Difference between revisions of "PSEAE CF.2010"

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|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i>
 
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i>
 
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
 
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
|journal=mBIO
+
|journal=mBio
 
|pub_year=2010
 
|pub_year=2010
|volume=
+
|volume=1(4)
|link=
+
|page=pii:e00199-10
|page=in press
+
|pubmed=20856824
 
}}'
 
}}'
 +
 +
== Figures ==
 +
{|cellspacing=20,
 +
| align="center"|
 +
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.thumb.jpg
 +
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.jpg JPEG]
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.tif TIFF]
 +
| align="center"|
 +
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.thumb.jpg
 +
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.jpg JPEG]
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.tif TIFF]
 +
 +
| align="center"|
 +
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.thumb.jpg
 +
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.jpg JPEG]
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.tif TIFF]
 +
 +
| align="center"|
 +
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.thumb.jpg
 +
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.jpg JPEG]
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.tif TIFF]
 +
 +
| align="center"|
 +
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.thumb.jpg
 +
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.jpg JPEG]
 +
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.tif TIFF]
 +
|}
  
 
== Supplement Tables ==
 
== Supplement Tables ==
* Table S1. Strains
+
* Table S1. ''P. aeruginosa'' strains used in this study [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS1.xls MS Excel]
* Table S2. ''P. aeruginosa'' orthologs
+
* Table S2. Orthologous genes from P. aeruginosa strains PAO1, PA14, PA7, and LESB58 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS2.xls MS Excel]
* Table S3. Affymetrix microarray annotation
+
* Table S3. Affymetrix microarray annotation [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS3.xls MS Excel]
* Table S4. ''P. aeruginosa'' annotation
+
* Table S4. Genes expressed differently in clonal groups [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS4.xls MS Excel]
* Table S5. Differentially expressed genes between progenitors
+
* Table S5. Genes expressed differently in ancestors and strain PA14 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS5.xls MS Excel]
* Table S6. Differentially expressed genes within isogenic groups (compared to each progenitor/first strain).  
+
* Table S6. Genes expressed differently within clonal groups over time [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS6.xls MS Excel]
* 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 ==
+
== Microarray data ==
 
=== CEL files ===
 
=== CEL files ===
 
* http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip
 
* http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.exp.txt.gz 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)
 
* You can also download it from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21966 (NCBI GEO)
  
=== Gzipped TXT files ===
+
=== TXT files ===
 +
Compressed by gzip.
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.raw.txt.gz RAW data, before pre-processing]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.raw.txt.gz RAW data, before pre-processing]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.corrected.txt.gz RMA pre-processing, PM corrected]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.corrected.txt.gz RMA pre-processing, PM corrected]
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* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls]
 
