Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.6.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84975	0.389
27DAP/17DAP	1.14982	0.849
39DAP/27DAP	1.4555	0.426
41DAP/39DAP	1.12239	0.822
42DAP/41DAP	1.10267	0.916
43DAP/42DAP	1.10835	1
47DAP/43DAP	1.26912	0.909
52DAP/47DAP	1.07541	0.984
57DAP/52DAP	0.98293	0.976

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8499	0.063
17DAP/reference	1.02999	0.874
27DAP/reference	0.93424	0.286
39DAP/reference	1.05126	0.57
41DAP/reference	1.0267	0.714
42DAP/reference	0.80902	0.001
43DAP/reference	1.03919	0.617
47DAP/reference	0.9132	0.046
52DAP/reference	0.93733	0.275
57DAP/reference	0.98247	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73132	0.289
27DAP/17DAP	0.96572	0.943
39DAP/27DAP	1.56156	0.324
41DAP/39DAP	2.19271	0.013
42DAP/41DAP	0.74815	0.032
43DAP/42DAP	0.77708	0.105
47DAP/43DAP	0.85536	0.382
52DAP/47DAP	1.34998	0.552
57DAP/52DAP	0.83306	0.528
57DAP/7DAP	0.98812

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13012	0.65
17DAP/reference	0.94944	0.389
27DAP/reference	1.12536	0.453
39DAP/reference	1.1487	0.077
41DAP/reference	1.02817	1
42DAP/reference	1.13297	0.308
43DAP/reference	1.11064	0.188
47DAP/reference	1.02805	0.804
52DAP/reference	0.94839	0.398
57DAP/reference	1.08845	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94113	0.518
17DAP/reference	0.96147	0.51
27DAP/reference	0.87171	0.123
39DAP/reference	1.0002	0.642
41DAP/reference	1.01401	0.718
42DAP/reference	0.92977	0.355
43DAP/reference	1.07568	0.802
47DAP/reference	0.92008	0.073
52DAP/reference	0.96082	0.433
57DAP/reference	0.86591	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37813	0.109
17DAP/reference	0.92732	0.308
27DAP/reference	1.16452	0.26
39DAP/reference	1.06411	0.65
41DAP/reference	1.14992	0.056
42DAP/reference	1.06089	0.759
43DAP/reference	1.12555	0.246
47DAP/reference	0.9415	0.348
52DAP/reference	0.97728	0.732
57DAP/reference	0.9744	0.543

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09593	0.966
26DAP/20DAP	1.55561	0.149
34DAP/26DAP	0.5575
51DAP/34DAP	0.76629	0.394
52DAP/51DAP	0.70353	1
53DAP/52DAP	1.83395	0.662
55DAP/53DAP	1.19246	0.826
57DAP/55DAP	0.74279	0.178
62DAP/57DAP	1.07886	1
68DAP/62DAP	1.21426	0.247
68DAP/14DAP	2.3037	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.49979	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.86913	0.034
Immature Eggplant/Mature Eggplant	2.15246
Ripe Pepper/Ripe Tomato	1.49076
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
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	1.50209	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.68306
IL12-4/WTpooled	0.8529	1
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.00676	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	1.92121	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19538	0.671
DC3000/delta hrp 6h	0.84048	0.95
DC3000/delta hrp 12h	0.96117	1
DC3000/delta hrp 24h	1.73857	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.90897	0.046
DC3000 delta B/DC3000 delta AB	3.97044	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94721	1
Exp 36h	1.52915	1
Exp 60h	1.01846	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99705	1
Var 0h	0.98587	1
Var 12h I row2-row1	0.75734	0.565
Var 12h NI row2-row1	2.51181	0.235
Var 36h I row2-row1	1.40594	0.742
Var 36h NI row2-row1	0.40167	0.478
Var 60h I row2-row1	0.58215	0.832
Var 60h NI row2-row1	0.605	0.313
Time course 0hI-0hNI	1.61804	0.719
Time course 12hI-12hNI	1.51175	0.599
Time course 36hI-36hNI	5.8935	0.004
Time course 60hI-60hNI	25.9985	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)	1.04523	0.541
transgenic ySAMdc/azygous control (breaker)	0.8939	0.251
transgenic ySAMdc/azygous control (red)	0.87674	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0018	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95474	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88259	1
Manapal/WT (break)	0.8635	0.333
Manapal/WT (red)	0.73792	0.424