cm2$GOF

[1] 0.646 0.646

> samm2 <- sammon(ALLdist2, trace = FALSE)

> ALLscol <- c("goldenrod", "skyblue")[as.integer(ALLs$mol.biol)]

> plot(cm1$points, col = ALLscol, ...)

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Figure 9: MDS plots of the ALL data. The patients with E2A/PBX are coloredred and those with ALL1/AF4 are colored blue. The four panels compare differ-ent methods of MDS and feature selection. a) metric MDS using t-test selectedfeatures, b) Sammon MDS using t-test selected features, c) metric MDS usingMAD selected features, d) Sammon MDS using MAD selected features.

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Using Heatmaps with Distances

� we can make use of the heatmap function for showing distances

� we call heatmap with both sym=TRUE and specify our owndistance function

� the resulting plot is symmetric and there is a strong indicationthat there are two (or possibly three) groups of samples.

> heatmap(as.matrix(ALLdist2), sym = TRUE, col = hmcol,

+ distfun = function(x) as.dist(x))

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E2A/PBX1 08018

Figure 10: A heatmap of the between sample distances.

74

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Plotting in Genomic Coordinates

� some of the genetic defects that are associated with cancer suchas deletions and amplifications induce correlations in expressionthat are related to chromosomal proximity.

� Genomic regions of correlated transcription have also beenidentified in normal tissues.

� This motivates the development of tools that relate geneexpression to chromosomal location.

� Genomic DNA is double stranded, one strand is called thesense strand, the other the antisense strand

� Both strands can contain coding sequences for genes, and thevisualization methods we consider reflect this.

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The geneplotter package

� We can build the object chrLoc using the code below> library("geneplotter")

> chrLoc <- buildChromLocation("hgu95av2")

� this creates an object of class chromLocation which containsthe location of all genes that were assayed on the HG-U95Av2chip (for different experiments you would use a different chip).

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Plotting chromosomal location

� select the highly expressing genes using s1 and s2 from aboveand compute the mean expression for each probe separately forthe two groups of patient samples, ALL1/AF4 and E2A/PBX1.> ALLch <- ALLs[s1 | s2, ]

> m1 <- rowMeans(exprs(ALLch)[, ALLch$mol.biol ==

+ "ALL1/AF4"])

> m2 <- rowMeans(exprs(ALLch)[, ALLch$mol.biol ==

+ "E2A/PBX1"])

� next compute the deciles of the combined data so the genes ineach decile can be colored differently.> deciles <- quantile(c(m1, m2), probs = seq(0,

+ 1, 0.1))

> s1dec <- cut(m1, deciles)

> s2dec <- cut(m2, deciles)

> gN <- names(s1dec) <- names(s2dec) <- geneNames(ALLch)

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> colors <- brewer.pal(10, "RdBu")

> layout(matrix(1:3, nr = 1), widths = c(5, 5, 2))

> cPlot(chrLoc, main = "ALL1/AF4")

> cColor(gN, colors[s1dec], chrLoc)

> cPlot(chrLoc, main = "E2A/PBX1")

> cColor(gN, colors[s2dec], chrLoc)

> image(1, 1:10, matrix(1:10, nc = 10), col = colors,

+ axes = FALSE, xlab = "", ylab = "")

> axis(2, at = (1:10), labels = levels(s1dec), las = 1)

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ALL1/AF4

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(7.75,8.07]

(8.07,8.52]

(8.52,9.31]

(9.31,13.7]

Figure 11: Side-by-side whole genome plots comparing expressionlevels in ALL1/AF4 and E2A/PBX1.

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Plotting Single Chromosomes

� plotChr produces one plot per chromosome.

� Each sample has two smooth lines; the one in the top half ofthe plot represents genes on the sense strand and the line in thebottom half of the plot represents expression for genes encodedon the antisense strand.

� Low expression values are near the center line and highexpression values are towards the edge of the plot.> par(mfrow = c(1, 1))

> msobj <- Makesense(ALLs, "hgu95av2")

> plotChr("22", msobj, col = ifelse(ALLs$mol.biol ==

+ "ALL1/AF4", "#EF8A62", "#67A9CF"), log = FALSE)

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Chromosome 22

Representative Genes

Sm

ooth

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xpre

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n

50

5

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at

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Figure 12: Plot of the expression data of individual ALL1/AF4 and E2A/PBX1samples. Each sample is plotted as a continuous line, the x-values are determinedby the location of the gene on the chromosome and the y values are expressionvalues. To remove some of the noise, the lines have been smoothed.

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Cumulative Expression

� for some genomic aberrations looking at cummulativeexpression can be helpful

� it is hypothesized that losing one copy of a chromosome mayonly slightly alter gene expression and that the amount bywhich it changes is less than the variability in the population

� the function alongChrom plots gene expression with the genesordered by their chromosomal location.

� the motivation for this is that on the level of individual loci,the technical and biological variability between samples can belarge enough to obscur systematic differences due to copynumber changes

� J.-P. Bourquin compared gene expression profiles betweenchildren with Down’s syndrome (trisomy 21) and a transientmyeloid disorder to children with different subtypes of AML.

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0e+

002e

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041e

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Cumulative expression levels by genes in chromosome 21 scaling method: none

Representative Genes

Cum

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3D

YR

K1A

KC

NJ1

5C

21or

f107

B3G

ALT

5R

IPK

4A

BC

G1

TM

PR

SS

3P

KN

OX

1C

21or

f124

C21

orf3

3P

FK

LU

BE

2G2

PO

FU

T2

SLC

19A

1C

OL6

A1

LSS

+ − + + + − + + + − − − + + − +

Figure 13: Cumulative expression profiles along Chromosome 21 for samplesfrom 10 children with trisomy 21 and a transient myeloid disorder, colored in red,and children with different subtypes of acute myeloid leukemia (M7), colored inblue.

85


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