Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.1.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87305	0.31
27DAP/17DAP	1.07168	0.88
39DAP/27DAP	1.58209	0.215
41DAP/39DAP	0.65727	0.062
42DAP/41DAP	0.93762	1
43DAP/42DAP	1.10101	1
47DAP/43DAP	1.06276	0.909
52DAP/47DAP	0.99133	0.842
57DAP/52DAP	1.07372	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96945	0.412
17DAP/reference	0.80719	0.012
27DAP/reference	1.2948	0.032
39DAP/reference	1.10696	0.079
41DAP/reference	1.03483	0.91
42DAP/reference	1.35001	0.001
43DAP/reference	1.09961	0.064
47DAP/reference	2.12021	0.001
52DAP/reference	1.5734	0.01
57DAP/reference	1.84006	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05121	0.728
27DAP/17DAP	0.83482	0.475
39DAP/27DAP	1.08632	0.742
41DAP/39DAP	1.09262	0.914
42DAP/41DAP	0.91181	0.384
43DAP/42DAP	1.08265	0.513
47DAP/43DAP	1.01978	1
52DAP/47DAP	1.00166	0.962
57DAP/52DAP	1.30962	0.156
57DAP/7DAP	1.40041	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32789	0.056
17DAP/reference	1.45112	0.017
27DAP/reference	1.34045	0.041
39DAP/reference	1.67647	0.007
41DAP/reference	1.23466	0.136
42DAP/reference	1.68353	0.021
43DAP/reference	1.54052	0.017
47DAP/reference	1.63401	0.022
52DAP/reference	1.39306	0.046
57DAP/reference	1.4935	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85462	0.19
17DAP/reference	0.93186	0.357
27DAP/reference	1.33501	0.203
39DAP/reference	1.35137	0.066
41DAP/reference	1.14364	0.309
42DAP/reference	1.30072	0.026
43DAP/reference	0.90236	0.314
47DAP/reference	1.22446	0.013
52DAP/reference	1.11832	0.279
57DAP/reference	0.80507	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19554	0.109
17DAP/reference	1.27655	0.298
27DAP/reference	1.44812	0.024
39DAP/reference	1.51767	0.009
41DAP/reference	1.33526	0.047
42DAP/reference	1.37745	0.023
43DAP/reference	1.82383	0.014
47DAP/reference	1.937	0.011
52DAP/reference	1.6093	0.031
57DAP/reference	3.21869	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04811	1
26DAP/20DAP	2.51536	0.099
34DAP/26DAP	0.82974	0.419
51DAP/34DAP	1.24581	0.581
52DAP/51DAP	0.71226	0.151
53DAP/52DAP	1.1075	0.517
55DAP/53DAP	0.84903	0.282
57DAP/55DAP	1.03886	0.997
62DAP/57DAP	0.787	0.681
68DAP/62DAP	1.76978	0.729
68DAP/14DAP	2.02496	0.053

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15846	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.7825	0.234
Mature Green Tomato/Ripe Tomato	0.99516	0.898
Immature Eggplant/Mature Eggplant	1.20914	0.081
Ripe Pepper/Ripe Tomato	0.91976	1
Mature Eggplant/Ripe Tomato	0.84947	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14133	0.742
1-1-2/M82	1.23729	0.977
12-2/M82	0.84125	0.661
12-4/M82	1.12863	1
1-3/M82	1.82527	0.248
2-1-1/M82	1.05803	0.764
2-1/M82	0.72243
2-6/M82	0.93279	1
3-2/M82	0.9358	0.752
4-1-1/M82	0.789	1
4-1/M82	1.69723	0.853
4-3-2/M82	1.15977	1
4-3/M82	1.25933	1
5-3/M82	1.17965	1
6-2/M82	1.1261	1
6-3/M82	1.01178	1
7-1/M82	0.83652	0.443
7-2/M82	1.04947	1
9-3-2/M82	1.38264	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31105	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.63151
IL12-4/WTpooled	1.04321
IL1-4/WTpooled	1.36807	1
WT/WTpooled	0.92988	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	1.09184	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09642	0.692
DC3000/delta hrp 6h	0.95281	0.95
DC3000/delta hrp 12h	1.05855	1
DC3000/delta hrp 24h	1.03629	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15223	0.042
DC3000 delta B/DC3000 delta AB	1.19203	0.215

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96993	1
Exp 36h	1.19687	0.489
Exp 60h	1.26482	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88487	1
Var 0h	0.94864	1
Var 12h I row2-row1	0.99697	1
Var 12h NI row2-row1	1.11976	1
Var 36h I row2-row1	1.32081	0.742
Var 36h NI row2-row1	1.0631	1
Var 60h I row2-row1	0.91889	0.832
Var 60h NI row2-row1	1.03299	1
Time course 0hI-0hNI	0.95935	0.765
Time course 12hI-12hNI	0.95089	0.725
Time course 36hI-36hNI	1.0461	0.651
Time course 60hI-60hNI	0.97612	0.646

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)	1.08519	0.748
transgenic ySAMdc/azygous control (breaker)	1.05147	1
transgenic ySAMdc/azygous control (red)	1.02874	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10602	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63899	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93916	1
Manapal/WT (break)	0.76583	0.333
Manapal/WT (red)	0.91077	0.315