Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77032	0.2
27DAP/17DAP	0.70427	0.162
39DAP/27DAP	1.13409	0.845
41DAP/39DAP	0.47208	0.041
42DAP/41DAP	1.06167	1
43DAP/42DAP	1.1497	0.84
47DAP/43DAP	0.65036	0.08
52DAP/47DAP	0.79265	0.502
57DAP/52DAP	1.004	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82477	0.077
17DAP/reference	0.70156	0.025
27DAP/reference	0.69619	0.04
39DAP/reference	0.7116	0.022
41DAP/reference	0.6464	0.013
42DAP/reference	0.78479	0.002
43DAP/reference	0.83451	0.135
47DAP/reference	0.81128	0.018
52DAP/reference	0.78862	0.111
57DAP/reference	0.97779	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01033	1
27DAP/17DAP	0.84791	0.39
39DAP/27DAP	0.65363	0.123
41DAP/39DAP	1.17331	0.705
42DAP/41DAP	0.89526	0.259
43DAP/42DAP	0.92256	0.293
47DAP/43DAP	0.84808	0.104
52DAP/47DAP	0.97395	0.899
57DAP/52DAP	0.89358	0.349
57DAP/7DAP	0.58676	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97513	0.55
17DAP/reference	0.8092	0.031
27DAP/reference	0.66984	0.011
39DAP/reference	0.5317	0.011
41DAP/reference	0.57651	0.01
42DAP/reference	0.49065	0.01
43DAP/reference	0.56879	0.011
47DAP/reference	0.56279	0.04
52DAP/reference	0.70536	0.049
57DAP/reference	0.65055	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54937	0.016
17DAP/reference	0.73997	0.011
27DAP/reference	0.92558	0.366
39DAP/reference	0.77993	0.087
41DAP/reference	0.96193	0.422
42DAP/reference	0.74304	0.046
43DAP/reference	0.46437	0.002
47DAP/reference	0.72823	0.05
52DAP/reference	0.57886	0.003
57DAP/reference	0.48732	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27529	0.021
17DAP/reference	1.36078	0.151
27DAP/reference	0.90696	0.257
39DAP/reference	0.84596	0.022
41DAP/reference	0.95215	0.56
42DAP/reference	1.06247	1
43DAP/reference	1.11759	0.679
47DAP/reference	0.64287	0.015
52DAP/reference	0.6807	0.073
57DAP/reference	1.35272	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35006	0.786
26DAP/20DAP	1.1739	0.718
34DAP/26DAP	0.94928	0.898
51DAP/34DAP	0.72985	0.112
52DAP/51DAP	1.05856	0.638
53DAP/52DAP	0.77003	0.057
55DAP/53DAP	0.92881	0.784
57DAP/55DAP	0.97943	0.914
62DAP/57DAP	0.97936	0.994
68DAP/62DAP	1.07135	0.936
68DAP/14DAP	0.68718	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57237	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.60636	0.058
Mature Green Tomato/Ripe Tomato	6.75491
Immature Eggplant/Mature Eggplant	0.53704	0.064
Ripe Pepper/Ripe Tomato	1.84873	1
Mature Eggplant/Ripe Tomato	1.97634	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86234	0.907
1-1-2/M82	1.11431	1
12-2/M82	0.91682	0.955
12-4/M82	0.53382	0.619
1-3/M82	1.93637	1
2-1-1/M82	0.891
2-1/M82	0.85437
2-6/M82	0.83036	0.501
3-2/M82	1.07597	0.84
4-1-1/M82	0.99474	1
4-1/M82	0.57874
4-3-2/M82	1.79717
4-3/M82	1.15214	0.268
5-3/M82	1.08215	1
6-2/M82	1.14784	1
6-3/M82	1.06691	1
7-1/M82	1.25305
7-2/M82	1.13637	1
9-3-2/M82	1.22604	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04704	0.493
IL2-6/WTpooled	1.04698	1
IL7-5/WTpooled	1.23552	0.792
IL7-3/WTpooled	0.98177	1
IL12-4/WTpooled	1.03694	1
IL1-4/WTpooled	0.73183	0.562
WT/WTpooled	1.03037	1

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	0.99642	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01309	1
DC3000/delta hrp 6h	1.07711	1
DC3000/delta hrp 12h	1.5154	1
DC3000/delta hrp 24h	0.86413	0.395

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.38031	0.023
DC3000 delta B/DC3000 delta AB	0.38739	0.02

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00604	1
Var 0h	1.09377	0.936
Var 12h I row2-row1	0.89478	0.565
Var 12h NI row2-row1	1.01168	1
Var 36h I row2-row1	0.85518	0.805
Var 36h NI row2-row1	0.94483	0.706
Var 60h I row2-row1	1.55554	0.562
Var 60h NI row2-row1	1.0446	1
Time course 0hI-0hNI	1.06168	0.63
Time course 12hI-12hNI	1.03387	0.668
Time course 36hI-36hNI	0.95953	0.101
Time course 60hI-60hNI	0.19823	0.006

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)	1.07401	0.748
transgenic ySAMdc/azygous control (breaker)	1.00737	1
transgenic ySAMdc/azygous control (red)	1.16466	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.60357	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.11185	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	10.069	0.086
Manapal/WT (break)	3.74453	0.123
Manapal/WT (red)	1.16657	0.413