Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87294	0.324
27DAP/17DAP	1.09913	0.881
39DAP/27DAP	2.73692	0.038
41DAP/39DAP	0.76407	0.229
42DAP/41DAP	1.04023	1
43DAP/42DAP	1.1239	1
47DAP/43DAP	0.86927	0.58
52DAP/47DAP	1.08538	0.989
57DAP/52DAP	1.17215	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08054	0.48
17DAP/reference	1.00971	0.813
27DAP/reference	1.02238	0.847
39DAP/reference	0.98189	0.68
41DAP/reference	0.99548	0.814
42DAP/reference	0.91178	0.041
43DAP/reference	0.97117	0.631
47DAP/reference	1.07844	0.136
52DAP/reference	0.94551	0.35
57DAP/reference	1.20509	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00525	0.801
27DAP/17DAP	1.51946	0.092
39DAP/27DAP	1.02923	0.977
41DAP/39DAP	1.53384	0.934
42DAP/41DAP	1.78532	0.263
43DAP/42DAP	0.92179	0.503
47DAP/43DAP	0.98353	0.928
52DAP/47DAP	0.89955	0.528
57DAP/52DAP	0.95102	0.668
57DAP/7DAP	0.82697

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9277	0.27
17DAP/reference	0.88973	0.013
27DAP/reference	0.95125	0.117
39DAP/reference	0.83957	0.011
41DAP/reference	0.85622	0.019
42DAP/reference	0.86361	0.01
43DAP/reference	0.78998	0.009
47DAP/reference	1.00686	1
52DAP/reference	0.79021	0.012
57DAP/reference	0.79347	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93753	0.386
17DAP/reference	0.9897	0.673
27DAP/reference	0.9481	0.423
39DAP/reference	0.95413	0.195
41DAP/reference	0.95385	0.242
42DAP/reference	0.96214	0.212
43DAP/reference	0.96167	0.459
47DAP/reference	1.0023	1
52DAP/reference	0.9486	0.143
57DAP/reference	0.93823	0.278

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87804	0.028
17DAP/reference	0.9497	0.328
27DAP/reference	0.84289	0.037
39DAP/reference	0.84087	0.014
41DAP/reference	0.90526	0.132
42DAP/reference	0.93157	0.108
43DAP/reference	0.89605	0.071
47DAP/reference	1.02991	0.847
52DAP/reference	0.94291	0.529
57DAP/reference	1.33897	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03958	0.966
26DAP/20DAP	1.66973	0.153
34DAP/26DAP	0.90741	0.735
51DAP/34DAP	3.07979	0.029
52DAP/51DAP	0.91925	1
53DAP/52DAP	1.77081
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.97514	0.819
62DAP/57DAP	0.96942	0.994
68DAP/62DAP	0.9379	0.81
68DAP/14DAP	0.95097	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32916	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.10245	0.287
Mature Green Tomato/Ripe Tomato	0.9519	0.132
Immature Eggplant/Mature Eggplant	0.85316	0.069
Ripe Pepper/Ripe Tomato	0.71506	0.293
Mature Eggplant/Ripe Tomato	0.98776	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09619	0.536
1-1-2/M82	1.08002	1
12-2/M82	0.92638	0.955
12-4/M82	1.04805	1
1-3/M82	1.04706
2-1-1/M82	0.89244	0.565
2-1/M82	0.87515	1
2-6/M82	1.00736	1
3-2/M82	1.08004	0.717
4-1-1/M82	1.105	1
4-1/M82	1.40278	0.853
4-3-2/M82	1.05938	1
4-3/M82	1.08012	0.268
5-3/M82	1.04067	1
6-2/M82	1.06658	1
6-3/M82	1.04362	1
7-1/M82	0.91859	1
7-2/M82	0.98644	1
9-3-2/M82	1.15551	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8946	0.247
IL2-6/WTpooled	1.01884	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80362	0.294
IL12-4/WTpooled	1.05942	0.891
IL1-4/WTpooled	1.05823	1
WT/WTpooled	1.17065	0.686

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	1.16205	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01491	1
DC3000/delta hrp 6h	1.03998	1
DC3000/delta hrp 12h	1.04601	1
DC3000/delta hrp 24h	0.95263	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21395	0.183
DC3000 delta B/DC3000 delta AB	1.33544	0.101

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91895	1
Exp 36h	0.97001	0.943
Exp 60h	1.07887	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99661	1
Var 0h	0.43923	0.291
Var 12h I row2-row1	1.06569	0.795
Var 12h NI row2-row1	1.00949	1
Var 36h I row2-row1	1.12375	0.742
Var 36h NI row2-row1	0.93699	0.645
Var 60h I row2-row1	0.6228	0.285
Var 60h NI row2-row1	1.13121	0.904
Time course 0hI-0hNI	1.05992	0.764
Time course 12hI-12hNI	1.18778	0.265
Time course 36hI-36hNI	1.38051	0.009
Time course 60hI-60hNI	2.76197	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)	0.87946	0.32
transgenic ySAMdc/azygous control (breaker)	0.98616	1
transgenic ySAMdc/azygous control (red)	1.01968	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03193	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95844	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79092	0.172
Manapal/WT (break)	0.91516	1
Manapal/WT (red)	0.8665	0.229