Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42425	0.325
27DAP/17DAP	0.70121	0.166
39DAP/27DAP	0.98859	0.798
41DAP/39DAP	0.70992	0.286
42DAP/41DAP	0.98786	1
43DAP/42DAP	0.95141	0.898
47DAP/43DAP	0.93849	0.773
52DAP/47DAP	0.90876	0.626
57DAP/52DAP	0.90079	0.903

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86928	0.128
17DAP/reference	0.82686	0.025
27DAP/reference	1.05452	0.894
39DAP/reference	0.85648	0.068
41DAP/reference	0.91573	0.341
42DAP/reference	1.00684	0.517
43DAP/reference	0.87919	0.211
47DAP/reference	0.92616	0.3
52DAP/reference	0.78089	0.082
57DAP/reference	0.95093	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23455	0.312
27DAP/17DAP	0.74975	0.179
39DAP/27DAP	0.99069	0.964
41DAP/39DAP	0.91467	0.781
42DAP/41DAP	1.00813	0.884
43DAP/42DAP	0.7076	0.025
47DAP/43DAP	1.29477	0.758
52DAP/47DAP	1.05143	0.892
57DAP/52DAP	0.89216	0.537
57DAP/7DAP	1.17719	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18796	0.051
17DAP/reference	0.9932	0.599
27DAP/reference	0.92752	0.062
39DAP/reference	1.00584	1
41DAP/reference	0.92788	0.247
42DAP/reference	0.928	0.13
43DAP/reference	1.00553	0.694
47DAP/reference	0.92419	0.383
52DAP/reference	0.84968	0.09
57DAP/reference	0.87004	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03723	0.724
17DAP/reference	1.07789	0.599
27DAP/reference	1.12038	0.648
39DAP/reference	0.8121	0.071
41DAP/reference	0.9053	0.25
42DAP/reference	0.95483	0.433
43DAP/reference	0.75442	0.102
47DAP/reference	0.82649	0.029
52DAP/reference	0.91784	0.351
57DAP/reference	0.9015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36512	0.019
17DAP/reference	1.173	0.212
27DAP/reference	1.02121	0.903
39DAP/reference	1.06021	0.353
41DAP/reference	0.97304	0.56
42DAP/reference	1.12655	0.51
43DAP/reference	1.1686	0.074
47DAP/reference	0.69673	0.045
52DAP/reference	0.93878	0.538
57DAP/reference	0.89576	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.3621	0.916
26DAP/20DAP	0.71751	0.512
34DAP/26DAP	0.78451	0.21
51DAP/34DAP	2.81748	0.241
52DAP/51DAP	0.89009	1
53DAP/52DAP	1.15071	0.845
55DAP/53DAP	1.33382	0.399
57DAP/55DAP	0.71749	0.159
62DAP/57DAP	0.92306	0.871
68DAP/62DAP	1.38815	0.984
68DAP/14DAP	1.70332

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00416	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	19.8392	0.064
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	8.07201
Mature Eggplant/Ripe Tomato	4.24652

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25689	0.877
1-1-2/M82	0.84384
12-2/M82	1.15542
12-4/M82	0.94271
1-3/M82	0.74154	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.09528	1
3-2/M82	N/A	N/A
4-1-1/M82	1.15936
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.02025
5-3/M82	1.02499	1
6-2/M82	0.93872
6-3/M82	1.12395
7-1/M82	1.28869
7-2/M82	1.12662
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	1.00351	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89768	1
IL12-4/WTpooled	0.72412	0.566
IL1-4/WTpooled	0.94218
WT/WTpooled	1.11611	0.87

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	1.09527	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04605	0.724
DC3000/delta hrp 6h	0.91502	0.95
DC3000/delta hrp 12h	1.12717	1
DC3000/delta hrp 24h	1.06367	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.92206
DC3000 delta B/DC3000 delta AB	0.66915

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.72882	0.661
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	1.06281	1
Var 0h	1.00331	1
Var 12h I row2-row1	1.01288	0.795
Var 12h NI row2-row1	0.79092	1
Var 36h I row2-row1	0.93662	1
Var 36h NI row2-row1	0.50003	0.31
Var 60h I row2-row1	1.04717	1
Var 60h NI row2-row1	0.84978	0.63
Time course 0hI-0hNI	0.93902	0.721
Time course 12hI-12hNI	0.96803	0.782
Time course 36hI-36hNI	0.94216	0.323
Time course 60hI-60hNI	0.48684	0.006

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)	0.9458	0.662
transgenic ySAMdc/azygous control (breaker)	1.47424	1
transgenic ySAMdc/azygous control (red)	1.33064	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98071	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11739	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89706	1
Manapal/WT (break)	1.18038	0.14
Manapal/WT (red)	2.38617	0.222