Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.1.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98913	0.839
27DAP/17DAP	1.11044	0.873
39DAP/27DAP	0.65382	0.392
41DAP/39DAP	1.43079	0.437
42DAP/41DAP	1.19295	0.913
43DAP/42DAP	0.97468	0.912
47DAP/43DAP	0.90096	0.667
52DAP/47DAP	1.28554	0.721
57DAP/52DAP	0.84703	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84514	0.101
17DAP/reference	0.82072	0.104
27DAP/reference	0.99604	0.741
39DAP/reference	0.8155	0.093
41DAP/reference	0.7228	0.039
42DAP/reference	0.86972	0.045
43DAP/reference	1.02339	0.957
47DAP/reference	0.88236	0.148
52DAP/reference	1.2075	0.167
57DAP/reference	1.13932	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0643	0.593
27DAP/17DAP	1.11994	0.658
39DAP/27DAP	1.02039	0.832
41DAP/39DAP	1.10554	0.895
42DAP/41DAP	0.98668	0.787
43DAP/42DAP	1.06881	0.699
47DAP/43DAP	0.99308	0.954
52DAP/47DAP	1.09344	0.718
57DAP/52DAP	1.0246	0.941
57DAP/7DAP	1.18321	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7922	0.066
17DAP/reference	0.85441	0.031
27DAP/reference	0.84733	0.01
39DAP/reference	0.82414	0.013
41DAP/reference	0.78677	0.013
42DAP/reference	0.71496	0.012
43DAP/reference	0.77674	0.017
47DAP/reference	0.85342	0.168
52DAP/reference	0.75226	0.026
57DAP/reference	0.69751	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81854	0.152
17DAP/reference	0.60382	0.01
27DAP/reference	0.86494	0.173
39DAP/reference	0.79838	0.105
41DAP/reference	0.95669	0.322
42DAP/reference	0.91226	0.081
43DAP/reference	0.74224	0.105
47DAP/reference	0.7114	0.014
52DAP/reference	0.62684	0.003
57DAP/reference	0.37148	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82483	0.065
17DAP/reference	0.90292	0.348
27DAP/reference	0.8037	0.025
39DAP/reference	0.81438	0.021
41DAP/reference	0.87251	0.064
42DAP/reference	0.9475	0.552
43DAP/reference	0.94699	0.416
47DAP/reference	0.99792	0.525
52DAP/reference	0.69355	0.05
57DAP/reference	1.42893	0.062

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06001	0.966
26DAP/20DAP	0.82095	0.317
34DAP/26DAP	1.17051	0.819
51DAP/34DAP	0.99692	0.893
52DAP/51DAP	1.02389	1
53DAP/52DAP	1.03312	0.895
55DAP/53DAP	1.16977	0.46
57DAP/55DAP	0.84178	0.508
62DAP/57DAP	1.11052	0.158
68DAP/62DAP	0.94994	0.787
68DAP/14DAP	1.03612	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71457	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.5403
Mature Green Tomato/Ripe Tomato	0.93132	0.522
Immature Eggplant/Mature Eggplant	1.24774	0.278
Ripe Pepper/Ripe Tomato	1.01264	1
Mature Eggplant/Ripe Tomato	1.46165	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04499	1
1-1-2/M82	0.86907	0.804
12-2/M82	1.16161	1
12-4/M82	1.10356
1-3/M82	0.82029	0.378
2-1-1/M82	1.26672	0.689
2-1/M82	N/A	N/A
2-6/M82	1.23808	0.594
3-2/M82	0.83638
4-1-1/M82	1.11253	0.968
4-1/M82	1.25014	1
4-3-2/M82	1.01012	1
4-3/M82	0.85114	1
5-3/M82	0.94961	1
6-2/M82	0.97772
6-3/M82	1.0697	1
7-1/M82	N/A	N/A
7-2/M82	1.04136	1
9-3-2/M82	0.98169	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8249	0.321
IL2-6/WTpooled	1.11051	0.584
IL7-5/WTpooled	1.48043	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.17653	0.737
IL1-4/WTpooled	1.05928	1
WT/WTpooled	0.93971	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	0.91989	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95008	1
DC3000/delta hrp 6h	1.07576	1
DC3000/delta hrp 12h	1.12428	1
DC3000/delta hrp 24h	0.99938	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95314	0.597
DC3000 delta B/DC3000 delta AB	1.01511	0.714

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93664	1
Exp 36h	0.73476	0.426
Exp 60h	1.00278	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97423	1
Var 0h	0.94709	1
Var 12h I row2-row1	0.99316	1
Var 12h NI row2-row1	0.99684	1
Var 36h I row2-row1	0.81633	0.805
Var 36h NI row2-row1	1.39785	1
Var 60h I row2-row1	1.53998	0.562
Var 60h NI row2-row1	1.20976	0.904
Time course 0hI-0hNI	0.99965	1
Time course 12hI-12hNI	0.93544	0.586
Time course 36hI-36hNI	0.81313	0.023
Time course 60hI-60hNI	0.88879	0.081

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)	0.96545	0.286
transgenic ySAMdc/azygous control (breaker)	1.25274	0.178
transgenic ySAMdc/azygous control (red)	0.98588	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02993	0.096

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69223	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20629	0.14
Manapal/WT (break)	1.17101	0.381
Manapal/WT (red)	1.18469	0.413