Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.1.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7707	0.055
27DAP/17DAP	0.84055	0.579
39DAP/27DAP	1.05246	1
41DAP/39DAP	0.90776	0.761
42DAP/41DAP	1.38567	0.514
43DAP/42DAP	0.93098	0.851
47DAP/43DAP	0.60889	0.084
52DAP/47DAP	1.0842	0.946
57DAP/52DAP	1.84453	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37546	0.278
17DAP/reference	0.88082	0.029
27DAP/reference	0.96068	0.525
39DAP/reference	0.99228	0.855
41DAP/reference	0.84673	0.031
42DAP/reference	0.95438	0.103
43DAP/reference	0.94138	0.084
47DAP/reference	0.91298	0.077
52DAP/reference	0.93746	0.25
57DAP/reference	1.06759	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	1.40627	0.579
39DAP/27DAP	0.90402	0.496
41DAP/39DAP	1.69264	0.674
42DAP/41DAP	0.91975	0.687
43DAP/42DAP	1.04289	1
47DAP/43DAP	1.13214	1
52DAP/47DAP	0.80836	0.538
57DAP/52DAP	0.75114	0.424
57DAP/7DAP	0.92828

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08525	0.399
17DAP/reference	0.87243	0.072
27DAP/reference	0.88207	0.117
39DAP/reference	0.93017	0.264
41DAP/reference	0.84284	0.086
42DAP/reference	0.86149	0.03
43DAP/reference	0.86472	0.082
47DAP/reference	0.95356	0.504
52DAP/reference	0.79394	0.043
57DAP/reference	0.84922	0.05

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07642	0.65
17DAP/reference	0.88762	0.062
27DAP/reference	0.92686	0.249
39DAP/reference	0.91377	0.298
41DAP/reference	0.94535	0.315
42DAP/reference	0.88613	0.061
43DAP/reference	0.88726	0.292
47DAP/reference	0.86285	0.037
52DAP/reference	0.77072	0.051
57DAP/reference	0.88929	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25955	0.022
17DAP/reference	1.05028	0.699
27DAP/reference	0.82248	0.063
39DAP/reference	1.00898	1
41DAP/reference	0.75893	0.058
42DAP/reference	0.82702	0.172
43DAP/reference	0.7159	0.059
47DAP/reference	0.88942	0.12
52DAP/reference	0.85659	0.242
57DAP/reference	1.12696	0.332

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21021	0.966
26DAP/20DAP	1.40656	1
34DAP/26DAP	1.15409	1
51DAP/34DAP	0.42189
52DAP/51DAP	1.65152	0.05
53DAP/52DAP	1.06794	1
55DAP/53DAP	0.8304	0.648
57DAP/55DAP	0.95198	0.845
62DAP/57DAP	1.08273	0.133
68DAP/62DAP	1.17164	0.139
68DAP/14DAP	1.05875	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.80856	0.627

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.373	0.073
Mature Green Tomato/Ripe Tomato	2.71302	0.237
Immature Eggplant/Mature Eggplant	1.05924	0.58
Ripe Pepper/Ripe Tomato	6.55251	0.256
Mature Eggplant/Ripe Tomato	2.98631	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.87644
12-2/M82	N/A	N/A
12-4/M82	0.89136
1-3/M82	N/A	N/A
2-1-1/M82	0.78739
2-1/M82	N/A	N/A
2-6/M82	1.06665	0.695
3-2/M82	0.9638
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	0.65068
5-3/M82	1.19998
6-2/M82	1.67022
6-3/M82	0.94793
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.89836

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84919	0.321
IL2-6/WTpooled	1.01332	1
IL7-5/WTpooled	1.15962	0.792
IL7-3/WTpooled	0.87776	1
IL12-4/WTpooled	0.76656	0.71
IL1-4/WTpooled	1.19484	1
WT/WTpooled	1.06705	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91084	1
DC3000/delta hrp 6h	1.09142	1
DC3000/delta hrp 12h	1.05685	1
DC3000/delta hrp 24h	0.74869	0.035

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	358.421

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90125	1
Exp 36h	0.78698	0.539
Exp 60h	0.83174	0.522

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)	1.04875	0.699
transgenic ySAMdc/azygous control (breaker)	0.77163	0.137
transgenic ySAMdc/azygous control (red)	1.03282	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09719	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1089	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.68828	0.087
Manapal/WT (break)	1.19756	0.381
Manapal/WT (red)	1.37444	0.222