Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84672	0.249
27DAP/17DAP	0.70016	0.287
39DAP/27DAP	0.85073	0.495
41DAP/39DAP	0.95535	0.815
42DAP/41DAP	1.05122	0.958
43DAP/42DAP	1.21291	0.724
47DAP/43DAP	1.19217	0.364
52DAP/47DAP	0.69785	0.515
57DAP/52DAP	1.04414	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29351	0.089
17DAP/reference	0.78273	0.041
27DAP/reference	0.89967	0.385
39DAP/reference	0.69644	0.028
41DAP/reference	0.63187	0.039
42DAP/reference	0.86223	0.054
43DAP/reference	0.89865	0.148
47DAP/reference	0.89759	0.161
52DAP/reference	1.18036	0.548
57DAP/reference	1.35271	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28715	0.04
27DAP/17DAP	0.88793	0.39
39DAP/27DAP	1.22089	0.314
41DAP/39DAP	1.05353	1
42DAP/41DAP	1.18453	0.042
43DAP/42DAP	1.00661	0.83
47DAP/43DAP	1.04338	0.822
52DAP/47DAP	1.08557	0.785
57DAP/52DAP	0.85046	0.215
57DAP/7DAP	0.84137	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65078	0.04
17DAP/reference	1.40377	0.02
27DAP/reference	1.00978	0.664
39DAP/reference	1.007	1
41DAP/reference	0.93647	0.203
42DAP/reference	1.03126	0.828
43DAP/reference	0.99813	0.694
47DAP/reference	0.87461	0.128
52DAP/reference	0.83343	0.017
57DAP/reference	0.76114	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78403	0.064
17DAP/reference	0.75117	0.031
27DAP/reference	0.90695	0.34
39DAP/reference	0.99197	0.539
41DAP/reference	1.06565	0.862
42DAP/reference	0.96972	0.433
43DAP/reference	0.64691	0.02
47DAP/reference	0.7171	0.016
52DAP/reference	0.81569	0.007
57DAP/reference	0.56144	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58988	0.037
17DAP/reference	1.43659	0.206
27DAP/reference	1.11729	0.284
39DAP/reference	1.07088	0.691
41DAP/reference	0.98103	0.618
42DAP/reference	1.40773	0.074
43DAP/reference	1.44114	0.134
47DAP/reference	0.85538	0.191
52DAP/reference	0.86	0.319
57DAP/reference	1.92978	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7006
26DAP/20DAP	1.13522	0.683
34DAP/26DAP	0.83643	0.095
51DAP/34DAP	2.07146	0.032
52DAP/51DAP	0.93497	1
53DAP/52DAP	1.08254	0.819
55DAP/53DAP	0.59432	0.016
57DAP/55DAP	0.90944	0.575
62DAP/57DAP	0.94564	0.871
68DAP/62DAP	1.14802	0.897
68DAP/14DAP	2.03874	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07592	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.28837	0.068
Mature Green Tomato/Ripe Tomato	1.24924	0.149
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	17.7712	0.256
Mature Eggplant/Ripe Tomato	0.89726

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08055	0.742
1-1-2/M82	1.27411
12-2/M82	0.96298
12-4/M82	0.83428	0.33
1-3/M82	8.74614
2-1-1/M82	1.36851
2-1/M82	N/A	N/A
2-6/M82	1.3597
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	1.02598
6-2/M82	N/A	N/A
6-3/M82	1.25997
7-1/M82	0.81162
7-2/M82	N/A	N/A
9-3-2/M82	1.31889

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83578	0.247
IL2-6/WTpooled	0.97223	1
IL7-5/WTpooled	1.07203	0.792
IL7-3/WTpooled	0.77515	0.31
IL12-4/WTpooled	0.95274	0.71
IL1-4/WTpooled	0.87692	0.415
WT/WTpooled	1.02529	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	0.97621	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17457	0.846
DC3000/delta hrp 6h	0.90252	0.95
DC3000/delta hrp 12h	1.29397	1
DC3000/delta hrp 24h	0.68384	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14996	0.11
DC3000 delta B/DC3000 delta AB	1.0606	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79442	0.328
Exp 36h	0.93565	0.879
Exp 60h	0.74841	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01787	1
Var 0h	0.77817	0.936
Var 12h I row2-row1	0.82371	0.344
Var 12h NI row2-row1	1.38055	0.228
Var 36h I row2-row1	1.00019	1
Var 36h NI row2-row1	1.12925	1
Var 60h I row2-row1	0.82689	0.439
Var 60h NI row2-row1	0.80338	0.572
Time course 0hI-0hNI	1.16656	0.603
Time course 12hI-12hNI	0.96098	0.632
Time course 36hI-36hNI	0.9452	0.211
Time course 60hI-60hNI	1.36936	0.053

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)	1.19764	0.289
transgenic ySAMdc/azygous control (breaker)	1.24593	0.248
transgenic ySAMdc/azygous control (red)	1.36561	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.59098	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.75704	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.06096	0.105
Manapal/WT (break)	2.3645	0.381
Manapal/WT (red)	2.45874	0.134