Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21978	0.681
27DAP/17DAP	1.3532	0.854
39DAP/27DAP	0.90501	0.631
41DAP/39DAP	1.05411	0.904
42DAP/41DAP	0.98039	1
43DAP/42DAP	0.80722	0.671
47DAP/43DAP	0.74033	0.274
52DAP/47DAP	1.1793	0.676
57DAP/52DAP	1.13556	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.082	0.567
17DAP/reference	1.29483	0.017
27DAP/reference	1.326	0.152
39DAP/reference	1.18787	0.453
41DAP/reference	1.06788	0.587
42DAP/reference	1.02134	0.756
43DAP/reference	0.89177	0.519
47DAP/reference	0.7764	0.077
52DAP/reference	0.71147	0.049
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26518	0.075
27DAP/17DAP	0.76828	0.121
39DAP/27DAP	1.19367	0.227
41DAP/39DAP	0.60475	0.018
42DAP/41DAP	1.05615	0.8
43DAP/42DAP	0.79365	0.082
47DAP/43DAP	0.86843	0.457
52DAP/47DAP	0.83863	0.389
57DAP/52DAP	0.98589	0.862
57DAP/7DAP	0.78558	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04489
17DAP/reference	1.12642	0.092
27DAP/reference	1.38125	0.006
39DAP/reference	1.10036	0.538
41DAP/reference	1.14435	0.402
42DAP/reference	1.24727
43DAP/reference	1.03739
47DAP/reference	0.93767	0.383
52DAP/reference	1.17625
57DAP/reference	1.43347	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03851	0.719
17DAP/reference	1.25548	0.092
27DAP/reference	1.03187	0.888
39DAP/reference	0.87668	0.119
41DAP/reference	1.05102	0.814
42DAP/reference	1.13196	0.18
43DAP/reference	0.8104	0.181
47DAP/reference	0.97051	0.459
52DAP/reference	0.89642	0.121
57DAP/reference	1.00527	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16318	0.095
17DAP/reference	1.43844	0.074
27DAP/reference	1.80736	0.033
39DAP/reference	1.44432	0.084
41DAP/reference	1.4145	0.074
42DAP/reference	1.29617	0.321
43DAP/reference	1.00922	0.767
47DAP/reference	0.89158	0.08
52DAP/reference	0.93395	0.637
57DAP/reference	0.85455	0.056

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16178	0.966
26DAP/20DAP	0.76693	0.223
34DAP/26DAP	0.96616	0.954
51DAP/34DAP	1.19373
52DAP/51DAP	1.34261	0.349
53DAP/52DAP	1.03218	0.848
55DAP/53DAP	1.05955	0.925
57DAP/55DAP	1.103	0.969
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.41129	0.185
68DAP/14DAP	0.92602	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41808	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.55426
Mature Green Tomato/Ripe Tomato	36.6679	0.016
Immature Eggplant/Mature Eggplant	3.75092	0.05
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.87769	0.26

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	0.95159
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.27776
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	0.83495	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.26366	0.541
IL7-3/WTpooled	0.66705
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.03712	1
WT/WTpooled	2.44152

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	0.8993	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93375	1
DC3000/delta hrp 6h	0.86284	0.95
DC3000/delta hrp 12h	1.06516	1
DC3000/delta hrp 24h	0.44767

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.29286
DC3000 delta B/DC3000 delta AB	0.53548	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10755	1
Exp 36h	0.7814	0.539
Exp 60h	0.68063	0.258

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	0.96501	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	1.25945	1
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	0.9443
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.37602	0.904
Time course 0hI-0hNI	0.96712	0.93
Time course 12hI-12hNI	0.94335	0.799
Time course 36hI-36hNI	0.78664	0.024
Time course 60hI-60hNI	0.47193	0.009

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)	0.82586	0.285
transgenic ySAMdc/azygous control (breaker)	1.90701	0.178
transgenic ySAMdc/azygous control (red)	1.30402	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96015	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.06634	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.63746	0.093
Manapal/WT (break)	2.27425	0.126
Manapal/WT (red)	1.52248	0.142