Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48549	0.244
27DAP/17DAP	0.57109	0.11
39DAP/27DAP	0.86536	0.564
41DAP/39DAP	0.95319	0.706
42DAP/41DAP	1.15464	0.745
43DAP/42DAP	0.95185	0.89
47DAP/43DAP	0.9839	0.895
52DAP/47DAP	0.86974	0.617
57DAP/52DAP	1.17033	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10063	0.441
17DAP/reference	1.23144	0.032
27DAP/reference	1.03359	0.782
39DAP/reference	0.91538	0.132
41DAP/reference	1.01523	1
42DAP/reference	0.94664	0.188
43DAP/reference	1.01642	0.758
47DAP/reference	1.00644	0.72
52DAP/reference	0.76905	0.021
57DAP/reference	0.84134	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32542	0.414
27DAP/17DAP	1.0129	1
39DAP/27DAP	0.38518	0.029
41DAP/39DAP	0.98155	0.986
42DAP/41DAP	1.20034	0.251
43DAP/42DAP	0.72524	0.022
47DAP/43DAP	1.02612	0.957
52DAP/47DAP	1.26197	0.681
57DAP/52DAP	1.19615	0.971
57DAP/7DAP	0.52827	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68318	0.049
17DAP/reference	1.13511	0.574
27DAP/reference	1.25717	0.371
39DAP/reference	1.16062	0.077
41DAP/reference	1.38956	0.136
42DAP/reference	0.93212	0.458
43DAP/reference	1.22006	0.325
47DAP/reference	1.04334	0.996
52DAP/reference	1.04621	0.526
57DAP/reference	1.53823	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14135	0.217
17DAP/reference	1.30798	0.063
27DAP/reference	1.08114	0.455
39DAP/reference	0.90842	0.113
41DAP/reference	1.07064	0.599
42DAP/reference	1.10304	0.247
43DAP/reference	0.82864	0.098
47DAP/reference	1.00799	1
52DAP/reference	0.87021	0.072
57DAP/reference	0.91284	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30132	0.13
17DAP/reference	1.3235	0.122
27DAP/reference	1.23178	0.373
39DAP/reference	0.97819	0.755
41DAP/reference	1.1705	0.984
42DAP/reference	1.02455	0.979
43DAP/reference	0.96969	0.639
47DAP/reference	0.89085	0.097
52DAP/reference	1.17106	0.79
57DAP/reference	0.89757	0.177

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21323	0.966
26DAP/20DAP	1.57561	0.099
34DAP/26DAP	0.60696	0.073
51DAP/34DAP	0.67845	0.06
52DAP/51DAP	0.91317	1
53DAP/52DAP	0.87975	0.21
55DAP/53DAP	1.24749	0.366
57DAP/55DAP	0.89519	0.583
62DAP/57DAP	1.20723	0.622
68DAP/62DAP	1.70425	0.021
68DAP/14DAP	1.12483	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.35423	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.88245	0.058
Mature Green Tomato/Ripe Tomato	5.75739	0.015
Immature Eggplant/Mature Eggplant	0.1722	0.057
Ripe Pepper/Ripe Tomato	2.04489
Mature Eggplant/Ripe Tomato	50.9045	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92586	1
IL2-6/WTpooled	0.96487	1
IL7-5/WTpooled	1.10411	0.792
IL7-3/WTpooled	1.06096	1
IL12-4/WTpooled	0.96652	0.581
IL1-4/WTpooled	1.0841	1
WT/WTpooled	0.94461	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	0.82939	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9993	1
DC3000/delta hrp 6h	1.12543	1
DC3000/delta hrp 12h	1.08196	1
DC3000/delta hrp 24h	0.46317	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4746	0.027
DC3000 delta B/DC3000 delta AB	0.42928	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95551	1
Exp 36h	0.66156	0.426
Exp 60h	0.5533	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97942	1
Var 0h	0.8302	1
Var 12h I row2-row1	0.78839	0.338
Var 12h NI row2-row1	1.06661	0.34
Var 36h I row2-row1	0.92164	0.313
Var 36h NI row2-row1	1.5521	0.482
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.03815	1
Time course 0hI-0hNI	0.96605	0.845
Time course 12hI-12hNI	0.70305	0.033
Time course 36hI-36hNI	0.53339	0.023
Time course 60hI-60hNI	0.11912	0.005

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)	0.88725	0.297
transgenic ySAMdc/azygous control (breaker)	0.9117	0.49
transgenic ySAMdc/azygous control (red)	1.18232	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96463	0.393

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.53448	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84177	0.172
Manapal/WT (break)	1.08355	1
Manapal/WT (red)	1.11753	1