Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.14.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00257	0.927
27DAP/17DAP	0.95933	0.945
39DAP/27DAP	1.36439	0.985
41DAP/39DAP	1.44104	0.426
42DAP/41DAP	1.10907	0.945
43DAP/42DAP	1.04119	1
47DAP/43DAP	0.96559	0.859
52DAP/47DAP	1.3203	0.521
57DAP/52DAP	1.07216	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02224	0.994
17DAP/reference	1.08705	0.108
27DAP/reference	1.03584	0.468
39DAP/reference	1.03115	0.486
41DAP/reference	1.11508	0.158
42DAP/reference	0.94079	0.069
43DAP/reference	1.07036	0.217
47DAP/reference	1.02572	1
52DAP/reference	0.9178	0.237
57DAP/reference	0.95319	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99147	0.782
27DAP/17DAP	0.95667	0.748
39DAP/27DAP	1.152	0.224
41DAP/39DAP	0.99723	1
42DAP/41DAP	1.10857	0.539
43DAP/42DAP	0.95166	0.522
47DAP/43DAP	0.97252	0.87
52DAP/47DAP	0.91144	0.389
57DAP/52DAP	0.89	0.119
57DAP/7DAP	1.0449	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91468	0.27
17DAP/reference	0.90372	0.025
27DAP/reference	0.89366	0.023
39DAP/reference	0.93762	0.043
41DAP/reference	0.92145	0.07
42DAP/reference	0.9067	0.017
43DAP/reference	0.89031	0.054
47DAP/reference	0.95866	0.504
52DAP/reference	0.85349	0.02
57DAP/reference	0.91474	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08064	0.337
17DAP/reference	1.10238	0.033
27DAP/reference	1.00388	1
39DAP/reference	1.00151	0.745
41DAP/reference	0.92387	0.156
42DAP/reference	0.87715	0.05
43DAP/reference	1.13443	0.137
47DAP/reference	1.04385	0.731
52DAP/reference	1.10581	0.279
57DAP/reference	1.38557	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89252	0.071
17DAP/reference	0.92605	0.198
27DAP/reference	0.90285	0.063
39DAP/reference	0.93	0.122
41DAP/reference	0.91664	0.096
42DAP/reference	0.91449	0.087
43DAP/reference	0.90469	0.179
47DAP/reference	1.11069	0.081
52DAP/reference	0.89432	0.238
57DAP/reference	1.10012	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96222	1
26DAP/20DAP	1.13021	0.663
34DAP/26DAP	1.1783	0.542
51DAP/34DAP	0.95451	0.727
52DAP/51DAP	1.07491	0.431
53DAP/52DAP	1.03186	0.921
55DAP/53DAP	0.92513	0.619
57DAP/55DAP	0.92592	0.612
62DAP/57DAP	1.09307	0.767
68DAP/62DAP	0.72823	0.118
68DAP/14DAP	0.8563	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70179	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.87665	0.063
Mature Green Tomato/Ripe Tomato	0.95283	0.522
Immature Eggplant/Mature Eggplant	0.81966	0.366
Ripe Pepper/Ripe Tomato	0.38608	0.224
Mature Eggplant/Ripe Tomato	0.65037	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05693	0.877
1-1-2/M82	0.74261
12-2/M82	0.99133	1
12-4/M82	1.11201	0.611
1-3/M82	1.16541	1
2-1-1/M82	1.07893	0.422
2-1/M82	1.0105	1
2-6/M82	1.1813	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.98154	1
4-1/M82	0.98559	1
4-3-2/M82	0.86907	1
4-3/M82	1.16834	0.268
5-3/M82	0.91249	1
6-2/M82	0.89306	0.481
6-3/M82	1.09695	1
7-1/M82	N/A	N/A
7-2/M82	1.05414	1
9-3-2/M82	0.82588	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99156	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04474	1
IL12-4/WTpooled	1.20952	0.525
IL1-4/WTpooled	1.08579	0.426
WT/WTpooled	0.95262	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	1.35975	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06775	0.846
DC3000/delta hrp 6h	0.95658	0.95
DC3000/delta hrp 12h	1.05783	1
DC3000/delta hrp 24h	1.02127	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95189	0.485
DC3000 delta B/DC3000 delta AB	1.03274	0.636

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15086	1
Exp 36h	1.13309	1
Exp 60h	1.00481	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96775	1
Var 0h	0.99495	1
Var 12h I row2-row1	0.86158	0.565
Var 12h NI row2-row1	1.01974	1
Var 36h I row2-row1	0.82971	1
Var 36h NI row2-row1	0.92787	0.522
Var 60h I row2-row1	0.77004	0.287
Var 60h NI row2-row1	0.98229	1
Time course 0hI-0hNI	1.05344	0.833
Time course 12hI-12hNI	0.91203	0.698
Time course 36hI-36hNI	1.23585	0.006
Time course 60hI-60hNI	3.22284	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)	1.00422	1
transgenic ySAMdc/azygous control (breaker)	1.22426	0.248
transgenic ySAMdc/azygous control (red)	0.96999	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02074	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04928	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83904	1
Manapal/WT (break)	0.85933	0.333
Manapal/WT (red)	1.19501	0.164