PSEAE CF.2010
From Marcotte Lab
Web supplement for 'Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M, Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo, mBIO, :in press (2010) PubMed '
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Supplement Tables
- Table S1. P. aeruginosa strains used in this study MS Excel
- Table S2. Orthologous genes from P. aeruginosa strains PAO1, PA14, PA7, and LESB58 MS Excel
- Table S3. Affymetrix microarray annotation MS Excel
- Table S4. Genes expressed differently in clonal groups MS Excel
- Table S5. Genes expressed differently in ancestors and strain PA14 MS Excel
- Table S6. Genes expressed differently within clonal groups over time MS Excel
Microarray data
CEL files
- http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip
- Description for CEL files (gzipped)
- You can also download it from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21966 (NCBI GEO)
TXT files
Compressed by gzip.
- RAW data, before pre-processing
- RMA pre-processing, PM corrected
- RMA pre-processing, Quantile normalized
- RMA pre-processing, ExpressSet
- MAS5 pre-processing, ExpressSet
- MAS5 pre-processing, P/M/A calls
Probe mapping to PAO1
A BASH shell script to run exonerate:
EXONERATE="/home/taejoon/bin64/exonerate" PROBE_FILE="PSEAE_1.affy_probes.fasta" GENOME_DIR="/home/taejoon/pkgenome.data/PCAP" TARGET_NAME="PSEAE_PAO1.NC_002516.fna" GENOME_FILE="$GENOME_DIR/$TARGET_NAME" GENOME_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate} echo "$PROBE_FILE vs. $GENOME_FILE" echo "#PROBE_FILE : $PROBE_FILE" > $GENOME_MAP_FILE echo "#GENOME_FILE : $GENOME_FILE" >> $GENOME_MAP_FILE $EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ --ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $GENOME_FILE >> $GENOME_MAP_FILE TARGET_NAME="PSEAE_PAO1.PCAP20091123.dna.fasta" CDNA_FILE="$GENOME_DIR/$TARGET_NAME" CDNA_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate} echo "$PROBE_FILE vs. $CDNA_FILE" echo "#PROBE_FILE : $PROBE_FILE" > $CDNA_MAP_FILE echo "#CDNA_FILE : $CDNA_FILE" >> $CDNA_MAP_FILE $EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ --ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE
R script for preprocessing
dataset_name <- 'Huse2010_GSE21966' library(affy) exp_table <- read.table(file="EXP",header=T,stringsAsFactors=FALSE,sep="\t") files_vector <- as.vector(exp_table$Filename,mode='character') samples_vector <- as.vector(exp_table$Sample,mode='character') affybatch_raw <- ReadAffy(filenames=files_vector,sampleNames=samples_vector) save(affybatch_raw, file=paste(dataset_name,'.affybatch_raw', sep='')) write.table(intensity(affybatch_raw), file=paste(dataset_name,'.raw.txt', sep='')) affybatch_corrected <- bg.correct(affybatch_raw, method='rma') save(affybatch_corrected, file=paste(dataset_name,'.affybatch_corrected', sep='')) write.table(intensity(affybatch_corrected), file=paste(dataset_name,'.corrected.txt', sep='')) affybatch_normalized <- normalize(affybatch_corrected, method='quantiles') save(affybatch_normalized, file=paste(dataset_name,'.affybatch_normalized',sep='')) write.table(intensity(affybatch_normalized), file=paste(dataset_name,'.norm.txt', sep='')) eset_rma <- rma(affybatch_raw) save(eset_rma, file=paste(dataset_name,'.eset_rma',sep='')) write.exprs(eset_rma, file=paste(dataset_name,'.eset_rma.txt',sep=''))
R script for ANOSIM test
library(vegan) tbl <- read.table('Huse2010_GSE21966.gene_mean.txt',header=T,row.names='Gene') t_tbl <- t(tbl) tbl_dist <- as.dist(1-cor(as.matrix(tbl),method='spearman')) igroup <- c('A','A','A','A','A','B','B','B','B','B','B','B','Ca','Ca','Cb','Cb','Cb','R','R') tbl_igroup_anosim <- anosim(tbl_dist,igroup) tgroup <- c('E','M','M','M','L','E','M','M','M','L','L','L','E','L','E','M','L','R','R') tbl_time_anosim <- anosim(tbl_dist,tgroup) mgroup <- c('C','C','M','D','D','C','C','D','M','M','C','M','C','M','M','D','M','R','R') tbl_morphology_anosim <- anosim(tbl_dist,mgroup)
R script for detecting differentially expressed genes
library(limma) library(affy) ## Read target information targets <- readTargets("EXP") affybatch_raw <- ReadAffy(filenames = targets$Filename) eset_rma <- rma(affybatch_raw) ## Patient - Splitting P3 igroup_detail <- factor(targets$Isogenic, levels=c("A","B","Ca","Cb","PAO1","PA14")) design_igroup_detail <- model.matrix(~0+igroup_detail) colnames(design_igroup_detail) <- c(levels(igroup_detail)) fit_igroup_detail <- lmFit(eset_rma, design_igroup_detail) fit_igroup_detail <- eBayes(fit_igroup_detail) contrast_igroup_detail <- makeContrasts(B-A,Ca-A,Cb-A,Ca-B,Cb-B,Cb-Ca, levels=design_igroup_detail) contrast_fit_igroup_detail <- contrasts.fit(fit_igroup_detail, contrast_igroup_detail) contrast_fit_igroup_detail <- eBayes(contrast_fit_igroup_detail) top_B_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=1, adjust="fdr", resort.by="logFC") write.table(top_B_A,"DE_between_group/igroup_B_A.top.txt") top_Ca_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=2, adjust="fdr", resort.by="logFC") write.table(top_Ca_A,"DE_between_group/igroup_Ca_A.top.txt") top_Cb_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=3, adjust="fdr", resort.by="logFC") write.table(top_Cb_A,"DE_between_group/igroup_Cb_A.top.txt") top_Ca_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=4, adjust="fdr", resort.by="logFC") write.table(top_Ca_B,"DE_between_group/igroup_Ca_B.top.txt") top_Cb_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=5, adjust="fdr", resort.by="logFC") write.table(top_Cb_B,"DE_between_group/igroup_Cb_B.top.txt") top_Cb_Ca <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail), coef=6, adjust="fdr", resort.by="logFC") write.table(top_Cb_Ca,"DE_between_group/igroup_Cb_Ca.top.txt")
Raw data for DE genes between clonal groups
Raw data for DE genes within clonal groups
Genome/Annotation data
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.
- P. aeruginosa PAO1
- Genomic DNA, Transcripts, Proteins, Annotation(TSV)
- Reciprocal BLAST best-hits: PA14, PA7, LESB58, Summary
- P. aeruginosa PA14
- P. aeruginosa PA7
- P. aeruginosa LESB58