Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.16.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06267	0.812
27DAP/17DAP	1.27393	0.742
39DAP/27DAP	1.20668	0.504
41DAP/39DAP	0.84271	0.412
42DAP/41DAP	1.07593	0.978
43DAP/42DAP	0.85086	0.576
47DAP/43DAP	1.0448	0.926
52DAP/47DAP	0.88294	0.662
57DAP/52DAP	1.07445	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86208	0.118
17DAP/reference	0.72376	0.007
27DAP/reference	1.03099	0.925
39DAP/reference	0.85207	0.121
41DAP/reference	0.77886	0.009
42DAP/reference	0.88131	0.01
43DAP/reference	0.9851	0.763
47DAP/reference	0.9742	0.418
52DAP/reference	1.13161	0.548
57DAP/reference	1.25016	0.032

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46301	0.036
27DAP/17DAP	1.01801	0.942
39DAP/27DAP	1.21522	0.267
41DAP/39DAP	0.96788	0.945
42DAP/41DAP	0.94591	0.612
43DAP/42DAP	0.7006	0.065
47DAP/43DAP	0.94806	0.757
52DAP/47DAP	0.88865	0.56
57DAP/52DAP	0.85711	0.391
57DAP/7DAP	1.20491	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99467	0.682
17DAP/reference	1.07139	0.477
27DAP/reference	1.19098	0.049
39DAP/reference	0.85226	0.031
41DAP/reference	0.82461	0.07
42DAP/reference	0.88522	0.13
43DAP/reference	0.96199	0.321
47DAP/reference	1.1569	0.149
52DAP/reference	0.85135	0.023
57DAP/reference	0.81417	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81266	0.034
17DAP/reference	0.75585	0.004
27DAP/reference	0.94627	0.381
39DAP/reference	1.0822	0.639
41DAP/reference	1.09328	0.362
42DAP/reference	0.90821	0.042
43DAP/reference	0.84546	0.095
47DAP/reference	0.9386	0.188
52DAP/reference	1.03791	1
57DAP/reference	0.74011	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05498	0.631
17DAP/reference	0.82216	0.143
27DAP/reference	0.92587	0.165
39DAP/reference	0.90578	0.147
41DAP/reference	1.03801	0.84
42DAP/reference	1.09142	0.364
43DAP/reference	1.04445	0.828
47DAP/reference	0.92725	0.315
52DAP/reference	1.07011	0.714
57DAP/reference	1.91704	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.131	1
26DAP/20DAP	0.72137	0.317
34DAP/26DAP	1.39872	0.819
51DAP/34DAP	0.65726	0.049
52DAP/51DAP	0.8572	1
53DAP/52DAP	1.0804	0.697
55DAP/53DAP	1.06561	0.911
57DAP/55DAP	0.98263	0.823
62DAP/57DAP	1.21925	0.393
68DAP/62DAP	1.30083	0.635
68DAP/14DAP	2.04039	0.061

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75961	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.77306
Mature Green Tomato/Ripe Tomato	2.64158	0.015
Immature Eggplant/Mature Eggplant	1.37225	0.058
Ripe Pepper/Ripe Tomato	0.24813	0.293
Mature Eggplant/Ripe Tomato	1.30471	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.58337	0.944
1-1-2/M82	N/A	N/A
12-2/M82	0.3453
12-4/M82	1.52443	0.611
1-3/M82	1.70973	0.277
2-1-1/M82	1.53626
2-1/M82	1.08388	1
2-6/M82	1.35591
3-2/M82	N/A	N/A
4-1-1/M82	0.77832
4-1/M82	0.93749
4-3-2/M82	1.51875
4-3/M82	1.35436	0.268
5-3/M82	1.25398	0.572
6-2/M82	1.15465
6-3/M82	0.70165	1
7-1/M82	1.79382	0.87
7-2/M82	0.73847
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	1.02539	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.29418	0.362
IL12-4/WTpooled	1.22688	0.516
IL1-4/WTpooled	0.95019
WT/WTpooled	1.01155	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05703	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01572	1
DC3000/delta hrp 24h	3.48239	0.072

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.9562
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.11138	1
Var 0h	0.59216	1
Var 12h I row2-row1	2.04744	0.506
Var 12h NI row2-row1	1.2049	1
Var 36h I row2-row1	0.69279	1
Var 36h NI row2-row1	0.99822	0.791
Var 60h I row2-row1	1.02234	0.562
Var 60h NI row2-row1	0.93391	1
Time course 0hI-0hNI	1.31334	0.63
Time course 12hI-12hNI	0.92175	0.6
Time course 36hI-36hNI	0.89979	0.194
Time course 60hI-60hNI	0.71533	0.161

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)	0.63164	0.286
transgenic ySAMdc/azygous control (breaker)	0.88249	0.251
transgenic ySAMdc/azygous control (red)	0.86129	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01016	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88599	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.05437	0.093
Manapal/WT (break)	0.98927	1
Manapal/WT (red)	0.80966	0.36