Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32883	0.61
27DAP/17DAP	1.17308	0.828
39DAP/27DAP	1.45597	0.507
41DAP/39DAP	0.91108	0.591
42DAP/41DAP	1.12491	0.938
43DAP/42DAP	1.37225	0.88
47DAP/43DAP	1.34533	0.618
52DAP/47DAP	0.74694	0.452
57DAP/52DAP	1.91661	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93454	0.262
17DAP/reference	1.04531	0.675
27DAP/reference	0.91635	0.395
39DAP/reference	1.01294	0.92
41DAP/reference	0.88484	0.267
42DAP/reference	0.96784	0.305
43DAP/reference	1.09007	0.866
47DAP/reference	0.81479	0.106
52DAP/reference	0.86484	0.158
57DAP/reference	0.8074	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96623	0.663
27DAP/17DAP	1.02273	0.942
39DAP/27DAP	1.07826	0.575
41DAP/39DAP	1.08346	0.393
42DAP/41DAP	0.96395	0.712
43DAP/42DAP	1.02158	0.585
47DAP/43DAP	1.00144	1
52DAP/47DAP	1.02828	0.915
57DAP/52DAP	0.97948	0.753
57DAP/7DAP	1.00943	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19943	0.205
17DAP/reference	1.28331	0.059
27DAP/reference	1.32535	0.02
39DAP/reference	1.16628	0.351
41DAP/reference	1.10758	0.375
42DAP/reference	1.05639	1
43DAP/reference	1.32957	0.066
47DAP/reference	0.86104	0.293
52DAP/reference	1.13436	0.229
57DAP/reference	1.06878	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90774	0.503
17DAP/reference	0.84144	0.214
27DAP/reference	0.78363	0.111
39DAP/reference	0.9829	0.526
41DAP/reference	0.80082	0.03
42DAP/reference	0.92499	0.098
43DAP/reference	0.8834	0.298
47DAP/reference	0.92502	0.141
52DAP/reference	0.94118	0.38
57DAP/reference	0.80196	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01473	1
17DAP/reference	0.92676	0.407
27DAP/reference	1.1728	0.067
39DAP/reference	1.12353	0.275
41DAP/reference	1.26662	0.027
42DAP/reference	1.0286	1
43DAP/reference	0.98788	0.712
47DAP/reference	0.85775	0.139
52DAP/reference	1.87682	0.335
57DAP/reference	0.74506	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23409	0.966
26DAP/20DAP	0.9258	0.512
34DAP/26DAP	1.04384	1
51DAP/34DAP	1.01545	0.962
52DAP/51DAP	0.94975	0.151
53DAP/52DAP	1.08028
55DAP/53DAP	0.90619	0.028
57DAP/55DAP	1.06485	0.898
62DAP/57DAP	0.93363	0.871
68DAP/62DAP	1.0754	0.914
68DAP/14DAP	0.86291	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9075	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.26057	1
Mature Eggplant/Ripe Tomato	0.4423

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25018
1-1-2/M82	0.9108
12-2/M82	N/A	N/A
12-4/M82	1.06033	1
1-3/M82	0.95399
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.39101
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.00926
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.04738	1
6-2/M82	N/A	N/A
6-3/M82	1.13584
7-1/M82	N/A	N/A
7-2/M82	0.95207
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1949	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.87103	0.699
WT/WTpooled	N/A	N/A

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	0.97416	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1554	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18582	1
DC3000/delta hrp 24h	0.80332	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04586	0.333
DC3000 delta B/DC3000 delta AB	1.03511	0.55

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08986	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07564	1
Var 0h	1.52915	1
Var 12h I row2-row1	1.20982	0.196
Var 12h NI row2-row1	0.90819	0.713
Var 36h I row2-row1	0.93623	1
Var 36h NI row2-row1	0.85415	0.584
Var 60h I row2-row1	1.53806	1
Var 60h NI row2-row1	1.23274	0.904
Time course 0hI-0hNI	1.14262	0.719
Time course 12hI-12hNI	1.0656	0.603
Time course 36hI-36hNI	0.96439	0.441
Time course 60hI-60hNI	1.28761	0.008

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)	1.61781	0.372
transgenic ySAMdc/azygous control (breaker)	0.99294	1
transgenic ySAMdc/azygous control (red)	1.119	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95533	0.305

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92791	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8259	1
Manapal/WT (break)	0.94035	1
Manapal/WT (red)	1.24128	0.222