Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.6.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01319	1
27DAP/17DAP	0.88184	0.72
39DAP/27DAP	1.06341	0.876
41DAP/39DAP	1.18978	0.357
42DAP/41DAP	0.80505	0.774
43DAP/42DAP	1.07756	1
47DAP/43DAP	1.2507	0.343
52DAP/47DAP	0.9531	0.754
57DAP/52DAP	1.03677	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04397	0.662
17DAP/reference	1.0318	0.787
27DAP/reference	1.39664	0.125
39DAP/reference	1.38048	0.096
41DAP/reference	1.25954	0.145
42DAP/reference	1.11536	0.13
43DAP/reference	1.07054	0.617
47DAP/reference	0.9712	0.418
52DAP/reference	1.27679	0.025
57DAP/reference	1.10736	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03629	1
27DAP/17DAP	0.96541	0.878
39DAP/27DAP	1.09053	0.611
41DAP/39DAP	1.07496	0.817
42DAP/41DAP	1.15883	0.478
43DAP/42DAP	1.02087	1
47DAP/43DAP	0.98363	0.919
52DAP/47DAP	1.0682	0.862
57DAP/52DAP	0.98234	0.75
57DAP/7DAP	0.78362	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95058	0.445
17DAP/reference	0.88591	0.167
27DAP/reference	0.78037	0.019
39DAP/reference	1.012	1
41DAP/reference	1.05557	0.539
42DAP/reference	0.95451	0.415
43DAP/reference	0.90602	0.22
47DAP/reference	1.13442	0.7
52DAP/reference	1.1109	0.286
57DAP/reference	1.0632	0.612

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06763	0.66
17DAP/reference	1.11602	0.197
27DAP/reference	1.29522	0.044
39DAP/reference	1.30833	0.071
41DAP/reference	1.11058	0.335
42DAP/reference	1.21807	0.009
43DAP/reference	1.11941	0.624
47DAP/reference	1.06737	0.589
52DAP/reference	1.1695	0.053
57DAP/reference	1.02286	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99238	0.653
17DAP/reference	0.98293	0.739
27DAP/reference	1.01278	1
39DAP/reference	1.03716	0.733
41DAP/reference	0.97536	0.618
42DAP/reference	1.01927	0.893
43DAP/reference	1.04591	0.688
47DAP/reference	0.87182	0.043
52DAP/reference	0.93567	0.464
57DAP/reference	0.93814	0.212

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1746	0.966
26DAP/20DAP	1.11192	0.66
34DAP/26DAP	0.78184	0.171
51DAP/34DAP	1.04733	0.759
52DAP/51DAP	0.9241	1
53DAP/52DAP	0.94715	0.79
55DAP/53DAP	0.88222	0.163
57DAP/55DAP	0.94367	0.78
62DAP/57DAP	1.68771
68DAP/62DAP	1.56497	0.305
68DAP/14DAP	1.29887

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.52676	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40941	0.089
Mature Green Tomato/Ripe Tomato	0.86752	0.347
Immature Eggplant/Mature Eggplant	1.2458	0.165
Ripe Pepper/Ripe Tomato	3.03986	1
Mature Eggplant/Ripe Tomato	5.70625	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.69468
12-2/M82	N/A	N/A
12-4/M82	0.98085	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.05038
4-1-1/M82	N/A	N/A
4-1/M82	0.94986
4-3-2/M82	0.68618	0.487
4-3/M82	N/A	N/A
5-3/M82	1.29835
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.22965
7-2/M82	N/A	N/A
9-3-2/M82	0.63096	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
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	N/A	N/A
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	0.87813	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82081	0.849
DC3000/delta hrp 6h	0.90639	0.95
DC3000/delta hrp 12h	0.97743	1
DC3000/delta hrp 24h	0.96154	0.84

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	0.74391

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06919	1
Exp 36h	0.81848	0.539
Exp 60h	0.82238	0.2

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98558	1
Var 0h	0.49139	1
Var 12h I row2-row1	0.93284	0.627
Var 12h NI row2-row1	1.02336	1
Var 36h I row2-row1	0.59245	0.805
Var 36h NI row2-row1	3.17792	1
Var 60h I row2-row1	0.82299	0.582
Var 60h NI row2-row1	1.00366	1
Time course 0hI-0hNI	0.94383	0.612
Time course 12hI-12hNI	0.95935	0.719
Time course 36hI-36hNI	0.87228	0.07
Time course 60hI-60hNI	0.64781	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)	1.07984	0.278
transgenic ySAMdc/azygous control (breaker)	0.70211	0.137
transgenic ySAMdc/azygous control (red)	1.01768	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13066	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87801	1
Manapal/WT (break)	0.71789	1
Manapal/WT (red)	1.24835	0.413