Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.12.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9742	0.689
27DAP/17DAP	1.01301	1
39DAP/27DAP	1.54367	0.092
41DAP/39DAP	0.7477	0.205
42DAP/41DAP	1.15943	0.929
43DAP/42DAP	1.13302	0.906
47DAP/43DAP	0.97072	0.868
52DAP/47DAP	0.91136	0.734
57DAP/52DAP	1.14441	0.77

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19107	0.265
17DAP/reference	1.29639	0.047
27DAP/reference	1.07812	0.637
39DAP/reference	1.35844	0.031
41DAP/reference	1.35918	0.093
42DAP/reference	1.76421	0.001
43DAP/reference	1.13752	0.678
47DAP/reference	0.99937	0.602
52DAP/reference	1.16691	0.158
57DAP/reference	0.90541	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95475	0.595
27DAP/17DAP	0.94677	0.748
39DAP/27DAP	0.88667	0.106
41DAP/39DAP	1.23962	0.663
42DAP/41DAP	0.94667	0.584
43DAP/42DAP	0.88093	0.065
47DAP/43DAP	1.19257	0.175
52DAP/47DAP	1.20373	0.424
57DAP/52DAP	1.58493	0.029
57DAP/7DAP	1.37399	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17357	0.461
17DAP/reference	1.10569	0.102
27DAP/reference	1.12935	0.197
39DAP/reference	1.10381	0.101
41DAP/reference	1.052	0.767
42DAP/reference	0.99317	0.641
43DAP/reference	0.88526	0.145
47DAP/reference	0.98721	0.671
52DAP/reference	1.07878	0.247
57DAP/reference	1.16632	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89604	0.374
17DAP/reference	1.06404	0.999
27DAP/reference	1.30799	0.283
39DAP/reference	0.98711	0.621
41DAP/reference	1.24965	0.149
42DAP/reference	0.92315	0.289
43DAP/reference	1.21175	0.135
47DAP/reference	1.20265	0.015
52DAP/reference	0.7112	0.025
57DAP/reference	1.05542	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08089	0.575
17DAP/reference	1.20051	0.627
27DAP/reference	0.95834	0.49
39DAP/reference	1.02078	0.711
41DAP/reference	0.89655	0.237
42DAP/reference	0.92836	0.445
43DAP/reference	0.89066	0.319
47DAP/reference	1.20049	0.877
52DAP/reference	1.38321	0.233
57DAP/reference	1.12999	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03877	0.966
26DAP/20DAP	0.98193	1
34DAP/26DAP	0.79848	0.15
51DAP/34DAP	1.12693	0.627
52DAP/51DAP	0.9043	1
53DAP/52DAP	0.98767	0.929
55DAP/53DAP	1.0091	0.939
57DAP/55DAP	1.12715	0.935
62DAP/57DAP	1.122	0.868
68DAP/62DAP	1.11831	0.944
68DAP/14DAP	1.13573

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2756	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.15	0.166
Immature Eggplant/Mature Eggplant	0.54137
Ripe Pepper/Ripe Tomato	1.20587
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.29398
12-2/M82	N/A	N/A
12-4/M82	1.18994
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	0.95449	1
4-1-1/M82	N/A	N/A
4-1/M82	2.02821
4-3-2/M82	1.28588
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	1.22876	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.3674	0.441
IL7-5/WTpooled	0.76711
IL7-3/WTpooled	0.90077	0.294
IL12-4/WTpooled	0.91319	1
IL1-4/WTpooled	0.97214	1
WT/WTpooled	0.93435	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	0.94489	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.48915	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.65848
DC3000/delta hrp 24h	0.58499	0.379

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53898	0.16
DC3000 delta B/DC3000 delta AB	1.29896	0.142

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	0.5884	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00559	1
Var 0h	1.05968	1
Var 12h I row2-row1	1.03644	1
Var 12h NI row2-row1	1.12787	1
Var 36h I row2-row1	0.86695	1
Var 36h NI row2-row1	1.05804	1
Var 60h I row2-row1	0.80197	0.285
Var 60h NI row2-row1	0.91013	0.63
Time course 0hI-0hNI	1.02332	0.852
Time course 12hI-12hNI	0.9746	0.836
Time course 36hI-36hNI	1.04794	0.651
Time course 60hI-60hNI	1.81918	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)	1.30139	0.431
transgenic ySAMdc/azygous control (breaker)	0.40106	0.139
transgenic ySAMdc/azygous control (red)	1.16696	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84943	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59672	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.51724	1
Manapal/WT (break)	0.54917	0.333
Manapal/WT (red)	1.30201	0.413