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 '
Contents |
Supplement Tables
- Table S1. Strains
- Table S2. P. aeruginosa orthologs
- Table S3. Affymetrix microarray annotation
- Table S4. P. aeruginosa annotation
- Table S5. Differentially expressed genes between progenitors
- Table S6. Differentially expressed genes within isogenic groups (compared to each progenitor/first strain).
- Table S7. Differentially expressed genes between isogenic groups.
- Table S8. Functional enrichment data for Table S7
- Table S9. Functional enrichment data for Table S6
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)
Gzipped TXT files
- 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)
Genome/Annotation data
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.
- P. aeruginosa PAO1
- P. aeruginosa PA14
- P. aeruginosa PA7
- P. aeruginosa LESB58