Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.6.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06216	0.912
27DAP/17DAP	0.97775	1
39DAP/27DAP	1.03803	0.99
41DAP/39DAP	0.9026	0.67
42DAP/41DAP	1.18138	0.997
43DAP/42DAP	1.00979	0.937
47DAP/43DAP	1.24036	0.618
52DAP/47DAP	1.11311	0.879
57DAP/52DAP	1.15773	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10003	0.059
17DAP/reference	1.0558	0.369
27DAP/reference	1.29719	0.285
39DAP/reference	0.95824	0.575
41DAP/reference	0.90599	0.267
42DAP/reference	0.94211	0.202
43DAP/reference	1.41935	0.252
47DAP/reference	0.88829	0.021
52DAP/reference	0.95075	0.35
57DAP/reference	1.03709	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8448	0.299
27DAP/17DAP	1.03816	0.951
39DAP/27DAP	1.03288	0.799
41DAP/39DAP	1.25233	0.531
42DAP/41DAP	0.76554	0.034
43DAP/42DAP	0.92063	0.466
47DAP/43DAP	0.9891	0.954
52DAP/47DAP	0.82599	0.316
57DAP/52DAP	1.19764	0.563
57DAP/7DAP	0.9514	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05622	0.761
17DAP/reference	1.20035	0.025
27DAP/reference	1.31869	0.246
39DAP/reference	0.91522	0.307
41DAP/reference	1.10674	0.507
42DAP/reference	1.18261	0.889
43DAP/reference	1.12027	0.079
47DAP/reference	1.029	0.868
52DAP/reference	1.10089	0.428
57DAP/reference	1.07121	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00562	0.884
17DAP/reference	1.03669	0.839
27DAP/reference	0.98255	0.576
39DAP/reference	0.89578	0.144
41DAP/reference	1.07395	1
42DAP/reference	1.07921	0.634
43DAP/reference	0.85812	0.084
47DAP/reference	0.96677	0.459
52DAP/reference	1.10517	0.471
57DAP/reference	1.00318	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9725	0.489
17DAP/reference	1.01604	0.918
27DAP/reference	0.88549	0.243
39DAP/reference	0.77425	0.023
41DAP/reference	0.98643	0.682
42DAP/reference	0.83187	0.22
43DAP/reference	0.86703	0.188
47DAP/reference	0.89963	0.139
52DAP/reference	0.89584	0.415
57DAP/reference	1.46533	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09419	0.966
26DAP/20DAP	1.30782	0.259
34DAP/26DAP	2.99018	0.542
51DAP/34DAP	0.93902	0.674
52DAP/51DAP	1.23384	0.904
53DAP/52DAP	0.90416	0.772
55DAP/53DAP	1.06429	0.722
57DAP/55DAP	1.10098	0.961
62DAP/57DAP	3.20204
68DAP/62DAP	0.97034	0.863
68DAP/14DAP	0.87348	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.33409	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.21869	0.881
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.3157
Mature Eggplant/Ripe Tomato	0.25881

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	0.85989
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	1.25995	0.274
IL2-6/WTpooled	0.91705	1
IL7-5/WTpooled	1.09739	0.75
IL7-3/WTpooled	1.15476	1
IL12-4/WTpooled	0.7957	0.71
IL1-4/WTpooled	0.94062	0.834
WT/WTpooled	1.05244	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	1.0758	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15944	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.51979	1
DC3000/delta hrp 24h	1.69284	0.095

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.38673
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	0.74887	1
Exp 36h	1.15151	1
Exp 60h	0.8652	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07902	1
Var 0h	0.88318	0.933
Var 12h I row2-row1	1.17311	0.228
Var 12h NI row2-row1	1.76337	1
Var 36h I row2-row1	1.16202	0.742
Var 36h NI row2-row1	0.73921	0.549
Var 60h I row2-row1	0.83968	0.285
Var 60h NI row2-row1	1.11573	1
Time course 0hI-0hNI	1.20375	0.799
Time course 12hI-12hNI	1.21818	0.482
Time course 36hI-36hNI	1.91032	0.005
Time course 60hI-60hNI	2.21149	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)	1.17071	0.331
transgenic ySAMdc/azygous control (breaker)	0.60022	0.15
transgenic ySAMdc/azygous control (red)	0.7502	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94969	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82009	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63649	0.172
Manapal/WT (break)	1.09093	1
Manapal/WT (red)	0.843	0.607