Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42799	0.264
27DAP/17DAP	0.99826	0.994
39DAP/27DAP	1.18414	0.663
41DAP/39DAP	0.76839	0.169
42DAP/41DAP	1.29647	0.691
43DAP/42DAP	0.97702	0.914
47DAP/43DAP	1.23554	0.459
52DAP/47DAP	1.041	0.916
57DAP/52DAP	1.02133	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94787	0.55
17DAP/reference	0.96519	0.597
27DAP/reference	1.09518	0.055
39DAP/reference	1.07061	0.106
41DAP/reference	0.9733	0.542
42DAP/reference	0.92128	0.03
43DAP/reference	0.9781	0.745
47DAP/reference	1.07382	0.11
52DAP/reference	0.93079	0.382
57DAP/reference	1.12841	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04204	0.708
27DAP/17DAP	0.97935	0.748
39DAP/27DAP	1.02258	0.691
41DAP/39DAP	0.96309	0.893
42DAP/41DAP	0.99315	0.882
43DAP/42DAP	0.96739	0.558
47DAP/43DAP	0.9839	0.902
52DAP/47DAP	1.03111	0.883
57DAP/52DAP	1.05271	0.659
57DAP/7DAP	1.07612	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93385	0.296
17DAP/reference	0.97799	0.447
27DAP/reference	1.16422	0.049
39DAP/reference	1.71661	0.005
41DAP/reference	0.93521	0.122
42DAP/reference	1.3383	0.008
43DAP/reference	1.16893	0.027
47DAP/reference	1.20797	0.254
52DAP/reference	1.10757	0.563
57DAP/reference	1.00308	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89867	0.062
17DAP/reference	0.90258	0.041
27DAP/reference	0.87727	0.188
39DAP/reference	0.99146	0.586
41DAP/reference	0.91652	0.16
42DAP/reference	0.89793	0.289
43DAP/reference	0.82854	0.087
47DAP/reference	0.94075	0.085
52DAP/reference	0.92036	0.006
57DAP/reference	0.8935	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83982	0.104
17DAP/reference	0.86351	0.072
27DAP/reference	0.99369	0.763
39DAP/reference	1.3162	0.057
41DAP/reference	1.25678	0.12
42DAP/reference	1.16796	0.233
43DAP/reference	0.95871	0.523
47DAP/reference	0.99913	0.731
52DAP/reference	1.12808	0.631
57DAP/reference	1.7164	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07339	0.966
26DAP/20DAP	1.00956	1
34DAP/26DAP	1.05749	0.819
51DAP/34DAP	0.94487	0.532
52DAP/51DAP	0.99992	1
53DAP/52DAP	1.17513	0.1
55DAP/53DAP	0.93228	0.796
57DAP/55DAP	0.93508	0.804
62DAP/57DAP	1.02453	0.902
68DAP/62DAP	1.04631	0.872
68DAP/14DAP	1.27545	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0482	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80851	0.261
Mature Green Tomato/Ripe Tomato	0.91378	0.446
Immature Eggplant/Mature Eggplant	1.8386	0.05
Ripe Pepper/Ripe Tomato	0.66553	0.224
Mature Eggplant/Ripe Tomato	0.5264	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92242	0.907
1-1-2/M82	1.02615	1
12-2/M82	0.93452	0.955
12-4/M82	1.03386	1
1-3/M82	1.09468	0.479
2-1-1/M82	0.75133	0.465
2-1/M82	0.99347	1
2-6/M82	0.94734	1
3-2/M82	0.99934	1
4-1-1/M82	1.01373	1
4-1/M82	1.57536	0.853
4-3-2/M82	1.30876	0.241
4-3/M82	0.96307	1
5-3/M82	0.96619	1
6-2/M82	1.02133	1
6-3/M82	0.97693	1
7-1/M82	1.04384
7-2/M82	0.91777	0.881
9-3-2/M82	1.44647	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.36245
IL2-6/WTpooled	1.33963
IL7-5/WTpooled	2.24628	0.792
IL7-3/WTpooled	1.3985
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.83151	0.834
WT/WTpooled	1.02539	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	1.0048	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10628	0.671
DC3000/delta hrp 6h	1.13871	1
DC3000/delta hrp 12h	1.00158	1
DC3000/delta hrp 24h	1.07548	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98303	1
DC3000 delta B/DC3000 delta AB	1.00958	0.694

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89894	0.235
Exp 36h	1.23278	1
Exp 60h	0.85182	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02834	1
Var 0h	0.90333	0.933
Var 12h I row2-row1	1.17867	0.189
Var 12h NI row2-row1	1.07605	1
Var 36h I row2-row1	0.78415	0.805
Var 36h NI row2-row1	0.89261	0.522
Var 60h I row2-row1	1.09007	1
Var 60h NI row2-row1	1.01356	1
Time course 0hI-0hNI	1.08673	0.833
Time course 12hI-12hNI	1.03432	0.818
Time course 36hI-36hNI	1.07939	0.28
Time course 60hI-60hNI	1.08494	0.254

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)	0.91189	0.567
transgenic ySAMdc/azygous control (breaker)	0.42302	0.139
transgenic ySAMdc/azygous control (red)	0.96957	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22924	0.039

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83365	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.63162	1
Manapal/WT (break)	0.95245	1
Manapal/WT (red)	0.43181	0.181