Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.45012	0.014
27DAP/17DAP	0.49784	0.031
39DAP/27DAP	0.83541	0.512
41DAP/39DAP	0.54179	0.045
42DAP/41DAP	0.77866	0.774
43DAP/42DAP	1.20765	0.861
47DAP/43DAP	1.02016	0.979
52DAP/47DAP	1.30957	0.374
57DAP/52DAP	0.90049	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.63061	0.008
17DAP/reference	1.25205	0.055
27DAP/reference	1.32303	0.052
39DAP/reference	0.88163	0.021
41DAP/reference	0.87637	0.031
42DAP/reference	0.82123	0.001
43DAP/reference	0.87424	0.143
47DAP/reference	0.75186	0.001
52DAP/reference	0.72113	0.077
57DAP/reference	0.75693	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.37643	0.029
27DAP/17DAP	1.8662	0.027
39DAP/27DAP	0.44624	0.028
41DAP/39DAP	0.3777	0.013
42DAP/41DAP	0.90385	0.265
43DAP/42DAP	1.3257	0.016
47DAP/43DAP	0.8121	0.036
52DAP/47DAP	0.97004	0.886
57DAP/52DAP	1.42318	0.043
57DAP/7DAP	0.30725	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.98253	0.024
17DAP/reference	1.16287	0.162
27DAP/reference	0.95969	0.231
39DAP/reference	0.77386	0.012
41DAP/reference	0.79801	0.01
42DAP/reference	0.92394	0.2
43DAP/reference	0.7847	0.011
47DAP/reference	0.65547	0.03
52DAP/reference	0.73042	0.014
57DAP/reference	0.83647	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58321	0.063
17DAP/reference	1.5963	0.027
27DAP/reference	1.28812	0.265
39DAP/reference	0.58491	0.011
41DAP/reference	0.77692	0.03
42DAP/reference	0.90452	0.15
43DAP/reference	0.74693	0.008
47DAP/reference	0.8055	0.01
52DAP/reference	0.6242	0.003
57DAP/reference	0.60362	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.69238	0.015
17DAP/reference	1.64733	0.115
27DAP/reference	1.62335	0.019
39DAP/reference	0.94763	0.271
41DAP/reference	0.93403	0.185
42DAP/reference	0.7336	0.015
43DAP/reference	0.67236	0.023
47DAP/reference	0.67066	0.005
52DAP/reference	0.61938	0.05
57DAP/reference	0.63584	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91731	1
26DAP/20DAP	1.26456	0.281
34DAP/26DAP	0.70441	0.093
51DAP/34DAP	0.59628	0.049
52DAP/51DAP	1.01163	0.86
53DAP/52DAP	0.73207	0.106
55DAP/53DAP	0.66106	0.031
57DAP/55DAP	0.83086	0.42
62DAP/57DAP	0.9594	0.994
68DAP/62DAP	1.2958	0.7
68DAP/14DAP	0.49445	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.18177	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53582	0.058
Mature Green Tomato/Ripe Tomato	1.82775	0.016
Immature Eggplant/Mature Eggplant	0.50057	0.068
Ripe Pepper/Ripe Tomato	18.9391	0.256
Mature Eggplant/Ripe Tomato	48.8432	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94643	0.944
1-1-2/M82	0.79662	1
12-2/M82	1.2817	1
12-4/M82	0.94785	1
1-3/M82	0.85985	0.501
2-1-1/M82	1.15425
2-1/M82	N/A	N/A
2-6/M82	1.17875	0.329
3-2/M82	0.89169
4-1-1/M82	0.98102	1
4-1/M82	0.86657	1
4-3-2/M82	1.07323
4-3/M82	0.83255	1
5-3/M82	0.96035	1
6-2/M82	0.81175	0.481
6-3/M82	1.21314	1
7-1/M82	0.92405	1
7-2/M82	1.11984	1
9-3-2/M82	0.92795	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.82816	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.91345	1
IL12-4/WTpooled	0.99993	1
IL1-4/WTpooled	1.17681
WT/WTpooled	1.0395	0.89

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	0.84161	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96029	1
DC3000/delta hrp 6h	0.86376	0.95
DC3000/delta hrp 12h	1.19168	1
DC3000/delta hrp 24h	0.79734	0.22

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.49443
DC3000 delta B/DC3000 delta AB	0.45218	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93082	1
Exp 36h	0.83058	0.449
Exp 60h	0.71603	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06259	1
Var 0h	0.79174	0.933
Var 12h I row2-row1	0.80191	0.338
Var 12h NI row2-row1	0.90163	0.627
Var 36h I row2-row1	1.024	1
Var 36h NI row2-row1	1.13212	1
Var 60h I row2-row1	1.03869	0.271
Var 60h NI row2-row1	1.10814	0.904
Time course 0hI-0hNI	1.01506	1
Time course 12hI-12hNI	0.98173	0.897
Time course 36hI-36hNI	0.78256	0.023
Time course 60hI-60hNI	0.11199	0.005

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)	0.82475	0.391
transgenic ySAMdc/azygous control (breaker)	2.10274	1
transgenic ySAMdc/azygous control (red)	0.93065	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81859	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.3524	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23808	0.14
Manapal/WT (break)	1.87616	1
Manapal/WT (red)	1.28492	1