Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.3.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23642	0.838
27DAP/17DAP	0.89978	0.822
39DAP/27DAP	1.03731	0.84
41DAP/39DAP	1.56563	0.516
42DAP/41DAP	1.8218	0.632
43DAP/42DAP	2.06369	0.14
47DAP/43DAP	0.79712	0.41
52DAP/47DAP	1.38122	0.521
57DAP/52DAP	0.7406	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16589	0.038
17DAP/reference	1.06253	0.1
27DAP/reference	1.06005	0.446
39DAP/reference	1.04706	0.654
41DAP/reference	1.21591	0.067
42DAP/reference	1.2111	0.006
43DAP/reference	0.97109	0.576
47DAP/reference	1.09081	0.069
52DAP/reference	1.1115	0.195
57DAP/reference	1.10015	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86488	0.27
27DAP/17DAP	1.27294	0.506
39DAP/27DAP	1.26592	0.296
41DAP/39DAP	1.40052	0.393
42DAP/41DAP	0.77506	0.116
43DAP/42DAP	1.23616	0.112
47DAP/43DAP	1.0723	0.906
52DAP/47DAP	0.97064	0.899
57DAP/52DAP	0.88322	0.43
57DAP/7DAP	0.82224	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65825	0.072
17DAP/reference	0.68254	0.014
27DAP/reference	0.82236	0.011
39DAP/reference	0.73909	0.014
41DAP/reference	0.72667	0.017
42DAP/reference	0.96892	0.458
43DAP/reference	0.78134	0.021
47DAP/reference	1.00352	1
52DAP/reference	0.61968	0.012
57DAP/reference	0.87839	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13337	0.501
17DAP/reference	1.23375	0.092
27DAP/reference	1.0989	0.244
39DAP/reference	1.17607	0.068
41DAP/reference	1.07491	0.799
42DAP/reference	1.00939	1
43DAP/reference	1.24243	0.072
47DAP/reference	0.99069	0.643
52DAP/reference	1.24244	0.006
57DAP/reference	1.18535	0.038

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70661	0.065
17DAP/reference	0.79443	0.189
27DAP/reference	0.63663	0.044
39DAP/reference	0.78769	0.069
41DAP/reference	0.75683	0.028
42DAP/reference	0.95276	0.552
43DAP/reference	0.93588	0.416
47DAP/reference	1.04455	0.792
52DAP/reference	0.8963	0.433
57DAP/reference	0.9213	0.359

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88196	0.193
26DAP/20DAP	0.87695	0.317
34DAP/26DAP	1.11904	0.19
51DAP/34DAP	0.88178	0.537
52DAP/51DAP	1.22493	0.704
53DAP/52DAP	0.89137	0.14
55DAP/53DAP	0.97607	0.796
57DAP/55DAP	1.16579	0.881
62DAP/57DAP	0.73414	0.466
68DAP/62DAP	0.83458	0.7
68DAP/14DAP	0.87439	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.62667	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95213	0.745
Mature Green Tomato/Ripe Tomato	0.14375	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.27368	1
Mature Eggplant/Ripe Tomato	0.42071	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.60891	0.526
1-1-2/M82	0.28582	N/A
12-2/M82	N/A	N/A
12-4/M82	0.99383	N/A
1-3/M82	1.00252	1
2-1-1/M82	1.30531	N/A
2-1/M82	N/A	N/A
2-6/M82	0.99613	1
3-2/M82	N/A	N/A
4-1-1/M82	0.85077	1
4-1/M82	1.11597	N/A
4-3-2/M82	1.07477	N/A
4-3/M82	N/A	N/A
5-3/M82	1.39954	1
6-2/M82	0.83787	N/A
6-3/M82	0.90111	1
7-1/M82	N/A	N/A
7-2/M82	0.84775	0.553
9-3-2/M82	1.36398	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92287	1
IL2-6/WTpooled	1.14453	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96678	1
IL12-4/WTpooled	0.78871	0.581
IL1-4/WTpooled	0.89091	0.562
WT/WTpooled	0.87555	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	4.25482	0.177

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08584	0.618
DC3000/delta hrp 6h	1.15051	0.95
DC3000/delta hrp 12h	1.09449	1
DC3000/delta hrp 24h	1.03573	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.97359	N/A
DC3000 delta B/DC3000 delta AB	0.67071	0.347

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01543	1
Exp 36h	1.45124	0.489
Exp 60h	1.02445	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95129	1
Var 0h	72.3577	0.936
Var 12h I row2-row1	0.93815	0.77
Var 12h NI row2-row1	0.91739	0.82
Var 36h I row2-row1	1.34694	0.601
Var 36h NI row2-row1	0.73589	0.522
Var 60h I row2-row1	1.00897	1
Var 60h NI row2-row1	1.1281	1
Time course 0hI-0hNI	1.10238	0.833
Time course 12hI-12hNI	1.22396	0.066
Time course 36hI-36hNI	2.49987	0.005
Time course 60hI-60hNI	5.46029	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)	1.03227	0.699
transgenic ySAMdc/azygous control (breaker)	1.80861	0.165
transgenic ySAMdc/azygous control (red)	1.07134	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90752	0.042

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02734	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83279	1
Manapal/WT (break)	1.11091	1
Manapal/WT (red)	1.17296	1