Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.3.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81688	0.303
27DAP/17DAP	0.50378	0.035
39DAP/27DAP	0.63668	0.326
41DAP/39DAP	0.93094	0.773
42DAP/41DAP	1.04771	1
43DAP/42DAP	1.50098	0.409
47DAP/43DAP	1.04017	0.949
52DAP/47DAP	1.11168	0.906
57DAP/52DAP	0.79951	0.74

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45649	0.038
17DAP/reference	0.86134	0.24
27DAP/reference	1.20361	0.806
39DAP/reference	0.59484	0.012
41DAP/reference	0.543	0.008
42DAP/reference	0.8332	0.103
43DAP/reference	N/A	N/A
47DAP/reference	0.68824	0.007
52DAP/reference	0.49869	0.012
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72532	0.038
27DAP/17DAP	0.96677	0.887
39DAP/27DAP	0.68246	0.029
41DAP/39DAP	0.87109	0.53
42DAP/41DAP	1.15824	0.159
43DAP/42DAP	1.11988	0.025
47DAP/43DAP	0.93065	0.418
52DAP/47DAP	0.64463	0.048
57DAP/52DAP	1.05235	0.679
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2	0.461
17DAP/reference	0.89532	0.253
27DAP/reference	0.64762	0.015
39DAP/reference	1.39957	0.391
41DAP/reference	1.03163	1
42DAP/reference	0.95715	0.371
43DAP/reference	1.03128	1
47DAP/reference	0.8506	0.168
52DAP/reference	0.96797	0.398
57DAP/reference	0.88781	0.123

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96777	0.706
17DAP/reference	0.91446	0.317
27DAP/reference	0.89201	0.16
39DAP/reference	0.80383	0.168
41DAP/reference	0.85845	0.148
42DAP/reference	0.83321	0.022
43DAP/reference	0.61759	0.003
47DAP/reference	0.62602	0.01
52DAP/reference	0.48618	0.004
57DAP/reference	0.51394	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03932	0.062
17DAP/reference	1.07589	1
27DAP/reference	1.29123	0.34
39DAP/reference	1.04255	0.755
41DAP/reference	0.90868	0.107
42DAP/reference	0.97315	0.671
43DAP/reference	1.0208	0.858
47DAP/reference	0.6734	0.016
52DAP/reference	0.78738	0.134
57DAP/reference	0.85937	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11204	0.966
26DAP/20DAP	1.46767	0.168
34DAP/26DAP	0.95845	0.94
51DAP/34DAP	0.99494	0.924
52DAP/51DAP	0.81744	0.151
53DAP/52DAP	0.71303	0.061
55DAP/53DAP	0.61107	0.017
57DAP/55DAP	0.91885	0.703
62DAP/57DAP	0.84015
68DAP/62DAP	1.83991	0.689
68DAP/14DAP	0.61243	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.40847	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.70404	0.058
Mature Green Tomato/Ripe Tomato	2.08787	0.025
Immature Eggplant/Mature Eggplant	0.44386	0.062
Ripe Pepper/Ripe Tomato	5.13607	1
Mature Eggplant/Ripe Tomato	11.298	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.13336	1
12-2/M82	N/A	N/A
12-4/M82	0.88007	0.619
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	0.80923
4-1/M82	N/A	N/A
4-3-2/M82	0.94277
4-3/M82	1.58283	0.268
5-3/M82	0.72757	0.642
6-2/M82	N/A	N/A
6-3/M82	0.82754
7-1/M82	0.8614
7-2/M82	1.15518
9-3-2/M82	0.90878	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88988	0.247
IL2-6/WTpooled	1.29941	0.659
IL7-5/WTpooled	1.02126	1
IL7-3/WTpooled	0.7181	0.298
IL12-4/WTpooled	1.03429	1
IL1-4/WTpooled	1.02917	1
WT/WTpooled	1.077	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	0.88216	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95871	1
DC3000/delta hrp 6h	1.05291	1
DC3000/delta hrp 12h	1.04481	1
DC3000/delta hrp 24h	1.3238	0.875

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.41789	0.025
DC3000 delta B/DC3000 delta AB	0.49763	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00906	1
Exp 36h	0.70681	0.539
Exp 60h	0.59305	0.259

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	1.104	1
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)	0.80939	0.301
transgenic ySAMdc/azygous control (breaker)	0.93694	1
transgenic ySAMdc/azygous control (red)	1.40597	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94297	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.6158	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.46757	0.083
Manapal/WT (break)	3.46525	0.123
Manapal/WT (red)	3.0243	0.142