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls]
 +
 +
=== Probe mapping to PAO1 ===
 +
A BASH shell script to run exonerate:
 +
<pre>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 >> $CDNA_MAP_FILE</pre>
 +
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.exonerate.gz Exonerate output against PAO1 transcripts]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset.gz ProbeSet - PAO1 gene mapping]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset_log.gz Log for bad probesets]
 +
 +
=== R script for preprocessing ===
 +
<pre>dataset_name <- 'Huse2010_GSE21966'
 +
library(affy)
 +
 +
exp_table <- read.table(file="EXP",header=T,stringsAsFactors=FALSE,sep="\t")
 +
files_vector <- as.vector(exp_table$Filename,mode='character')
 +
samples_vector <- as.vector(exp_table$Sample,mode='character')
 +
affybatch_raw <- ReadAffy(filenames=files_vector,sampleNames=samples_vector)
 +
 +
save(affybatch_raw, file=paste(dataset_name,'.affybatch_raw', sep=''))
 +
write.table(intensity(affybatch_raw),
 +
            file=paste(dataset_name,'.raw.txt', sep=''))
 +
 +
affybatch_corrected <- bg.correct(affybatch_raw, method='rma')
 +
save(affybatch_corrected,
 +
            file=paste(dataset_name,'.affybatch_corrected', sep=''))
 +
write.table(intensity(affybatch_corrected),
 +
            file=paste(dataset_name,'.corrected.txt', sep=''))
 +
 +
affybatch_normalized <- normalize(affybatch_corrected, method='quantiles')
 +
save(affybatch_normalized,
 +
            file=paste(dataset_name,'.affybatch_normalized',sep=''))
 +
write.table(intensity(affybatch_normalized),
 +
            file=paste(dataset_name,'.norm.txt', sep=''))
 +
 +
eset_rma <- rma(affybatch_raw)
 +
save(eset_rma, file=paste(dataset_name,'.eset_rma',sep=''))
 +
write.exprs(eset_rma,
 +
            file=paste(dataset_name,'.eset_rma.txt',sep=''))</pre>
 +
 +
=== R script for ANOSIM test ===
 +
<pre>library(vegan)
 +
tbl <- read.table('Huse2010_GSE21966.gene_mean.txt',header=T,row.names='Gene')
 +
t_tbl <- t(tbl)
 +
 +
tbl_dist <-  as.dist(1-cor(as.matrix(tbl),method='spearman'))
 +
igroup <- c('A','A','A','A','A','B','B','B','B','B','B','B','Ca','Ca','Cb','Cb','Cb','R','R')
 +
tbl_igroup_anosim <- anosim(tbl_dist,igroup)
 +
 +
tgroup <- c('E','M','M','M','L','E','M','M','M','L','L','L','E','L','E','M','L','R','R')
 +
tbl_time_anosim <- anosim(tbl_dist,tgroup)
 +
 +
mgroup <- c('C','C','M','D','D','C','C','D','M','M','C','M','C','M','M','D','M','R','R')
 +
tbl_morphology_anosim <- anosim(tbl_dist,mgroup)</pre>
 +
 +
=== R script for detecting differentially expressed genes ===
 +
<pre>library(limma)
 +
library(affy)
 +
 +
## Read target information
 +
targets <- readTargets("EXP")
 +
affybatch_raw <- ReadAffy(filenames = targets$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")</pre>
 +
 +
=== Raw data for DE genes between clonal groups ===
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_B_A.top.txt.gz B vs. A]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_A.top.txt.gz Ca vs. A]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_A.top.txt.gz Cb vs. A]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_B.top.txt.gz Ca vs. B]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_B.top.txt.gz Cb vs. B]
 +
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_Ca.top.txt.gz Cb vs. Ca]
 +
 +
=== Raw data for DE genes within clonal groups ===
 +
* Clonal group A: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A2_A1.top.txt.gz A2 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A31_A1.top.txt.gz A31 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A32_A1.top.txt.gz A32 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A4_A1.top.txt.gz A4 vs. A1]
 +
* Clonal group B: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B21_B1.top.txt.gz B21 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B22_B1.top.txt.gz B22 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B23_B1.top.txt.gz B23 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B31_B1.top.txt.gz B31 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B32_B1.top.txt.gz B32 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B33_B1.top.txt.gz B33 vs. B1]
 +
* Clonal group Ca: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Ca2_Ca1.top.txt.gz Ca2 vs. Ca1]
 +
* Clonal group Cb: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb2_Cb1.top.txt.gz Cb2 vs. Cb1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb3_Cb1.top.txt.gz Cb3 vs. Cb1]
 +
 +
== Genome/Annotation data ==
 +
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.
 +
 +
* ''P. aeruginosa'' PAO1
 +
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.NC_002516.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.tsv.gz Annotation(TSV)]
 +
** Reciprocal BLAST best-hits: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA14.BBH.txt.gz PA14], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA7.BBH.txt.gz PA7], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_LESB58.BBH.txt.gz LESB58], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.ortholog_summary.txt.gz Summary]
 +
 +
* ''P. aeruginosa'' PA14
 +
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.NC_008563.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.tsv.gz Annotation(TSV)]
 +
 +
* ''P. aeruginosa'' PA7
 +
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.NC_009656.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.tsv.gz Annotation(TSV)]
 +
 +
* ''P. aeruginosa'' LESB58
 +
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.NC_011770.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.tsv.gz Annotation(TSV)]
  
 
----
 
----
 
[[Category:Publication]]
 
[[Category:Publication]]

Latest revision as of 04:59, 30 May 2013

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, 1(4):pii:e00199-10 (2010) PubMed '

Contents

Figures

Fig1_PatientDiagram.1col.thumb.jpg

JPEG TIFF

Fig2_Microarray_Clustering.1col.thumb.jpg

JPEG TIFF

Fig3_Heatmap_DE_between_groups.2col.thumb.jpg

JPEG TIFF

Fig4_DEFC_within_group.1col.thumb.jpg

JPEG TIFF

Fig5_DE_VennDiagram.1col.thumb.jpg

JPEG TIFF

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

TXT files

Compressed by gzip.

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.