Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.13.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83618	0.221
27DAP/17DAP	1.14433	0.849
39DAP/27DAP	0.92564	0.67
41DAP/39DAP	1.44937	0.413
42DAP/41DAP	1.16013	0.873
43DAP/42DAP	1.26115	0.867
47DAP/43DAP	1.25172	0.769
52DAP/47DAP	1.20045	0.688
57DAP/52DAP	0.89852	0.869

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92822	0.205
17DAP/reference	1.07013	0.044
27DAP/reference	1.01707	0.771
39DAP/reference	1.01416	0.691
41DAP/reference	0.98781	0.814
42DAP/reference	0.93194	0.045
43DAP/reference	1.00099	0.942
47DAP/reference	0.9724	0.174
52DAP/reference	0.91017	0.135
57DAP/reference	0.91485	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96463	0.697
27DAP/17DAP	0.88251	0.614
39DAP/27DAP	1.07057	0.526
41DAP/39DAP	0.95201	0.959
42DAP/41DAP	1.03382	0.984
43DAP/42DAP	1.24563	0.056
47DAP/43DAP	0.9271	0.525
52DAP/47DAP	0.94311	0.753
57DAP/52DAP	1.01238	1
57DAP/7DAP	1.32901	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85194	0.104
17DAP/reference	0.87159	0.082
27DAP/reference	0.93616	0.283
39DAP/reference	0.86702	0.02
41DAP/reference	0.86749	0.047
42DAP/reference	0.89723	0.073
43DAP/reference	0.73038	0.019
47DAP/reference	0.90029	0.168
52DAP/reference	0.63303	0.015
57DAP/reference	0.79445	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03305	0.605
17DAP/reference	1.04736	0.348
27DAP/reference	0.92621	0.352
39DAP/reference	0.89467	0.178
41DAP/reference	0.91351	0.021
42DAP/reference	0.94718	0.289
43DAP/reference	1.04879	0.582
47DAP/reference	1.00745	1
52DAP/reference	0.99468	0.666
57DAP/reference	0.98902	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92627	0.147
17DAP/reference	1.04514	0.746
27DAP/reference	0.90382	0.119
39DAP/reference	0.72782	0.015
41DAP/reference	0.98733	0.682
42DAP/reference	0.79546	0.032
43DAP/reference	0.88673	0.237
47DAP/reference	0.94526	0.335
52DAP/reference	0.78394	0.177
57DAP/reference	0.69144	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10457	0.735
26DAP/20DAP	0.94573	1
34DAP/26DAP	1.18078	1
51DAP/34DAP	0.81071	0.328
52DAP/51DAP	1.2395	0.842
53DAP/52DAP	1.14204	0.961
55DAP/53DAP	0.95102	0.709
57DAP/55DAP	1.00678	0.923
62DAP/57DAP	1.14528	0.868
68DAP/62DAP	0.89548	0.7
68DAP/14DAP	1.20548	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3573	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83545	0.41
Mature Green Tomato/Ripe Tomato	0.33456	0.018
Immature Eggplant/Mature Eggplant	1.06996	0.334
Ripe Pepper/Ripe Tomato	0.30894	0.224
Mature Eggplant/Ripe Tomato	0.4471	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03307	0.877
1-1-2/M82	1.3523
12-2/M82	N/A	N/A
12-4/M82	0.97751
1-3/M82	0.82788
2-1-1/M82	1.08163
2-1/M82	N/A	N/A
2-6/M82	0.9238
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	0.93263
4-3/M82	1.28433
5-3/M82	1.01348	1
6-2/M82	N/A	N/A
6-3/M82	0.81544	0.796
7-1/M82	N/A	N/A
7-2/M82	1.08388
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94947	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.26148	0.362
IL12-4/WTpooled	1.11487	0.737
IL1-4/WTpooled	0.99253
WT/WTpooled	0.88957	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	0.98866	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18648	0.921
DC3000/delta hrp 6h	1.04083	1
DC3000/delta hrp 12h	1.10579	1
DC3000/delta hrp 24h	1.1062	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55464
DC3000 delta B/DC3000 delta AB	1.88198

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96621	1
Exp 36h	1.19097	1
Exp 60h	1.1675	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05763	1
Var 0h	1.06229	0.936
Var 12h I row2-row1	1.18576	0.254
Var 12h NI row2-row1	0.98621	1
Var 36h I row2-row1	0.89838	1
Var 36h NI row2-row1	0.76265	0.61
Var 60h I row2-row1	0.90321	0.287
Var 60h NI row2-row1	0.99905	1
Time course 0hI-0hNI	0.88789	0.265
Time course 12hI-12hNI	1.14787	0.102
Time course 36hI-36hNI	1.26887	0.028
Time course 60hI-60hNI	1.90456	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)	1.05276	0.339
transgenic ySAMdc/azygous control (breaker)	1.0491	1
transgenic ySAMdc/azygous control (red)	0.99438	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9688	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13255	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77191	1
Manapal/WT (break)	0.84872	1
Manapal/WT (red)	0.72563	0.181