Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.7.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86942	0.405
27DAP/17DAP	0.92874	0.863
39DAP/27DAP	1.29254	0.458
41DAP/39DAP	0.89261	0.566
42DAP/41DAP	1.29122	0.681
43DAP/42DAP	1.06846	1
47DAP/43DAP	0.88367	0.613
52DAP/47DAP	1.63547	0.156
57DAP/52DAP	0.75164	0.649

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0399	0.814
17DAP/reference	1.02134	0.355
27DAP/reference	1.04928	0.135
39DAP/reference	1.04251	0.343
41DAP/reference	0.99956	1
42DAP/reference	0.95919	0.163
43DAP/reference	0.99897	0.924
47DAP/reference	0.97616	0.3
52DAP/reference	0.9533	0.341
57DAP/reference	0.83003	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93414	0.402
27DAP/17DAP	1.03621	0.881
39DAP/27DAP	1.0855	0.453
41DAP/39DAP	0.97214	0.968
42DAP/41DAP	1.02214	1
43DAP/42DAP	1.06094	0.273
47DAP/43DAP	0.98454	0.923
52DAP/47DAP	1.01314	0.956
57DAP/52DAP	1.01074	1
57DAP/7DAP	1.12224	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77446	0.138
17DAP/reference	0.7725	0.011
27DAP/reference	0.74294	0.01
39DAP/reference	0.76187	0.011
41DAP/reference	0.79097	0.02
42DAP/reference	0.70714	0.013
43DAP/reference	0.75354	0.013
47DAP/reference	0.79984	0.079
52DAP/reference	0.69767	0.012
57DAP/reference	0.74629	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02944	0.634
17DAP/reference	1.07118	0.216
27DAP/reference	0.96535	0.438
39DAP/reference	0.98821	0.554
41DAP/reference	0.96312	0.322
42DAP/reference	0.96357	0.237
43DAP/reference	1.028	0.809
47DAP/reference	0.93674	0.06
52DAP/reference	1.01301	0.988
57DAP/reference	1.07949	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81874	0.158
17DAP/reference	0.93489	0.398
27DAP/reference	0.78193	0.039
39DAP/reference	0.7738	0.028
41DAP/reference	0.81764	0.028
42DAP/reference	0.71512	0.036
43DAP/reference	0.7896	0.018
47DAP/reference	0.96479	0.296
52DAP/reference	0.76956	0.141
57DAP/reference	0.71914	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93769	0.733
26DAP/20DAP	0.83943	0.317
34DAP/26DAP	0.96016	0.917
51DAP/34DAP	0.93225	0.504
52DAP/51DAP	0.99546	1
53DAP/52DAP	1.02897	0.753
55DAP/53DAP	1.06725	0.689
57DAP/55DAP	1.06786	0.865
62DAP/57DAP	0.99002	0.994
68DAP/62DAP	0.90678	0.579
68DAP/14DAP	0.92792	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86101	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95576
Mature Green Tomato/Ripe Tomato	1.51851	0.023
Immature Eggplant/Mature Eggplant	1.07052	0.439
Ripe Pepper/Ripe Tomato	1.87091	1
Mature Eggplant/Ripe Tomato	0.95699

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08938
1-1-2/M82	0.88688
12-2/M82	0.91212	0.862
12-4/M82	N/A	N/A
1-3/M82	0.83864	0.378
2-1-1/M82	1.04654
2-1/M82	N/A	N/A
2-6/M82	0.99998
3-2/M82	0.86567
4-1-1/M82	0.98877	1
4-1/M82	N/A	N/A
4-3-2/M82	0.99922
4-3/M82	0.88806	1
5-3/M82	1.00855	1
6-2/M82	1.11903
6-3/M82	0.86452
7-1/M82	N/A	N/A
7-2/M82	1.11193
9-3-2/M82	0.77347

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85305
IL2-6/WTpooled	0.9791	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95805	1
IL12-4/WTpooled	1.15734	0.646
IL1-4/WTpooled	0.89681
WT/WTpooled	0.98322	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	0.94612	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00927	0.921
DC3000/delta hrp 6h	1.15299	1
DC3000/delta hrp 12h	1.06244	1
DC3000/delta hrp 24h	1.07368	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99522	1
DC3000 delta B/DC3000 delta AB	0.87913	0.406

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99757	1
Exp 36h	1.2043	0.409
Exp 60h	1.07485	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02135	1
Var 0h	1.01305	0.98
Var 12h I row2-row1	1.1241	0.204
Var 12h NI row2-row1	0.98465	0.906
Var 36h I row2-row1	0.87599	0.575
Var 36h NI row2-row1	0.8881	0.478
Var 60h I row2-row1	1.68086	0.562
Var 60h NI row2-row1	1.30309	0.904
Time course 0hI-0hNI	1.12983	0.719
Time course 12hI-12hNI	0.97606	0.87
Time course 36hI-36hNI	0.94561	0.169
Time course 60hI-60hNI	1.20402	0.029

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)	0.96374	0.32
transgenic ySAMdc/azygous control (breaker)	0.89333	0.49
transgenic ySAMdc/azygous control (red)	1.06438	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02296	0.372

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81053	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12241	0.307
Manapal/WT (break)	0.91379	1
Manapal/WT (red)	1.17065	0.413