Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61103	0.071
27DAP/17DAP	0.93996	0.882
39DAP/27DAP	1.96942	0.384
41DAP/39DAP	1.2756	0.437
42DAP/41DAP	0.40279	0.259
43DAP/42DAP	0.57049	0.483
47DAP/43DAP	0.51883	0.052
52DAP/47DAP	1.01458	0.875
57DAP/52DAP	1.15656	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87223	0.013
17DAP/reference	1.13813	0.014
27DAP/reference	1.13773	0.048
39DAP/reference	1.0203	0.828
41DAP/reference	1.21515	0.111
42DAP/reference	0.9017	0.05
43DAP/reference	1.06274	0.646
47DAP/reference	0.82612	0.019
52DAP/reference	0.81157	0.037
57DAP/reference	0.83251	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.48792	0.035
27DAP/17DAP	0.94354	0.821
39DAP/27DAP	0.99072	0.997
41DAP/39DAP	0.89979	0.68
42DAP/41DAP	0.92744	0.511
43DAP/42DAP	0.92824	0.522
47DAP/43DAP	0.81513	0.045
52DAP/47DAP	0.78359	0.452
57DAP/52DAP	0.90083	0.359
57DAP/7DAP	0.6197

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81943	0.024
17DAP/reference	0.9617	0.389
27DAP/reference	1.15665	0.049
39DAP/reference	0.95237	0.411
41DAP/reference	0.92533	0.271
42DAP/reference	1.02488	1
43DAP/reference	0.92432	0.23
47DAP/reference	1.5006	0.018
52DAP/reference	0.9967	0.74
57DAP/reference	0.89927	0.144

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0686	0.042
17DAP/reference	1.27384	0.019
27DAP/reference	1.25188	0.097
39DAP/reference	1.10238	0.463
41DAP/reference	0.97125	0.441
42DAP/reference	0.9412	0.355
43DAP/reference	1.35659	0.027
47DAP/reference	1.03814	0.675
52DAP/reference	1.03583	1
57DAP/reference	1.39359	0.031

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89125	0.016
17DAP/reference	1.07647	0.699
27DAP/reference	0.98244	0.624
39DAP/reference	1.06114	0.711
41DAP/reference	1.0621	0.714
42DAP/reference	0.98958	0.816
43DAP/reference	0.75964	0.057
47DAP/reference	0.96677	0.478
52DAP/reference	0.98747	0.8
57DAP/reference	0.67701	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29065	0.966
26DAP/20DAP	1.46026
34DAP/26DAP	0.84255
51DAP/34DAP	1.28339	0.339
52DAP/51DAP	0.69597
53DAP/52DAP	0.6444	0.527
55DAP/53DAP	1.19028	0.876
57DAP/55DAP	1.03715	0.997
62DAP/57DAP	0.91496	0.871
68DAP/62DAP	1.00597	0.834
68DAP/14DAP	0.90639	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.10622	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	7.21736	0.022
Immature Eggplant/Mature Eggplant	1.23674	0.123
Ripe Pepper/Ripe Tomato	0.04541
Mature Eggplant/Ripe Tomato	4.73174	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.04804
1-3/M82	N/A	N/A
2-1-1/M82	0.9552
2-1/M82	N/A	N/A
2-6/M82	0.95683
3-2/M82	1.17932	0.463
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	0.64581
5-3/M82	1.0469
6-2/M82	0.9075
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.06988	1
IL7-5/WTpooled	1.51309
IL7-3/WTpooled	1.05945	1
IL12-4/WTpooled	1.05054	0.695
IL1-4/WTpooled	1.07912	1
WT/WTpooled	1.02475	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	1.21337	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99594	1
DC3000/delta hrp 6h	1.32896	1
DC3000/delta hrp 12h	0.83591	1
DC3000/delta hrp 24h	4.80354	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.64805	0.042
DC3000 delta B/DC3000 delta AB	1.28171	0.162

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02509	1
Exp 36h	1.22188	0.693
Exp 60h	1.38901	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9864	1
Var 0h	1.01694	1
Var 12h I row2-row1	1.02119	0.795
Var 12h NI row2-row1	0.97994	0.906
Var 36h I row2-row1	0.85095	0.298
Var 36h NI row2-row1	1.02441	1
Var 60h I row2-row1	0.91805	0.832
Var 60h NI row2-row1	0.91354	0.977
Time course 0hI-0hNI	1.27073	0.297
Time course 12hI-12hNI	0.99659	1
Time course 36hI-36hNI	1.18182	0.063
Time course 60hI-60hNI	2.05636	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)	1.00201	1
transgenic ySAMdc/azygous control (breaker)	0.70537	0.173
transgenic ySAMdc/azygous control (red)	1.19226	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93609	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84775	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09142	0.14
Manapal/WT (break)	0.74534	0.333
Manapal/WT (red)	0.75567	0.315