Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86372	0.436
27DAP/17DAP	0.87117	0.674
39DAP/27DAP	1.1644	0.643
41DAP/39DAP	0.95348	0.791
42DAP/41DAP	1.20909	0.745
43DAP/42DAP	0.97545	0.898
47DAP/43DAP	1.04528	0.979
52DAP/47DAP	0.94542	0.814
57DAP/52DAP	0.98078	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95684	0.317
17DAP/reference	1.05743	0.127
27DAP/reference	1.00461	1
39DAP/reference	1.0086	0.903
41DAP/reference	0.93184	0.085
42DAP/reference	0.87811	0.019
43DAP/reference	1.07867	0.306
47DAP/reference	0.89944	0.055
52DAP/reference	0.84199	0.131
57DAP/reference	0.88572	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.58839	0.319
27DAP/17DAP	1.04986	0.9
39DAP/27DAP	1.0546	0.636
41DAP/39DAP	0.98348	1
42DAP/41DAP	1.17973	0.872
43DAP/42DAP	0.97797	0.902
47DAP/43DAP	1.09005	0.92
52DAP/47DAP	0.97311	0.902
57DAP/52DAP	1.2492	0.393
57DAP/7DAP	1.2348

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54509	0.035
17DAP/reference	1.324	0.022
27DAP/reference	1.46502	0.007
39DAP/reference	1.43127	0.008
41DAP/reference	1.12248	0.171
42DAP/reference	1.22687	0.03
43DAP/reference	1.09891	0.2
47DAP/reference	0.96581	0.504
52DAP/reference	1.6295	0.01
57DAP/reference	1.4863	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08441	0.443
17DAP/reference	0.9844	0.576
27DAP/reference	0.94923	0.393
39DAP/reference	0.89631	0.136
41DAP/reference	1.08478	1
42DAP/reference	0.77827	0.039
43DAP/reference	1.08166	0.479
47DAP/reference	0.81516	0.066
52DAP/reference	1.02822	0.789
57DAP/reference	1.12198	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50939	0.016
17DAP/reference	1.10053	0.522
27DAP/reference	1.1411	0.07
39DAP/reference	1.11981	0.151
41DAP/reference	1.16715	0.129
42DAP/reference	1.1709	0.199
43DAP/reference	1.07423	0.827
47DAP/reference	0.91671	0.296
52DAP/reference	1.06914	0.724
57DAP/reference	0.62948	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98879	1
26DAP/20DAP	1.39928	0.281
34DAP/26DAP	0.8217	0.893
51DAP/34DAP	1.13014	0.775
52DAP/51DAP	1.07991	0.733
53DAP/52DAP	1.17791	0.935
55DAP/53DAP	1.0695	0.869
57DAP/55DAP	1.06128	1
62DAP/57DAP	0.77817
68DAP/62DAP	N/A	N/A
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12199	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.44989	0.095
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.26339
Mature Eggplant/Ripe Tomato	1.01083	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25121	0.742
1-1-2/M82	1.27311
12-2/M82	N/A	N/A
12-4/M82	1.20807	1
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	1.75305
4-3/M82	1.10138	1
5-3/M82	1.104	1
6-2/M82	N/A	N/A
6-3/M82	1.10344
7-1/M82	1.08031
7-2/M82	1.19005
9-3-2/M82	1.04698

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.17155	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80482	0.418
IL12-4/WTpooled	1.10927	0.839
IL1-4/WTpooled	0.91765
WT/WTpooled	1.00494	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	0.92057	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99016	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.28935	1
DC3000/delta hrp 24h	1.13642	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.04495	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89919	1
Var 0h	0.54812	0.255
Var 12h I row2-row1	1.14361	0.654
Var 12h NI row2-row1	1.68058	1
Var 36h I row2-row1	0.70241	1
Var 36h NI row2-row1	1.00418	1
Var 60h I row2-row1	0.91879	0.374
Var 60h NI row2-row1	0.95595	1
Time course 0hI-0hNI	0.8349	0.269
Time course 12hI-12hNI	0.99538	1
Time course 36hI-36hNI	1.06155	0.218
Time course 60hI-60hNI	1.6585	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)	1.13408	0.482
transgenic ySAMdc/azygous control (breaker)	0.97814	1
transgenic ySAMdc/azygous control (red)	1.21744	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01448	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80412	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82732	1
Manapal/WT (break)	1.32005	0.183
Manapal/WT (red)	1.08151	0.413