Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09332	0.878
27DAP/17DAP	0.7229	0.415
39DAP/27DAP	0.68861	0.194
41DAP/39DAP	1.08288	0.893
42DAP/41DAP	0.89377	1
43DAP/42DAP	1.06881	1
47DAP/43DAP	0.99461	0.799
52DAP/47DAP	0.71797	0.357
57DAP/52DAP	1.06277	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93641	0.101
17DAP/reference	0.8344	0.026
27DAP/reference	0.98007	0.668
39DAP/reference	1.11232	0.129
41DAP/reference	1.00805	1
42DAP/reference	0.9617	0.242
43DAP/reference	0.97538	0.519
47DAP/reference	0.992	0.568
52DAP/reference	0.93849	0.23
57DAP/reference	0.96415	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30255	0.179
27DAP/17DAP	0.88665	0.537
39DAP/27DAP	0.80401	0.194
41DAP/39DAP	0.95782	0.934
42DAP/41DAP	1.25217	0.861
43DAP/42DAP	0.90092	0.383
47DAP/43DAP	0.99213	0.939
52DAP/47DAP	1.08273	0.804
57DAP/52DAP	0.98604	0.81
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24971	0.058
17DAP/reference	1.17365	0.07
27DAP/reference	0.93	0.159
39DAP/reference	0.97258	0.411
41DAP/reference	0.86704	0.058
42DAP/reference	0.90812	0.077
43DAP/reference	0.86171	0.105
47DAP/reference	0.92358	0.222
52DAP/reference	0.94067	0.179
57DAP/reference	0.80489	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17581	0.104
17DAP/reference	0.8339	0.037
27DAP/reference	1.00229	1
39DAP/reference	0.95498	0.33
41DAP/reference	0.86917	0.085
42DAP/reference	0.97716	0.534
43DAP/reference	1.11606	0.441
47DAP/reference	0.99263	0.66
52DAP/reference	0.82226	0.034
57DAP/reference	0.88472	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43447	0.018
17DAP/reference	1.10922	0.118
27DAP/reference	1.04763	0.596
39DAP/reference	1.1248	0.203
41DAP/reference	1.07594	0.734
42DAP/reference	1.01655	1
43DAP/reference	1.11094	0.403
47DAP/reference	0.86122	0.097
52DAP/reference	0.78799	0.123
57DAP/reference	1.04059	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30049	0.966
26DAP/20DAP	0.52536	0.223
34DAP/26DAP	2.01239	0.126
51DAP/34DAP	1.22207
52DAP/51DAP	0.96881	1
53DAP/52DAP	1.51507	0.783
55DAP/53DAP	0.9886	0.82
57DAP/55DAP	1.4406	0.728
62DAP/57DAP	0.77276	0.681
68DAP/62DAP	1.38181	0.682
68DAP/14DAP	0.57338	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8638	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.58566

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08922	0.877
1-1-2/M82	0.94744	1
12-2/M82	N/A	N/A
12-4/M82	1.33323
1-3/M82	0.71982
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.13635	0.594
3-2/M82	0.86077
4-1-1/M82	N/A	N/A
4-1/M82	1.13422
4-3-2/M82	1.02788
4-3/M82	N/A	N/A
5-3/M82	0.957	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.01399	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.72154	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02028	1
IL12-4/WTpooled	1.0264	1
IL1-4/WTpooled	0.97794
WT/WTpooled	1.0027	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	0.79517	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95436	1
DC3000/delta hrp 6h	1.02422	1
DC3000/delta hrp 12h	1.05787	1
DC3000/delta hrp 24h	0.6121	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7574
DC3000 delta B/DC3000 delta AB	0.57307	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01998	1
Exp 36h	0.78636	0.699
Exp 60h	0.60243	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98291	1
Var 0h	0.57368	0.936
Var 12h I row2-row1	0.73033	0.39
Var 12h NI row2-row1	0.96967	0.546
Var 36h I row2-row1	0.92013	1
Var 36h NI row2-row1	1.26356	0.482
Var 60h I row2-row1	0.75881	0.562
Var 60h NI row2-row1	1.02552	1
Time course 0hI-0hNI	0.95644	0.699
Time course 12hI-12hNI	0.92506	0.287
Time course 36hI-36hNI	0.87815	0.117
Time course 60hI-60hNI	0.10242	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)	1.15649	0.654
transgenic ySAMdc/azygous control (breaker)	1.06609	1
transgenic ySAMdc/azygous control (red)	1.34974	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9706	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.74152	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.07703	0.083
Manapal/WT (break)	1.66251	0.183
Manapal/WT (red)	1.39134	0.164