Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.8.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08107	0.964
27DAP/17DAP	0.90533	0.796
39DAP/27DAP	1.20192	0.708
41DAP/39DAP	1.3113	0.334
42DAP/41DAP	1.13873	0.962
43DAP/42DAP	1.05548	0.945
47DAP/43DAP	1.0452	0.966
52DAP/47DAP	0.97616	0.812
57DAP/52DAP	1.0062	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89482	0.087
17DAP/reference	1.00586	0.843
27DAP/reference	0.93389	0.187
39DAP/reference	0.96405	0.475
41DAP/reference	0.93247	0.341
42DAP/reference	0.85243	0.006
43DAP/reference	1.09488	0.175
47DAP/reference	0.88666	0.065
52DAP/reference	0.77587	0.037
57DAP/reference	0.76392	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98395	0.75
27DAP/17DAP	1.10816	0.598
39DAP/27DAP	1.05539	0.728
41DAP/39DAP	1.06033	0.827
42DAP/41DAP	1.00654	0.939
43DAP/42DAP	1.05882	0.446
47DAP/43DAP	1.05911	0.749
52DAP/47DAP	1.1127	0.676
57DAP/52DAP	1.03038	0.846
57DAP/7DAP	1.25829	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84864	0.157
17DAP/reference	0.87515	0.056
27DAP/reference	0.90994	0.055
39DAP/reference	0.82238	0.011
41DAP/reference	0.75391	0.023
42DAP/reference	0.68118	0.01
43DAP/reference	0.81218	0.031
47DAP/reference	0.86485	0.168
52DAP/reference	0.73199	0.038
57DAP/reference	0.85914	0.038

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04179	0.66
17DAP/reference	1.06559	0.415
27DAP/reference	0.81845	0.079
39DAP/reference	0.83759	0.14
41DAP/reference	0.82334	0.05
42DAP/reference	0.84106	0.055
43DAP/reference	1.13284	0.263
47DAP/reference	0.93287	0.246
52DAP/reference	1.0002	0.713
57DAP/reference	1.10741	0.398

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88911	0.068
17DAP/reference	0.98116	0.681
27DAP/reference	0.90368	0.165
39DAP/reference	0.80365	0.01
41DAP/reference	0.85944	0.026
42DAP/reference	0.89453	0.22
43DAP/reference	0.81515	0.048
47DAP/reference	0.94466	0.396
52DAP/reference	0.86371	0.167
57DAP/reference	0.52405	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96803	1
26DAP/20DAP	0.89431	0.512
34DAP/26DAP	1.07003	1
51DAP/34DAP	0.96728	0.743
52DAP/51DAP	1.0542	0.676
53DAP/52DAP	1.12736	0.738
55DAP/53DAP	1.01731	0.917
57DAP/55DAP	1.1237	0.818
62DAP/57DAP	1.25662	0.257
68DAP/62DAP	0.97416	0.834
68DAP/14DAP	0.9428	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88311	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.56545	0.042
Immature Eggplant/Mature Eggplant	1.59768
Ripe Pepper/Ripe Tomato	0.93404	1
Mature Eggplant/Ripe Tomato	1.30167	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0063	1
1-1-2/M82	0.77576	1
12-2/M82	1.05552	1
12-4/M82	1.00072	1
1-3/M82	0.90036	0.378
2-1-1/M82	0.93193	0.784
2-1/M82	0.95885
2-6/M82	1.10745	0.695
3-2/M82	1.0183	1
4-1-1/M82	1.02414	1
4-1/M82	1.08139	1
4-3-2/M82	0.81451	0.698
4-3/M82	0.91408
5-3/M82	0.91832	0.49
6-2/M82	0.91639	1
6-3/M82	0.94159	0.796
7-1/M82	0.88982
7-2/M82	0.90084	0.881
9-3-2/M82	0.80717	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02978	1
IL2-6/WTpooled	1.10133	0.441
IL7-5/WTpooled	1.78605
IL7-3/WTpooled	0.99566	1
IL12-4/WTpooled	1.00688	1
IL1-4/WTpooled	1.11216	1
WT/WTpooled	0.8989	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	0.94685	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03764	0.921
DC3000/delta hrp 6h	1.3872	0.978
DC3000/delta hrp 12h	1.41797	1
DC3000/delta hrp 24h	1.0487	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91267	0.538
DC3000 delta B/DC3000 delta AB	1.0398	0.601

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.24676	0.693
Exp 60h	1.1624	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.74697	1
Var 0h	0.96429	1
Var 12h I row2-row1	1.05868	0.654
Var 12h NI row2-row1	0.8907	0.494
Var 36h I row2-row1	0.82841	1
Var 36h NI row2-row1	0.84393	0.549
Var 60h I row2-row1	1.15317	0.562
Var 60h NI row2-row1	1.2286	0.904
Time course 0hI-0hNI	1.04611	0.799
Time course 12hI-12hNI	1.01112	0.892
Time course 36hI-36hNI	0.93922	0.269
Time course 60hI-60hNI	1.144	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)	0.95429	0.409
transgenic ySAMdc/azygous control (breaker)	1.12794	1
transgenic ySAMdc/azygous control (red)	0.85883	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03211	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81088	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06759	1
Manapal/WT (break)	0.90602	1
Manapal/WT (red)	0.81204	0.181