Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98483	0.839
27DAP/17DAP	1.15616	0.844
39DAP/27DAP	1.09796	0.946
41DAP/39DAP	1.05726	0.78
42DAP/41DAP	1.14913	0.755
43DAP/42DAP	1.00761	0.937
47DAP/43DAP	0.90275	0.667
52DAP/47DAP	1.21631	0.873
57DAP/52DAP	1.41398	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85589	0.051
17DAP/reference	0.84329	0.024
27DAP/reference	0.997	0.847
39DAP/reference	1.12313	0.841
41DAP/reference	0.72296	0.085
42DAP/reference	1.08955	0.191
43DAP/reference	1.0624	0.646
47DAP/reference	1.08169	0.34
52DAP/reference	1.17385	0.031
57DAP/reference	0.96112	0.456

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11723	0.445
27DAP/17DAP	1.18873	0.429
39DAP/27DAP	1.03807	0.691
41DAP/39DAP	0.84589	0.372
42DAP/41DAP	1.14892	0.663
43DAP/42DAP	0.98226	0.831
47DAP/43DAP	0.96164	0.796
52DAP/47DAP	1.43398	0.199
57DAP/52DAP	1.60881	0.056
57DAP/7DAP	1.24415	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17991	0.091
17DAP/reference	1.161	0.112
27DAP/reference	1.07279	0.371
39DAP/reference	1.33047	0.005
41DAP/reference	1.2658	0.011
42DAP/reference	1.25813	0.01
43DAP/reference	1.21298	0.013
47DAP/reference	1.36781	0.121
52DAP/reference	1.40876	0.015
57DAP/reference	1.81461	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99952	0.848
17DAP/reference	1.54035	0.723
27DAP/reference	0.95712	0.292
39DAP/reference	0.95942	0.469
41DAP/reference	1.19329	0.076
42DAP/reference	1.19377	0.274
43DAP/reference	0.76475	0.03
47DAP/reference	0.90219	0.105
52DAP/reference	0.94701	0.433
57DAP/reference	0.77709	0.156

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96461	0.455
17DAP/reference	0.92011	0.292
27DAP/reference	1.10386	0.164
39DAP/reference	1.12885	0.078
41DAP/reference	1.00751	1
42DAP/reference	1.0893	0.481
43DAP/reference	1.06449	0.779
47DAP/reference	0.95907	0.278
52DAP/reference	1.13972	0.448
57DAP/reference	1.29213	0.126

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1195	0.966
26DAP/20DAP	1.94211	0.153
34DAP/26DAP	1.079	1
51DAP/34DAP	1.25642	0.185
52DAP/51DAP	1.19502	0.503
53DAP/52DAP	1.06417	0.806
55DAP/53DAP	0.99958	0.917
57DAP/55DAP	0.94499	0.795
62DAP/57DAP	1.02263	1
68DAP/62DAP	1.3423	0.182
68DAP/14DAP	2.37027	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65662	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01305	1
Mature Green Tomato/Ripe Tomato	0.87459	0.377
Immature Eggplant/Mature Eggplant	1.38831	0.096
Ripe Pepper/Ripe Tomato	0.99867	1
Mature Eggplant/Ripe Tomato	0.89825	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03999	0.591
1-1-2/M82	1.09677	0.942
12-2/M82	0.97593	0.955
12-4/M82	1.07525	1
1-3/M82	0.99802	1
2-1-1/M82	1.22047
2-1/M82	0.83785	0.345
2-6/M82	1.1184	0.505
3-2/M82	1.35341
4-1-1/M82	1.00985
4-1/M82	0.98758
4-3-2/M82	N/A	N/A
4-3/M82	1.17978	1
5-3/M82	1.00818	1
6-2/M82	1.01446
6-3/M82	1.05674	1
7-1/M82	1.02006	1
7-2/M82	1.20114	0.385
9-3-2/M82	0.74961

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.71679
IL1-4/WTpooled	1.30494
WT/WTpooled	1.39745

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	1.20712	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98173	1
DC3000/delta hrp 6h	0.79488	0.95
DC3000/delta hrp 12h	0.90458	1
DC3000/delta hrp 24h	1.05857	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12739	0.042
DC3000 delta B/DC3000 delta AB	1.22009	0.246

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98419	1
Exp 36h	1.88186	1
Exp 60h	1.20868	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.06177	0.482
transgenic ySAMdc/azygous control (breaker)	1.30545	0.248
transgenic ySAMdc/azygous control (red)	1.04465	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98549	0.393

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01583	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93652	1
Manapal/WT (break)	0.87347	0.333
Manapal/WT (red)	0.97836	0.728