Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73004	0.11
27DAP/17DAP	0.85312	0.686
39DAP/27DAP	0.9098	0.573
41DAP/39DAP	1.19555	0.168
42DAP/41DAP	1.08771	0.941
43DAP/42DAP	1.09961	1
47DAP/43DAP	1.18674	0.809
52DAP/47DAP	0.9838	0.886
57DAP/52DAP	1.20614	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92732	0.317
17DAP/reference	1.07346	0.185
27DAP/reference	1.01165	0.831
39DAP/reference	0.99431	0.921
41DAP/reference	1.03479	0.48
42DAP/reference	0.87522	0.095
43DAP/reference	1.07385	0.471
47DAP/reference	0.90417	0.148
52DAP/reference	1.05865	0.8
57DAP/reference	1.06769	0.6

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98157	0.763
27DAP/17DAP	0.79222	0.172
39DAP/27DAP	0.79757	0.529
41DAP/39DAP	1.13549	0.868
42DAP/41DAP	1.09328	1
43DAP/42DAP	1.0398	1
47DAP/43DAP	1.08935	0.941
52DAP/47DAP	1.43513	0.286
57DAP/52DAP	0.90726	0.566
57DAP/7DAP	1.17619	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04322	0.98
17DAP/reference	1.11716	0.199
27DAP/reference	0.99253	0.614
39DAP/reference	1.05014	1
41DAP/reference	1.22072	0.303
42DAP/reference	1.17296	0.889
43DAP/reference	1.1832	0.289
47DAP/reference	0.89634	0.383
52DAP/reference	1.05179	0.781
57DAP/reference	0.97896	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87897	0.115
17DAP/reference	0.73926	0.005
27DAP/reference	0.82077	0.031
39DAP/reference	0.95838	0.339
41DAP/reference	0.96238	0.348
42DAP/reference	0.86139	0.022
43DAP/reference	0.94778	0.423
47DAP/reference	0.945	0.178
52DAP/reference	0.93126	0.171
57DAP/reference	0.8041	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05266	0.75
17DAP/reference	1.02114	1
27DAP/reference	1.29696	0.025
39DAP/reference	1.0094	0.889
41DAP/reference	1.11964	0.657
42DAP/reference	0.76212	0.108
43DAP/reference	0.94927	0.468
47DAP/reference	0.98394	0.558
52DAP/reference	1.03673	0.705
57DAP/reference	1.23044	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13461	0.945
26DAP/20DAP	1.66832
34DAP/26DAP	2.48641	1
51DAP/34DAP	N/A	N/A
52DAP/51DAP	0.40607
53DAP/52DAP	0.61466
55DAP/53DAP	0.60371	0.125
57DAP/55DAP	0.59037	0.19
62DAP/57DAP	1.19863	0.868
68DAP/62DAP	1.6271	0.31
68DAP/14DAP	1.36216	0.108

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18813	0.347

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	1.27113

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90315	0.944
1-1-2/M82	1.28237
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	0.96016	1
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	0.85312	0.642
6-2/M82	N/A	N/A
6-3/M82	1.11203
7-1/M82	N/A	N/A
7-2/M82	1.13832	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74131	0.247
IL2-6/WTpooled	1.04986	0.584
IL7-5/WTpooled	0.78704	1
IL7-3/WTpooled	0.95545	1
IL12-4/WTpooled	1.01959	1
IL1-4/WTpooled	0.83376	0.562
WT/WTpooled	0.97611	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	1.40398	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08332	0.875
DC3000/delta hrp 6h	1.40441	0.672
DC3000/delta hrp 12h	1.02626	1
DC3000/delta hrp 24h	1.06219	0.467

Experiment: DC3000 effector mutants

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

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96967	1
Exp 36h	N/A	N/A
Exp 60h	1.16826	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97159	1
Var 0h	0.97811
Var 12h I row2-row1	0.97302
Var 12h NI row2-row1	0.87898
Var 36h I row2-row1	1.62052	0.601
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	1.01055
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.90066	0.485
Time course 12hI-12hNI	1.06681	1
Time course 36hI-36hNI	1.70104	0.005
Time course 60hI-60hNI	1.86774	0.06

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)	1.02789	0.541
transgenic ySAMdc/azygous control (breaker)	2.26343	0.161
transgenic ySAMdc/azygous control (red)	1.28894	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98634	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87247	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96881	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.09824	0.164