Difference between revisions of "PSEAE CF.2010"
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== Supplement Tables == | == Supplement Tables == |
Revision as of 14:48, 8 September 2010
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 |
Figures
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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
- Genomic DNA, Transcripts, Proteins, Annotation(TSV)
- Reciprocal BLAST best-hits: PA14, PA7, LESB58, Summary
- P. aeruginosa PA14
- P. aeruginosa PA7
- P. aeruginosa LESB58