Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23136	0.534
27DAP/17DAP	1.10017	0.911
39DAP/27DAP	0.72325	0.338
41DAP/39DAP	1.03522	0.992
42DAP/41DAP	0.9786	1
43DAP/42DAP	1.0072	0.937
47DAP/43DAP	1.13009	0.825
52DAP/47DAP	0.92713	0.761
57DAP/52DAP	0.90217	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13751	0.421
17DAP/reference	0.94215	0.419
27DAP/reference	1.26105	0.034
39DAP/reference	1.2031	0.343
41DAP/reference	1.19662	0.171
42DAP/reference	1.20198	0.191
43DAP/reference	1.06576	0.596
47DAP/reference	1.22694	0.009
52DAP/reference	1.44925	0.016
57DAP/reference	1.3703	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35968	0.558
27DAP/17DAP	1.04326	0.912
39DAP/27DAP	0.83319	0.154
41DAP/39DAP	1.0375	0.914
42DAP/41DAP	0.96541	0.649
43DAP/42DAP	0.97683	0.801
47DAP/43DAP	0.86534	0.179
52DAP/47DAP	0.95872	0.77
57DAP/52DAP	0.94721	0.709
57DAP/7DAP	0.67496

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98344	0.613
17DAP/reference	1.06386	0.399
27DAP/reference	0.96262	0.231
39DAP/reference	1.14207	0.05
41DAP/reference	0.98183	0.538
42DAP/reference	1.02591	0.686
43DAP/reference	1.07106	0.637
47DAP/reference	1.06045	0.854
52DAP/reference	1.02895	0.886
57DAP/reference	1.0558	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88663	0.503
17DAP/reference	0.96703	0.561
27DAP/reference	1.39428	0.133
39DAP/reference	1.20964	0.29
41DAP/reference	1.7115	0.162
42DAP/reference	1.41049	0.029
43DAP/reference	1.03793	0.997
47DAP/reference	1.00976	0.695
52DAP/reference	1.02705	0.368
57DAP/reference	0.87716	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93274	0.249
17DAP/reference	0.99281	0.739
27DAP/reference	1.12401	0.105
39DAP/reference	1.08726	0.39
41DAP/reference	1.05758	0.605
42DAP/reference	1.29426	0.097
43DAP/reference	1.40988	0.044
47DAP/reference	1.17394	0.163
52DAP/reference	0.93415	0.529
57DAP/reference	1.27433	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14329	0.966
26DAP/20DAP	0.95756
34DAP/26DAP	1.2153	1
51DAP/34DAP	0.81095	0.436
52DAP/51DAP	0.95795	1
53DAP/52DAP	0.89321	0.767
55DAP/53DAP	1.17091	0.589
57DAP/55DAP	0.7643
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.55851	0.174
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.58	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.48837
Mature Green Tomato/Ripe Tomato	2.15254	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.7304
Mature Eggplant/Ripe Tomato	0.30595	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06071	0.473
1-1-2/M82	1.21948	1
12-2/M82	N/A	N/A
12-4/M82	0.98926	1
1-3/M82	0.69174	0.441
2-1-1/M82	0.95144
2-1/M82	N/A	N/A
2-6/M82	0.93802	1
3-2/M82	0.904
4-1-1/M82	N/A	N/A
4-1/M82	1.21082	0.853
4-3-2/M82	1.13019
4-3/M82	1.09463
5-3/M82	0.9041	0.49
6-2/M82	0.87018	1
6-3/M82	0.93026	1
7-1/M82	0.90781
7-2/M82	0.76293	0.578
9-3-2/M82	0.97931

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1766	0.277
IL2-6/WTpooled	0.92254	1
IL7-5/WTpooled	1.3735	0.75
IL7-3/WTpooled	0.89162	0.294
IL12-4/WTpooled	0.93776	1
IL1-4/WTpooled	0.88713	0.562
WT/WTpooled	1.04202	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	0.83508	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06206	0.921
DC3000/delta hrp 6h	1.203	1
DC3000/delta hrp 12h	1.10091	1
DC3000/delta hrp 24h	1.04655	0.553

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
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	N/A	N/A
Var 0h	1.13067	0.374
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.2379	0.213
transgenic ySAMdc/azygous control (breaker)	0.89842	0.49
transgenic ySAMdc/azygous control (red)	0.91614	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87226	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03763	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03526	1
Manapal/WT (break)	1.53943	0.183
Manapal/WT (red)	2.5561	0.15