Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.1.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.8554	0.061
27DAP/17DAP	1.26068	0.766
39DAP/27DAP	0.99609	0.782
41DAP/39DAP	0.80927	0.315
42DAP/41DAP	0.70814	0.397
43DAP/42DAP	1.10895	0.94
47DAP/43DAP	1.22623	0.438
52DAP/47DAP	0.75189	0.377
57DAP/52DAP	1.01315	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0122	1
17DAP/reference	1.0643	0.606
27DAP/reference	1.1011	0.375
39DAP/reference	1.04423	0.8
41DAP/reference	0.9399	0.341
42DAP/reference	1.16235	0.103
43DAP/reference	0.86114	0.394
47DAP/reference	1.14988	0.306
52DAP/reference	0.96291	0.438
57DAP/reference	0.76825	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27699	0.04
27DAP/17DAP	1.09191	0.664
39DAP/27DAP	0.98015	0.852
41DAP/39DAP	0.98284	0.997
42DAP/41DAP	0.98898	0.84
43DAP/42DAP	0.88176	0.121
47DAP/43DAP	0.98633	0.928
52DAP/47DAP	1.00413	0.979
57DAP/52DAP	0.96747	0.691
57DAP/7DAP	0.98707	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12926	0.257
17DAP/reference	0.87918	0.064
27DAP/reference	0.98985	0.614
39DAP/reference	1.24296	0.282
41DAP/reference	0.96175	0.538
42DAP/reference	0.84069	0.16
43DAP/reference	1.06893	0.672
47DAP/reference	1.10647	1
52DAP/reference	0.71278	0.115
57DAP/reference	1.0088	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30706	0.325
17DAP/reference	1.10699	0.892
27DAP/reference	1.09807	0.552
39DAP/reference	1.6234	0.065
41DAP/reference	1.13594	0.599
42DAP/reference	1.16511	0.129
43DAP/reference	1.20735	0.347
47DAP/reference	1.10954	0.048
52DAP/reference	1.10718
57DAP/reference	1.05767	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96885	0.526
17DAP/reference	1.11434	0.503
27DAP/reference	0.70776	0.048
39DAP/reference	1.13196	0.752
41DAP/reference	0.82696	0.209
42DAP/reference	1.08063	0.893
43DAP/reference	1.13228	0.88
47DAP/reference	1.23959	0.009
52DAP/reference	1.27076	0.335
57DAP/reference	1.25342	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.36349	0.966
26DAP/20DAP	0.92415	1
34DAP/26DAP	1.07247	1
51DAP/34DAP	1.12617	0.597
52DAP/51DAP	1.17632	0.218
53DAP/52DAP	1.03677	0.819
55DAP/53DAP	1.22955	0.113
57DAP/55DAP	0.88383	0.587
62DAP/57DAP	0.78879	0.681
68DAP/62DAP	0.8448	0.7
68DAP/14DAP	0.84328	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85102	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94088
Mature Green Tomato/Ripe Tomato	2.19089	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.24877	0.293
Mature Eggplant/Ripe Tomato	0.65326	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.26257
12-2/M82	N/A	N/A
12-4/M82	0.94592
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	0.54613
4-3/M82	N/A	N/A
5-3/M82	0.74181
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.76343
7-2/M82	N/A	N/A
9-3-2/M82	0.95333

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12997	0.365
IL2-6/WTpooled	1.32287	0.659
IL7-5/WTpooled	1.65554
IL7-3/WTpooled	0.99089	1
IL12-4/WTpooled	1.26599	0.737
IL1-4/WTpooled	0.9798	0.834
WT/WTpooled	1.24836	0.999

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	0.98267	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1823	1
DC3000/delta hrp 6h	1.2801	1
DC3000/delta hrp 12h	2.18142
DC3000/delta hrp 24h	1.89196	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76734	0.024
DC3000 delta B/DC3000 delta AB	0.91899	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.8628	1
Exp 36h	0.91642	0.82
Exp 60h	0.90284	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98657	1
Var 0h	1.00025	1
Var 12h I row2-row1	0.95342	0.856
Var 12h NI row2-row1	0.98457	1
Var 36h I row2-row1	1.04203	1
Var 36h NI row2-row1	1.25338	0.253
Var 60h I row2-row1	1.1634	0.562
Var 60h NI row2-row1	1.10133	0.904
Time course 0hI-0hNI	1.02897	0.852
Time course 12hI-12hNI	1.00072	1
Time course 36hI-36hNI	0.92838	0.317
Time course 60hI-60hNI	0.37062	0.005

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)	0.99271	0.862
transgenic ySAMdc/azygous control (breaker)	0.94727	1
transgenic ySAMdc/azygous control (red)	0.96537	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94178	0.093

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98385	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26071	0.105
Manapal/WT (break)	1.21406	1
Manapal/WT (red)	0.78507	0.181