Arabidopsis transcriptome/hormone response to flg22

The row data used to generate the data in this set: (GEO
GSE78735) Arabidopsis thaliana RNA-3seq data collected from 17 genotypes (JEPS,
jEPS, JePS, JEpS, JEPs, jePS, jEpS, jEPs, JepS, JePs, JEps, jepS, jePs, jEps,
Jeps, jeps, fls2) x 7 time points (0, 1, 2, 3, 5, 9, 18 hours after flg22 treatment)
x 3 biological replicates.

Contents of this set:

All are tab-delimited text. The number of columns does not
include the row name column.

1.      
The mean and standard error estimates for each
combination of the genotype and the time (119 columns) for each of 18750 genes
(rows).

a.      
Mean: “genotype.time.mean.estimates.txt”

b.      
Standard error: “genotype.time.std.err.txt”

2.      
The same as 1. but for 37 hormones (rows) and
related compounds (hormones, hereafter). Note that for JA, all 8 j-containing
genotypes (such as jEPS, jEps) were handled as a single genotype, so they have
the same values for a single time point.

a.      
Mean: “hormone.genotype.time.mean.estimates.txt”

b.      
Standard error: “hormone.genotype.time.std.err.txt”

3.      
The transcript response change (difference in
differences) for the comparisons of each of the 15 combinatorial genotypes (not
including the jeps) vs. jeps at each of 6 time points (1, 2, 3, 5, 9, 18 hours;
15 * 6 = 90 columns), for 18750 genes (rows).

a.      
Mean: “did.vs.quad.txt”

b.      
Associated p-value: “did.pval.vs.quad.txt”

4.      
The transcript response change (difference in
differences) for the comparisons of each of the 15 combinatorial genotypes (not
including JEPS) vs. JEPS (WT) at each of 6 time points (90 columns), for 18750
genes (rows).

a.      
Mean: “did.vs.wt.txt”

b.      
Associated p-value: “did.pval.vs.wt.txt”

5.      
The transcript response change (difference in
differences) for the comparisons between fls2 and JEPS (WT) at each of 6 time
points (6 columns), for 18750 genes (rows).

a.      
Mean: “did.fls2.vs.wt.txt”

b.      
Associated p-value: “did.pval.fls2.vs.wt.txt”

6.      
The same as 3., but for 37 hormones

a.      
Mean: “hormone.did.vs.quad.txt”

b.      
Associated p-value: “hormone.did.pval.vs.quad.txt”

7.      
The same as 5., but for 37 hormones

a.      
Mean: “hormone.did.fls2.vs.wt.txt”

b.      
Associated p-value: “hormone.did.pval.fls2.vs.wt.txt”

8.      
The signaling allocation results (16 allocations
x 6 time points = 96 columns) with the model selected based on AICc. (used in most
Figs for signaling allocations, including Fig 2 heatmap) for 5235 genes plus
two hormones (rows).

a.      
Mean: “allocation.AICc.model.mean.txt”

b.      
Associated p-value: “allocation.AICc.model.pval.txt”

9.      
The signaling allocation results (16 allocations
x 6 time points = 96 columns) with the full (unregularized) model. (used in the
Fig 3 and S3 Fig A) for 5259 genes plus two hormones (rows).

a.      
Mean: “allocation.full.model.mean.txt”

b.      
Associated p-value: “allocation.full.model.pval.txt”

10.  
The signaling allocation results (16 allocations
x 6 time points = 96 columns) with the model selected based on BIC. (used in S3
Fig B) for 4954 genes plus 2 hormones (rows).

a.      
Mean: “allocation.AICc.model.mean.txt”

b.      
Associated p-value: “allocation.AICc.model.pval.txt”

11.  
“genes.for.allocation.figs.txt”: The gene sets
used in the figures indicated below among the genes in 8. (5235 genes plus 2
hormones; rows). A value of 0 indicates not used in the figure. For clusters
and randomly selected genes, a value of 1 indicates the membership. For
heatmaps, non-zero values indicate the order of the genes from the top in the
figure. The figures are indicated in the column (22 columns):  'Fig2.heatmap', 'Fig2.column.a', 'Fig2.column.b',
'Fig6A.heatmap', 'Fig6B.heatmap', 'Fig6C.heatmap', 'Fig8.heatmap', 'Fig8.clusterS1',
'Fig8.clusterS2', 'Fig8.clusterS3', 'Fig9A.heatmap', 'Fig9B.heatmap', 'Fig9C.heatmap',
'Fig9A.clusterE1', 'Fig9A.clusterE2', 'Fig9A.clusterE3', 'Fig10A.heatmap', 'Fig10E.heatmap',
'Fig10F.heatmap', 'Fig10G.heatmap',  'S4Fig.heatmap', 'S7Fig.ET.geneset'

12.  
“S2Fig.genes.txt”: The gene sets used in the S2
Fig (panels A and B; 2 columns) among the genes in 1. (18750 genes; rows). A value
of 0 indicates not used in the figure. Non-zero values indicate the order of
the genes from the top in the figure.
13.  
“cor.design.mat.txt”:
The cosine correlation among the signaling allocation terms in linear model.
The design matrix for only one time point was used.