Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75681	0.226
27DAP/17DAP	1.01431	0.958
39DAP/27DAP	0.71814	0.392
41DAP/39DAP	1.15102	0.78
42DAP/41DAP	0.86828	1
43DAP/42DAP	1.06277	1
47DAP/43DAP	0.77277	0.308
52DAP/47DAP	1.00114	0.948
57DAP/52DAP	0.77906	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38176	0.101
17DAP/reference	1.54282	0.1
27DAP/reference	1.09446	0.478
39DAP/reference	1.20017	0.04
41DAP/reference	1.11546	0.093
42DAP/reference	1.21255	0.001
43DAP/reference	1.00454	1
47DAP/reference	0.95732	0.345
52DAP/reference	1.07003	0.524
57DAP/reference	1.00852	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77486	0.135
27DAP/17DAP	1.10071	0.761
39DAP/27DAP	0.70679	0.068
41DAP/39DAP	1.00673	1
42DAP/41DAP	0.77736	0.174
43DAP/42DAP	1.03243	0.664
47DAP/43DAP	0.81951	0.056
52DAP/47DAP	1.00668	0.935
57DAP/52DAP	1.7874	0.165
57DAP/7DAP	0.53071	0.181

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8902	0.27
17DAP/reference	1.28967	0.035
27DAP/reference	1.00367	1
39DAP/reference	0.88638	0.17
41DAP/reference	1.15058	0.215
42DAP/reference	1.00268	0.751
43DAP/reference	0.95156	0.351
47DAP/reference	0.81902	0.128
52DAP/reference	0.8594	0.072
57DAP/reference	0.99582	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30241	0.049
17DAP/reference	2.25256	0.007
27DAP/reference	1.45596	0.014
39DAP/reference	1.0941	0.514
41DAP/reference	0.97882	0.459
42DAP/reference	1.41533	0.011
43DAP/reference	1.57498	0.022
47DAP/reference	1.11304	0.092
52DAP/reference	1.0887	0.444
57DAP/reference	1.1616	0.193

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01228	0.804
17DAP/reference	1.49824	0.094
27DAP/reference	1.33522	0.014
39DAP/reference	1.04392	0.711
41DAP/reference	1.0045	0.682
42DAP/reference	1.0757	0.612
43DAP/reference	0.91753	0.319
47DAP/reference	0.97998	0.525
52DAP/reference	0.83657	0.204
57DAP/reference	1.1832	0.2

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12616	0.916
26DAP/20DAP	0.9157	1
34DAP/26DAP	1.5503	0.819
51DAP/34DAP	0.8752	0.579
52DAP/51DAP	0.96403	1
53DAP/52DAP	1.16959	0.819
55DAP/53DAP	1.18685	0.748
57DAP/55DAP	0.86638	0.479
62DAP/57DAP	0.84128	0.681
68DAP/62DAP	0.79083	0.406
68DAP/14DAP	0.73199	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.45982	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.98412	0.07
Immature Eggplant/Mature Eggplant	0.25762	0.063
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.42388

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.27514	0.877
1-1-2/M82	1.64075
12-2/M82	N/A	N/A
12-4/M82	1.24427
1-3/M82	0.58661	0.441
2-1-1/M82	0.67951
2-1/M82	N/A	N/A
2-6/M82	0.84792
3-2/M82	1.35608
4-1-1/M82	0.99468	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.8927	1
6-2/M82	0.34396
6-3/M82	0.74432
7-1/M82	1.02998
7-2/M82	0.64288	0.565
9-3-2/M82	0.70234

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76231	0.243
IL2-6/WTpooled	1.01566	0.788
IL7-5/WTpooled	1.45473	0.792
IL7-3/WTpooled	0.98917	1
IL12-4/WTpooled	1.0423	0.891
IL1-4/WTpooled	0.94944	0.562
WT/WTpooled	1.05499	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	0.77881	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.004	1
DC3000/delta hrp 6h	1.09632	1
DC3000/delta hrp 12h	0.90533	1
DC3000/delta hrp 24h	1.00938	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86593	0.629
DC3000 delta B/DC3000 delta AB	0.87436	0.03

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87959	1
Exp 36h	0.44034	0.434
Exp 60h	0.50834	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98433	1
Var 0h	0.96001	1
Var 12h I row2-row1	0.86636	0.338
Var 12h NI row2-row1	0.90894	0.713
Var 36h I row2-row1	0.89937	0.805
Var 36h NI row2-row1	1.03808	1
Var 60h I row2-row1	1.0435	1
Var 60h NI row2-row1	1.08742	1
Time course 0hI-0hNI	1.00304	1
Time course 12hI-12hNI	0.86173	0.044
Time course 36hI-36hNI	0.76346	0.057
Time course 60hI-60hNI	0.40716	0.005

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)	1.08624	0.654
transgenic ySAMdc/azygous control (breaker)	0.27536	0.119
transgenic ySAMdc/azygous control (red)	1.02397	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98882	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85986	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68255	1
Manapal/WT (break)	0.68867	1
Manapal/WT (red)	1.62116	0.413