Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.34305	0.029
27DAP/17DAP	1.19069	0.793
39DAP/27DAP	1.15377	0.752
41DAP/39DAP	0.60387	0.053
42DAP/41DAP	0.66411	0.774
43DAP/42DAP	1.16647	0.835
47DAP/43DAP	1.17058	0.52
52DAP/47DAP	0.65559	0.198
57DAP/52DAP	0.83091	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97913	0.578
17DAP/reference	2.35392	0.028
27DAP/reference	4.27403	0.007
39DAP/reference	2.357	0.012
41DAP/reference	1.91232	0.014
42DAP/reference	1.6031	0.001
43DAP/reference	1.38988	0.009
47DAP/reference	1.496	0.006
52DAP/reference	1.15146	0.053
57DAP/reference	1.32999	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.21774	0.036
27DAP/17DAP	1.17132	0.811
39DAP/27DAP	0.84622	0.477
41DAP/39DAP	0.99672	0.875
42DAP/41DAP	1.0717	0.984
43DAP/42DAP	0.52365	0.022
47DAP/43DAP	0.7868	0.034
52DAP/47DAP	1.31995	0.317
57DAP/52DAP	1.56254	0.082
57DAP/7DAP	1.0552	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23602	0.088
17DAP/reference	1.61945	0.006
27DAP/reference	1.91438	0.006
39DAP/reference	2.67166	0.006
41DAP/reference	2.02459	0.01
42DAP/reference	1.46149	0.076
43DAP/reference	1.47588	0.02
47DAP/reference	2.62311	0.014
52DAP/reference	2.69281	0.007
57DAP/reference	3.4314	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71011	0.134
17DAP/reference	1.11838	0.806
27DAP/reference	1.98709	0.014
39DAP/reference	2.36813	0.011
41DAP/reference	1.81056	0.006
42DAP/reference	1.87983	0.007
43DAP/reference	1.48145	0.076
47DAP/reference	1.84632	0.008
52DAP/reference	1.78051	0.106
57DAP/reference	0.89142	0.318

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7418	0.026
17DAP/reference	1.38537	0.201
27DAP/reference	2.86594	0.013
39DAP/reference	2.2889	0.005
41DAP/reference	1.72168	0.012
42DAP/reference	2.17006	0.025
43DAP/reference	2.35371	0.007
47DAP/reference	3.77976	0.006
52DAP/reference	2.95538	0.027
57DAP/reference	7.3668	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09291	0.966
26DAP/20DAP	1.75911	0.137
34DAP/26DAP	1.1551	0.819
51DAP/34DAP	1.24026	0.132
52DAP/51DAP	1.3616	0.108
53DAP/52DAP	0.52356	0.049
55DAP/53DAP	0.46658	0.017
57DAP/55DAP	0.61444	0.103
62DAP/57DAP	1.11937	0.868
68DAP/62DAP	1.39123	0.033
68DAP/14DAP	1.01564	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14772	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.50095	0.058
Mature Green Tomato/Ripe Tomato	3.40122
Immature Eggplant/Mature Eggplant	0.6138	0.062
Ripe Pepper/Ripe Tomato	0.47444	0.224
Mature Eggplant/Ripe Tomato	1.22368	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.49073	0.557
1-1-2/M82	1.27741	1
12-2/M82	0.75151	0.727
12-4/M82	1.09065	1
1-3/M82	1.91599	0.248
2-1-1/M82	0.82863	0.465
2-1/M82	0.48672	0.322
2-6/M82	1.36928	0.329
3-2/M82	1.26821
4-1-1/M82	1.10782	1
4-1/M82	1.15015	1
4-3-2/M82	0.67171	0.487
4-3/M82	0.6783	0.72
5-3/M82	1.25551	1
6-2/M82	1.2031	1
6-3/M82	1.03266	1
7-1/M82	N/A	N/A
7-2/M82	1.9804	0.385
9-3-2/M82	1.07294	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87042	1
IL2-6/WTpooled	1.10738	0.788
IL7-5/WTpooled	0.14862
IL7-3/WTpooled	1.06707
IL12-4/WTpooled	0.9235	1
IL1-4/WTpooled	0.84117	0.834
WT/WTpooled	0.98492	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	0.76168	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91652	1
DC3000/delta hrp 6h	1.19059	0.95
DC3000/delta hrp 12h	1.08759	1
DC3000/delta hrp 24h	0.80283	0.058

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.52958	0.023
DC3000 delta B/DC3000 delta AB	0.56523	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94932	1
Exp 36h	0.81525	0.539
Exp 60h	0.77313	0.32

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	N/A	N/A
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)	1.06257	0.748
transgenic ySAMdc/azygous control (breaker)	0.9125	1
transgenic ySAMdc/azygous control (red)	1.7185	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86902	0.104

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.65312	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38724	0.307
Manapal/WT (break)	1.53449	0.14
Manapal/WT (red)	2.90349	0.15