Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25027	0.452
27DAP/17DAP	0.48755	0.027
39DAP/27DAP	0.51175	0.241
41DAP/39DAP	1.02986	0.894
42DAP/41DAP	0.63725	0.397
43DAP/42DAP	1.27831	0.44
47DAP/43DAP	0.78774	0.382
52DAP/47DAP	1.11785	0.991
57DAP/52DAP	1.09051	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96522	0.432
17DAP/reference	0.54479	0.012
27DAP/reference	0.60968	0.029
39DAP/reference	0.48624	0.013
41DAP/reference	0.37348	0.009
42DAP/reference	0.68086	0.002
43DAP/reference	0.52509	0.015
47DAP/reference	0.44983	0.001
52DAP/reference	0.40244	0.014
57DAP/reference	0.58956	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44976	0.158
27DAP/17DAP	0.80564	0.363
39DAP/27DAP	0.59961	0.033
41DAP/39DAP	1.5815	0.735
42DAP/41DAP	0.97603	0.734
43DAP/42DAP	0.79658	0.07
47DAP/43DAP	0.86393	0.08
52DAP/47DAP	0.96094	0.868
57DAP/52DAP	0.6728	0.049
57DAP/7DAP	0.39563	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97196	0.495
17DAP/reference	0.81115	0.039
27DAP/reference	0.84049	0.051
39DAP/reference	0.85786	0.095
41DAP/reference	0.7141	0.023
42DAP/reference	0.81308	0.016
43DAP/reference	0.83241	0.027
47DAP/reference	0.57373	0.026
52DAP/reference	0.79413	0.04
57DAP/reference	0.91534	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51492	0.016
17DAP/reference	0.60983	0.033
27DAP/reference	0.6649	0.044
39DAP/reference	0.63477	0.062
41DAP/reference	0.56669	0.005
42DAP/reference	0.60377	0.012
43DAP/reference	0.48191	0.027
47DAP/reference	0.4894	0.007
52DAP/reference	0.4046	0.007
57DAP/reference	0.23802	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94722	0.422
17DAP/reference	0.92333	0.426
27DAP/reference	0.76351	0.037
39DAP/reference	0.7393	0.015
41DAP/reference	0.90147	0.119
42DAP/reference	0.74401	0.041
43DAP/reference	0.7668	0.106
47DAP/reference	0.54044	0.006
52DAP/reference	0.54787	0.053
57DAP/reference	0.94718	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35108	0.945
26DAP/20DAP	0.96966	1
34DAP/26DAP	0.95825	0.834
51DAP/34DAP	0.53197	0.059
52DAP/51DAP	1.06255	0.742
53DAP/52DAP	0.7248	0.128
55DAP/53DAP	1.21984	0.782
57DAP/55DAP	0.74881	0.281
62DAP/57DAP	0.75865
68DAP/62DAP	0.95567	0.834
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.97499	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.58429	0.058
Mature Green Tomato/Ripe Tomato	6.54615	0.015
Immature Eggplant/Mature Eggplant	0.95851	0.651
Ripe Pepper/Ripe Tomato	1.88203	0.256
Mature Eggplant/Ripe Tomato	12.2888	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.86353
12-2/M82	0.34766	0.955
12-4/M82	0.77112	0.358
1-3/M82	0.62643
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.87865
3-2/M82	1.16967
4-1-1/M82	N/A	N/A
4-1/M82	0.77383
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.17697	1
6-2/M82	N/A	N/A
6-3/M82	0.77661
7-1/M82	1.25109
7-2/M82	0.94133
9-3-2/M82	1.23851

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96218
IL2-6/WTpooled	1.48743	0.584
IL7-5/WTpooled	3.2848
IL7-3/WTpooled	0.98899	1
IL12-4/WTpooled	1.04051	1
IL1-4/WTpooled	0.95058	1
WT/WTpooled	1.11569	0.874

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	1.00139	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97184	1
DC3000/delta hrp 6h	0.90625	0.95
DC3000/delta hrp 12h	0.89126	1
DC3000/delta hrp 24h	0.79833	0.257

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15079	0.16
DC3000 delta B/DC3000 delta AB	0.86271	0.431

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10138	0.254
Exp 36h	1.07911	1
Exp 60h	1.00466	1

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	0.92973	1
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)	0.97248	0.789
transgenic ySAMdc/azygous control (breaker)	1.14191	1
transgenic ySAMdc/azygous control (red)	1.0042	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.82144	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33665	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.7751	0.084
Manapal/WT (break)	2.58497	0.123
Manapal/WT (red)	1.46784	1