Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-4.4.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75891	0.29
27DAP/17DAP	1.3993	0.699
39DAP/27DAP	1.20501	0.82
41DAP/39DAP	1.2278	0.871
42DAP/41DAP	0.87322	1
43DAP/42DAP	0.78149	0.51
47DAP/43DAP	0.94083	0.744
52DAP/47DAP	1.23109	0.654
57DAP/52DAP	0.7142	0.613

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04235	0.872
17DAP/reference	1.0451	0.096
27DAP/reference	0.99861	0.904
39DAP/reference	1.06586	0.581
41DAP/reference	1.0752	0.067
42DAP/reference	0.96058	0.287
43DAP/reference	1.04146	0.646
47DAP/reference	0.87145	0.004
52DAP/reference	0.81282	0.05
57DAP/reference	0.87786	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17623	0.205
27DAP/17DAP	0.9729	0.887
39DAP/27DAP	1.14097	0.505
41DAP/39DAP	1.25428	0.077
42DAP/41DAP	0.88919	0.292
43DAP/42DAP	1.26428	0.049
47DAP/43DAP	0.93889	0.606
52DAP/47DAP	1.35177	0.255
57DAP/52DAP	2.16798	0.07
57DAP/7DAP	2.16454	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93987	0.203
17DAP/reference	0.88864	0.094
27DAP/reference	0.93449	0.135
39DAP/reference	0.86157	0.025
41DAP/reference	0.92433	0.06
42DAP/reference	0.88929	0.111
43DAP/reference	0.9122	0.086
47DAP/reference	1.01523	1
52DAP/reference	0.83752	0.028
57DAP/reference	0.86831	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0956	0.201
17DAP/reference	0.94951	0.378
27DAP/reference	0.94803	0.423
39DAP/reference	0.99348	0.586
41DAP/reference	0.94185	0.25
42DAP/reference	0.91266	0.121
43DAP/reference	1.09535	0.368
47DAP/reference	1.0365	0.353
52DAP/reference	0.96536	0.239
57DAP/reference	0.97701	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97763	0.566
17DAP/reference	0.94192	0.342
27DAP/reference	0.86129	0.032
39DAP/reference	0.8693	0.069
41DAP/reference	0.97704	0.618
42DAP/reference	0.88737	0.036
43DAP/reference	0.92618	0.294
47DAP/reference	1.12127	0.115
52DAP/reference	1.02356	0.871
57DAP/reference	0.86574	0.149

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00798	1
26DAP/20DAP	0.93647	0.512
34DAP/26DAP	1.01345	1
51DAP/34DAP	0.98938	0.893
52DAP/51DAP	1.08482	0.579
53DAP/52DAP	1.01657	1
55DAP/53DAP	1.10877	0.527
57DAP/55DAP	0.95161	0.698
62DAP/57DAP	1.26999	0.515
68DAP/62DAP	0.85875	0.429
68DAP/14DAP	0.81353	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.94899	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.68326	0.107
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33892	0.293
Mature Eggplant/Ripe Tomato	0.29475	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13471	N/A
1-1-2/M82	0.9875	N/A
12-2/M82	1.10029	0.61
12-4/M82	1.14904	N/A
1-3/M82	1.0865	N/A
2-1-1/M82	1.43096	N/A
2-1/M82	1.13495	N/A
2-6/M82	0.84866	1
3-2/M82	1.3541	0.717
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.44066	N/A
4-3/M82	1.17454	1
5-3/M82	0.88814	0.642
6-2/M82	1.68053	N/A
6-3/M82	0.83226	N/A
7-1/M82	1.54514	N/A
7-2/M82	1.3705	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	0.65996	0.243
IL2-6/WTpooled	1.24568	0.584
IL7-5/WTpooled	1.33484	0.792
IL7-3/WTpooled	0.83789	1
IL12-4/WTpooled	1.1076	0.891
IL1-4/WTpooled	0.95017	0.834
WT/WTpooled	1.01462	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	1.26804	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10547	0.921
DC3000/delta hrp 6h	0.89694	0.95
DC3000/delta hrp 12h	1.09502	1
DC3000/delta hrp 24h	1.07577	0.69

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	1.07347	0.196
Exp 36h	N/A	N/A
Exp 60h	1.20036	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97329	1
Var 0h	1.07655	0.98
Var 12h I row2-row1	1.04633	0.473
Var 12h NI row2-row1	0.96664	0.466
Var 36h I row2-row1	1.06046	1
Var 36h NI row2-row1	0.73493	0.61
Var 60h I row2-row1	1.01302	0.562
Var 60h NI row2-row1	0.94721	0.904
Time course 0hI-0hNI	1.19468	0.662
Time course 12hI-12hNI	0.90644	0.334
Time course 36hI-36hNI	0.80015	0.067
Time course 60hI-60hNI	1.14341	0.037

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)	1.17502	0.36
transgenic ySAMdc/azygous control (breaker)	0.42566	0.142
transgenic ySAMdc/azygous control (red)	1.13663	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98794	0.353

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6135	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73187	1
Manapal/WT (break)	0.97815	1
Manapal/WT (red)	1.01115	1