Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2534	0.359
27DAP/17DAP	1.16577	0.849
39DAP/27DAP	1.69589	0.236
41DAP/39DAP	0.85208	0.563
42DAP/41DAP	1.02075	1
43DAP/42DAP	2.22729	0.159
47DAP/43DAP	1.04452	0.856
52DAP/47DAP	1.62501	0.729
57DAP/52DAP	0.85117	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27053	0.384
17DAP/reference	1.02187	0.904
27DAP/reference	0.75507	0.232
39DAP/reference	0.89081	0.487
41DAP/reference	0.87634	0.542
42DAP/reference	1.07061	0.995
43DAP/reference	1.01772	0.942
47DAP/reference	0.99617	0.568
52DAP/reference	0.91974	0.319
57DAP/reference	1.15909	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18183	0.305
27DAP/17DAP	1.19485	0.617
39DAP/27DAP	0.83061	0.356
41DAP/39DAP	0.99432	0.959
42DAP/41DAP	1.21012	0.526
43DAP/42DAP	1.06555	0.585
47DAP/43DAP	1.1019	0.906
52DAP/47DAP	0.84138	0.553
57DAP/52DAP	1.46853	0.047
57DAP/7DAP	0.79796	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80324	0.402
17DAP/reference	0.7029	0.044
27DAP/reference	0.85277	0.117
39DAP/reference	0.83848	0.126
41DAP/reference	1.18735	0.577
42DAP/reference	0.96779	0.458
43DAP/reference	0.99293	0.637
47DAP/reference	1.11644	1
52DAP/reference	0.95198	0.304
57DAP/reference	1.00283	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67569	0.14
17DAP/reference	1.0547	0.873
27DAP/reference	1.0207	0.79
39DAP/reference	0.85588	0.208
41DAP/reference	0.96163	0.403
42DAP/reference	1.03651	1
43DAP/reference	1.0876	0.417
47DAP/reference	0.98775	0.59
52DAP/reference	1.02758	0.666
57DAP/reference	1.01082	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73831	0.077
17DAP/reference	1.10198	0.966
27DAP/reference	N/A	N/A
39DAP/reference	1.12025	0.189
41DAP/reference	0.923	0.417
42DAP/reference	1.06641	0.863
43DAP/reference	0.99482	0.796
47DAP/reference	1.38781	0.63
52DAP/reference	1.04107	0.928
57DAP/reference	1.24699	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01211	1
26DAP/20DAP	0.78281	0.512
34DAP/26DAP	0.66811	0.329
51DAP/34DAP	0.80304	0.298
52DAP/51DAP	1.41091	0.534
53DAP/52DAP	1.10174	1
55DAP/53DAP	1.24595	0.301
57DAP/55DAP	1.23616	0.249
62DAP/57DAP	0.93467	0.871
68DAP/62DAP	1.1128	1
68DAP/14DAP	2.54285

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14575	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.17101

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	N/A	N/A
IL2-6/WTpooled	0.95804	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83259	0.418
IL12-4/WTpooled	0.93385	1
IL1-4/WTpooled	0.84592	0.457
WT/WTpooled	1.11778	0.957

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	0.89985	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.25263	0.758
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.34674	1
DC3000/delta hrp 24h	1.1622	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63505	0.023
DC3000 delta B/DC3000 delta AB	0.63388	0.021

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	1.00962	1
Var 0h	0.96335	1
Var 12h I row2-row1	0.82551	0.338
Var 12h NI row2-row1	1.03751	0.649
Var 36h I row2-row1	0.82338	1
Var 36h NI row2-row1	1.91548	1
Var 60h I row2-row1	0.99829	1
Var 60h NI row2-row1	0.95964	1
Time course 0hI-0hNI	1.05736	0.852
Time course 12hI-12hNI	0.97538	0.864
Time course 36hI-36hNI	0.95827	0.411
Time course 60hI-60hNI	0.48749	0.006

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.41427	0.063

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.55877	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A