Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.16.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74874	0.178
27DAP/17DAP	0.79433	0.38
39DAP/27DAP	1.2618	0.692
41DAP/39DAP	1.08792	0.929
42DAP/41DAP	0.95793	1
43DAP/42DAP	1.0132	0.931
47DAP/43DAP	1.01167	0.835
52DAP/47DAP	1.07326	0.783
57DAP/52DAP	0.91145	0.903

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93025	0.284
17DAP/reference	0.92069	0.194
27DAP/reference	1.01772	0.966
39DAP/reference	1.00588	0.92
41DAP/reference	0.89101	0.154
42DAP/reference	0.90085	0.013
43DAP/reference	0.95144	0.234
47DAP/reference	0.95614	0.322
52DAP/reference	0.96641	0.461
57DAP/reference	1.04181	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86631	0.219
27DAP/17DAP	0.93079	0.748
39DAP/27DAP	1.1375	0.353
41DAP/39DAP	0.97335	0.959
42DAP/41DAP	0.9602	0.666
43DAP/42DAP	0.96399	0.729
47DAP/43DAP	1.04539	0.844
52DAP/47DAP	1.04507	0.9
57DAP/52DAP	1.18708	0.161
57DAP/7DAP	1.16362	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87931	0.115
17DAP/reference	0.81052	0.014
27DAP/reference	0.81728	0.017
39DAP/reference	0.81124	0.025
41DAP/reference	0.88286	0.116
42DAP/reference	0.88824	0.169
43DAP/reference	0.75049	0.013
47DAP/reference	0.86314	0.293
52DAP/reference	0.80409	0.038
57DAP/reference	0.78834	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89382	0.296
17DAP/reference	0.8385	0.049
27DAP/reference	0.81644	0.06
39DAP/reference	0.80707	0.032
41DAP/reference	0.85676	0.02
42DAP/reference	0.79328	0.073
43DAP/reference	0.88092	0.212
47DAP/reference	0.91784	0.113
52DAP/reference	0.83877	0.008
57DAP/reference	1.04	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95133	0.391
17DAP/reference	0.89968	0.243
27DAP/reference	0.81889	0.036
39DAP/reference	0.85402	0.063
41DAP/reference	0.7233	0.07
42DAP/reference	0.80449	0.049
43DAP/reference	0.75779	0.016
47DAP/reference	0.98824	0.593
52DAP/reference	0.74382	0.223
57DAP/reference	0.86974	0.129

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98441	1
26DAP/20DAP	0.99712	1
34DAP/26DAP	1.02223	1
51DAP/34DAP	1.01259	1
52DAP/51DAP	0.94863	1
53DAP/52DAP	0.94484	0.732
55DAP/53DAP	1.02179	1
57DAP/55DAP	1.07411	0.947
62DAP/57DAP	1.13152	0.678
68DAP/62DAP	1.02059	1
68DAP/14DAP	1.35782	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75347	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.16433
Mature Green Tomato/Ripe Tomato	2.08335	0.015
Immature Eggplant/Mature Eggplant	2.03182	0.05
Ripe Pepper/Ripe Tomato	1.51663	1
Mature Eggplant/Ripe Tomato	0.75453	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05929	0.877
1-1-2/M82	0.94408	0.804
12-2/M82	1.30987	0.375
12-4/M82	0.99005	1
1-3/M82	0.92983	1
2-1-1/M82	1.47639
2-1/M82	1.33491
2-6/M82	1.13384	0.695
3-2/M82	0.93447
4-1-1/M82	0.97015	1
4-1/M82	N/A	N/A
4-3-2/M82	1.21732	1
4-3/M82	0.91296	1
5-3/M82	1.04627	1
6-2/M82	0.8225
6-3/M82	1.08507	1
7-1/M82	N/A	N/A
7-2/M82	0.94711	0.881
9-3-2/M82	1.09145	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07135
IL2-6/WTpooled	1.03381	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04291	1
IL12-4/WTpooled	1.08671	0.695
IL1-4/WTpooled	0.87971	0.444
WT/WTpooled	1.09839	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	0.98579	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08427	0.894
DC3000/delta hrp 6h	1.10844	1
DC3000/delta hrp 12h	1.19527	1
DC3000/delta hrp 24h	0.99465	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12666	0.333
DC3000 delta B/DC3000 delta AB	1.32676	0.253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0424	1
Exp 36h	1.08965	1
Exp 60h	1.20513	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98273	1
Var 0h	0.4977	0.457
Var 12h I row2-row1	1.18054	0.473
Var 12h NI row2-row1	0.84292	0.403
Var 36h I row2-row1	0.93034	1
Var 36h NI row2-row1	0.88972	0.706
Var 60h I row2-row1	1.01675	1
Var 60h NI row2-row1	1.07487	0.904
Time course 0hI-0hNI	1.09856	0.574
Time course 12hI-12hNI	1.08734	0.097
Time course 36hI-36hNI	1.16623	0.011
Time course 60hI-60hNI	1.37589	0.008

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)	0.9679	0.614
transgenic ySAMdc/azygous control (breaker)	1.03514	1
transgenic ySAMdc/azygous control (red)	0.84092	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01365	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73552	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93909	1
Manapal/WT (break)	0.82096	0.333
Manapal/WT (red)	0.75133	0.199