Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.14.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09381	0.839
27DAP/17DAP	0.87625	0.677
39DAP/27DAP	1.27592	0.546
41DAP/39DAP	0.8253	0.419
42DAP/41DAP	0.91922	1
43DAP/42DAP	0.94909	0.877
47DAP/43DAP	1.23403	0.809
52DAP/47DAP	0.8905	0.626
57DAP/52DAP	1.50131	0.77

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15774	0.334
17DAP/reference	1.05555	0.653
27DAP/reference	1.11266	0.457
39DAP/reference	0.92651	0.446
41DAP/reference	1.12182	0.365
42DAP/reference	1.00569	0.587
43DAP/reference	1.11372	0.083
47DAP/reference	1.40305	0.001
52DAP/reference	1.20883	0.065
57DAP/reference	1.30668	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0027	0.871
27DAP/17DAP	0.99369	0.943
39DAP/27DAP	1.60232	0.267
41DAP/39DAP	0.76811	0.209
42DAP/41DAP	0.96023	0.712
43DAP/42DAP	1.06731	0.788
47DAP/43DAP	0.94023	0.722
52DAP/47DAP	1.24048	0.36
57DAP/52DAP	0.92435	0.603
57DAP/7DAP	0.98081	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23564	0.08
17DAP/reference	1.22157	0.014
27DAP/reference	0.96031	0.101
39DAP/reference	1.79907	0.005
41DAP/reference	1.276	0.019
42DAP/reference	1.57155	0.007
43DAP/reference	1.61041	0.007
47DAP/reference	1.76051	0.018
52DAP/reference	1.41037	0.01
57DAP/reference	1.41297	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11868	0.373
17DAP/reference	0.98401	0.642
27DAP/reference	1.17743	0.292
39DAP/reference	1.38837	0.015
41DAP/reference	0.96537	0.412
42DAP/reference	1.25941	0.041
43DAP/reference	1.2372	0.041
47DAP/reference	1.39115	0.016
52DAP/reference	0.95998	0.28
57DAP/reference	1.18779	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09381	0.162
17DAP/reference	0.94386	0.499
27DAP/reference	0.94582	0.337
39DAP/reference	1.03378	0.546
41DAP/reference	0.98462	0.618
42DAP/reference	1.041	0.635
43DAP/reference	1.26085	0.067
47DAP/reference	1.25612	0.081
52DAP/reference	1.10539	0.683
57DAP/reference	2.04939	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01654	1
26DAP/20DAP	1.10339	0.713
34DAP/26DAP	1.10295	1
51DAP/34DAP	1.74088	0.039
52DAP/51DAP	1.01346	0.965
53DAP/52DAP	1.80496	0.032
55DAP/53DAP	1.24298	0.295
57DAP/55DAP	0.93666	0.748
62DAP/57DAP	0.67775	0.088
68DAP/62DAP	1.06026	0.931
68DAP/14DAP	1.07565	0.889

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52393	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.16773	0.064
Mature Green Tomato/Ripe Tomato	4.81581	0.149
Immature Eggplant/Mature Eggplant	0.35296	0.069
Ripe Pepper/Ripe Tomato	18.4867	0.258
Mature Eggplant/Ripe Tomato	7.11498	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.56024	0.503
1-1-2/M82	1.00308
12-2/M82	0.72322
12-4/M82	0.90901	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.45115	0.967
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.69853	0.698
4-3/M82	2.24846	1
5-3/M82	1.09055	1
6-2/M82	N/A	N/A
6-3/M82	1.05059	1
7-1/M82	1.31197
7-2/M82	0.98591	1
9-3-2/M82	0.60462	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.67163	0.277
IL2-6/WTpooled	0.84192	0.473
IL7-5/WTpooled	1.39433	0.722
IL7-3/WTpooled	1.04029	1
IL12-4/WTpooled	1.05711	0.839
IL1-4/WTpooled	0.91744	0.834
WT/WTpooled	1.02816	0.874

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.96319	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03465	0.921
DC3000/delta hrp 6h	0.86329	0.95
DC3000/delta hrp 12h	0.99358	1
DC3000/delta hrp 24h	0.8485	0.236

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1099	0.102
DC3000 delta B/DC3000 delta AB	1.83599	0.259

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.00916	0.399

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.14013	1
Var 0h	2.58353	0.98
Var 12h I row2-row1	1.81972	0.348
Var 12h NI row2-row1	1.20428	1
Var 36h I row2-row1	0.81996	0.805
Var 36h NI row2-row1	1.24749	1
Var 60h I row2-row1	0.93674	0.832
Var 60h NI row2-row1	1.13502	0.904
Time course 0hI-0hNI	1.03495	0.852
Time course 12hI-12hNI	0.94015	0.632
Time course 36hI-36hNI	0.90179	0.15
Time course 60hI-60hNI	0.88796	0.081

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.37189	0.218
transgenic ySAMdc/azygous control (breaker)	2.0643	0.248
transgenic ySAMdc/azygous control (red)	1.08111	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08871	0.042

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09141	0.231

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15711	0.307
Manapal/WT (break)	0.55365	0.333
Manapal/WT (red)	0.66692	0.242