Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76942	0.098
27DAP/17DAP	1.03416	0.876
39DAP/27DAP	1.7769	0.391
41DAP/39DAP	1.54971	0.293
42DAP/41DAP	0.79117	0.774
43DAP/42DAP	1.27433	0.985
47DAP/43DAP	0.97446	0.599
52DAP/47DAP	0.98324	0.821
57DAP/52DAP	1.02038	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19681	0.179
17DAP/reference	0.73881	0.007
27DAP/reference	0.94848	0.514
39DAP/reference	0.81156	0.083
41DAP/reference	0.69085	0.018
42DAP/reference	0.97801	0.337
43DAP/reference	0.90972	0.17
47DAP/reference	0.94039	0.207
52DAP/reference	1.26804	0.021
57DAP/reference	1.15394	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11983	0.975
27DAP/17DAP	1.01681	0.957
39DAP/27DAP	0.88524	0.26
41DAP/39DAP	1.08055	0.837
42DAP/41DAP	0.97089	0.751
43DAP/42DAP	1.09585	0.554
47DAP/43DAP	0.93002	0.559
52DAP/47DAP	1.12427	0.645
57DAP/52DAP	1.36892	0.127
57DAP/7DAP	1.32037	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84007	0.071
17DAP/reference	0.81207	0.012
27DAP/reference	0.79978	0.01
39DAP/reference	0.86222	0.02
41DAP/reference	0.86713	0.037
42DAP/reference	0.8098	0.014
43DAP/reference	0.78318	0.02
47DAP/reference	0.89573	0.383
52DAP/reference	0.76103	0.019
57DAP/reference	0.72621	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75827	0.037
17DAP/reference	0.8612	0.058
27DAP/reference	0.95861	0.423
39DAP/reference	1.11699	0.657
41DAP/reference	1.10556	0.318
42DAP/reference	1.06974	0.794
43DAP/reference	0.87262	0.186
47DAP/reference	0.90347	0.178
52DAP/reference	0.93544	0.203
57DAP/reference	0.78383	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73932	0.035
17DAP/reference	0.8731	0.217
27DAP/reference	0.75656	0.024
39DAP/reference	0.78414	0.016
41DAP/reference	0.87894	0.026
42DAP/reference	0.83282	0.059
43DAP/reference	0.88883	0.197
47DAP/reference	0.89542	0.063
52DAP/reference	0.73697	0.058
57DAP/reference	1.24804	0.274

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.57142	0.496
26DAP/20DAP	0.98068	1
34DAP/26DAP	1.66493	1
51DAP/34DAP	1.10726	0.967
52DAP/51DAP	1.67184	0.054
53DAP/52DAP	0.81885	0.621
55DAP/53DAP	1.06349	0.955
57DAP/55DAP	0.99888	0.875
62DAP/57DAP	1.14547	0.115
68DAP/62DAP	1.58942	0.153
68DAP/14DAP	1.66116	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18274	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.257	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.51193	0.224
Mature Eggplant/Ripe Tomato	0.35942	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.96077
1-1-2/M82	0.96045	1
12-2/M82	0.73569	0.955
12-4/M82	N/A	N/A
1-3/M82	1.00965	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.33107	0.501
3-2/M82	N/A	N/A
4-1-1/M82	1.20862	1
4-1/M82	0.48334
4-3-2/M82	N/A	N/A
4-3/M82	0.97918	1
5-3/M82	1.30999
6-2/M82	1.25758	1
6-3/M82	0.27818
7-1/M82	N/A	N/A
7-2/M82	0.80137	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.38007	0.277
IL2-6/WTpooled	0.93439	1
IL7-5/WTpooled	0.91668	1
IL7-3/WTpooled	1.48451	1
IL12-4/WTpooled	1.24334	0.624
IL1-4/WTpooled	1.16866	1
WT/WTpooled	1.02748	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	0.79194	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1496	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.96485	1
DC3000/delta hrp 24h	1.15225	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.54965

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10585	1
Exp 36h	0.65846	0.749
Exp 60h	0.4241	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00144	1
Var 0h	1.05177	1
Var 12h I row2-row1	1.01456	0.654
Var 12h NI row2-row1	0.89378	0.494
Var 36h I row2-row1	0.56249	0.805
Var 36h NI row2-row1	0.97372	0.743
Var 60h I row2-row1	1.30205	0.562
Var 60h NI row2-row1	1.07358	0.904
Time course 0hI-0hNI	0.98016	0.935
Time course 12hI-12hNI	1.0104	0.867
Time course 36hI-36hNI	0.78688	0.027
Time course 60hI-60hNI	0.4608	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)	1.43398	0.273
transgenic ySAMdc/azygous control (breaker)	1.21123	0.248
transgenic ySAMdc/azygous control (red)	0.83193	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00802	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74601	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72222	1
Manapal/WT (break)	1.13947	0.381
Manapal/WT (red)	0.91247	0.424