Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20488	0.523
27DAP/17DAP	0.57421	0.04
39DAP/27DAP	0.99433	0.749
41DAP/39DAP	0.60455	0.055
42DAP/41DAP	0.96762	1
43DAP/42DAP	1.04661	1
47DAP/43DAP	0.72963	0.248
52DAP/47DAP	1.0186	0.959
57DAP/52DAP	1.11825	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72568	0.075
17DAP/reference	0.57088	0.026
27DAP/reference	0.60752	0.015
39DAP/reference	0.62741	0.031
41DAP/reference	0.37186	0.008
42DAP/reference	0.57482	0.001
43DAP/reference	0.42172	0.012
47DAP/reference	0.49501	0.001
52DAP/reference	0.7049	0.028
57DAP/reference	0.70921	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62542	0.055
27DAP/17DAP	0.76932	0.363
39DAP/27DAP	0.49039	0.032
41DAP/39DAP	1.0758	0.837
42DAP/41DAP	0.98035	0.781
43DAP/42DAP	0.76844	0.034
47DAP/43DAP	1.00267	0.973
52DAP/47DAP	1.06111	0.892
57DAP/52DAP	1.03417	0.874
57DAP/7DAP	0.54589	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03102	0.813
17DAP/reference	0.95353	0.253
27DAP/reference	0.86476	0.082
39DAP/reference	0.63553	0.011
41DAP/reference	0.62301	0.012
42DAP/reference	0.6118	0.01
43DAP/reference	0.57431	0.011
47DAP/reference	0.69781	0.101
52DAP/reference	0.5282	0.012
57DAP/reference	0.57556	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45327	0.005
17DAP/reference	0.44326	0.004
27DAP/reference	0.77955	0.167
39DAP/reference	0.73647	0.095
41DAP/reference	0.9932	0.615
42DAP/reference	0.86699	0.03
43DAP/reference	0.32097	0.002
47DAP/reference	0.62631	0.01
52DAP/reference	0.6673	0.005
57DAP/reference	0.33742	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64226	0.029
17DAP/reference	1.85858	0.191
27DAP/reference	1.65728	0.025
39DAP/reference	1.19074	0.1
41DAP/reference	0.96931	0.56
42DAP/reference	0.92737	0.445
43DAP/reference	0.86339	0.216
47DAP/reference	0.72401	0.057
52DAP/reference	0.58464	0.047
57DAP/reference	1.88166	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05904	1
26DAP/20DAP	1.16828	0.806
34DAP/26DAP	0.91682	0.816
51DAP/34DAP	0.52156	0.049
52DAP/51DAP	0.91857	0.151
53DAP/52DAP	0.89953	0.595
55DAP/53DAP	0.65865	0.023
57DAP/55DAP	0.7392	0.229
62DAP/57DAP	1.80667	0.133
68DAP/62DAP	9.89569	0.025
68DAP/14DAP	5.66762	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89258	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.5213	0.058
Mature Green Tomato/Ripe Tomato	2.53116	0.017
Immature Eggplant/Mature Eggplant	0.37506	0.062
Ripe Pepper/Ripe Tomato	39.9229	0.256
Mature Eggplant/Ripe Tomato	68.4361	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05257	1
1-1-2/M82	1.09819	1
12-2/M82	0.90782	0.955
12-4/M82	1.26996	1
1-3/M82	0.92073	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.9714	1
3-2/M82	N/A	N/A
4-1-1/M82	1.03246	1
4-1/M82	1.29511	1
4-3-2/M82	1.00569	1
4-3/M82	N/A	N/A
5-3/M82	1.00012	1
6-2/M82	0.75244
6-3/M82	1.24906
7-1/M82	0.88409
7-2/M82	1.0006	1
9-3-2/M82	1.00813	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05347	1
IL2-6/WTpooled	1.06192	0.456
IL7-5/WTpooled	0.74836
IL7-3/WTpooled	1.15963	1
IL12-4/WTpooled	0.85968	0.543
IL1-4/WTpooled	1.06437	1
WT/WTpooled	0.92568	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	1.05652	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93209	0.664
DC3000/delta hrp 6h	0.82502	0.95
DC3000/delta hrp 12h	0.99487	1
DC3000/delta hrp 24h	0.9447	0.354

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61619
DC3000 delta B/DC3000 delta AB	0.44946	0.022

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	0.97075	1
Var 0h	1.27313	0.98
Var 12h I row2-row1	0.95457	0.77
Var 12h NI row2-row1	0.96961	0.906
Var 36h I row2-row1	1.00668	1
Var 36h NI row2-row1	1.01528	1
Var 60h I row2-row1	1.26763	0.562
Var 60h NI row2-row1	1.05351	0.904
Time course 0hI-0hNI	0.98971	1
Time course 12hI-12hNI	1.02499	0.788
Time course 36hI-36hNI	1.00058	0.857
Time course 60hI-60hNI	0.50296	0.015

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)	1.01058	0.931
transgenic ySAMdc/azygous control (breaker)	5.11093	0.162
transgenic ySAMdc/azygous control (red)	1.22022	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.59496	0.081

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35225	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	46.7296	0.088
Manapal/WT (break)	16.2178	0.123
Manapal/WT (red)	2.85449	1