Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.3.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76585	0.156
27DAP/17DAP	1.30884	0.714
39DAP/27DAP	1.3912	0.387
41DAP/39DAP	0.93283	0.706
42DAP/41DAP	0.9172	1
43DAP/42DAP	0.93972	0.877
47DAP/43DAP	0.91594	0.696
52DAP/47DAP	1.82286	0.11
57DAP/52DAP	0.83383	0.602

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21805	0.188
17DAP/reference	1.00812	1
27DAP/reference	0.96671	0.417
39DAP/reference	0.90104	0.315
41DAP/reference	0.78253	0.267
42DAP/reference	1.20389	0.01
43DAP/reference	1.03012
47DAP/reference	0.87589	0.065
52DAP/reference	0.99183	0.668
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78454	0.039
27DAP/17DAP	1.00645	1
39DAP/27DAP	1.00536	0.862
41DAP/39DAP	1.31931	0.077
42DAP/41DAP	0.89619	0.329
43DAP/42DAP	1.22302	0.042
47DAP/43DAP	1.07343	0.664
52DAP/47DAP	1.10263	0.639
57DAP/52DAP	1.5815	0.056
57DAP/7DAP	1.24413	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98051	0.495
17DAP/reference	0.89096	0.014
27DAP/reference	0.95761	0.109
39DAP/reference	0.89127	0.011
41DAP/reference	0.88081	0.122
42DAP/reference	0.95877	0.338
43DAP/reference	1.04093	0.178
47DAP/reference	1.051	1
52DAP/reference	0.88069	0.061
57DAP/reference	0.89313	0.101

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21182	0.037
17DAP/reference	1.52789	0.007
27DAP/reference	1.68061	0.016
39DAP/reference	1.76409	0.011
41DAP/reference	1.50164	0.008
42DAP/reference	1.54921	0.108
43DAP/reference	1.40546	0.036
47DAP/reference	1.37226	0.128
52DAP/reference	1.45191	0.006
57DAP/reference	1.32649	0.012

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92182	0.048
17DAP/reference	1.15209	0.298
27DAP/reference	1.02882	0.695
39DAP/reference	1.05049	0.67
41DAP/reference	0.93282	0.293
42DAP/reference	1.08901	0.556
43DAP/reference	1.13534	0.59
47DAP/reference	1.00747	1
52DAP/reference	1.08198	0.558
57DAP/reference	2.3965	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.997	1
26DAP/20DAP	0.97156	1
34DAP/26DAP	0.97118	0.945
51DAP/34DAP	0.85132	0.197
52DAP/51DAP	1.02804	0.925
53DAP/52DAP	1.04125	0.678
55DAP/53DAP	1.04639	0.696
57DAP/55DAP	1.0185	1
62DAP/57DAP	0.75125
68DAP/62DAP	1.01868	0.962
68DAP/14DAP	0.98214	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12813	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.10278	0.058
Mature Green Tomato/Ripe Tomato	0.5751	0.107
Immature Eggplant/Mature Eggplant	0.37197	0.062
Ripe Pepper/Ripe Tomato	0.41335	0.224
Mature Eggplant/Ripe Tomato	0.53085	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93305	0.944
1-1-2/M82	0.87412	1
12-2/M82	1.55834
12-4/M82	0.93453	1
1-3/M82	1.06746	1
2-1-1/M82	1.06844	1
2-1/M82	N/A	N/A
2-6/M82	1.17484	0.695
3-2/M82	0.94689
4-1-1/M82	1.02801	1
4-1/M82	1.03742
4-3-2/M82	1.02457
4-3/M82	0.78175	0.72
5-3/M82	0.80882	0.278
6-2/M82	1.15571	1
6-3/M82	0.96535	0.916
7-1/M82	0.81219	0.803
7-2/M82	1.13385	0.324
9-3-2/M82	0.78977

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72685	0.243
IL2-6/WTpooled	1.11771	0.441
IL7-5/WTpooled	0.99658	1
IL7-3/WTpooled	0.70582	0.31
IL12-4/WTpooled	0.85641	1
IL1-4/WTpooled	0.99143	1
WT/WTpooled	1.03068	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	1.15687	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02931	0.921
DC3000/delta hrp 6h	1.00913	0.95
DC3000/delta hrp 12h	1.00032	1
DC3000/delta hrp 24h	1.0708	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97056	1
DC3000 delta B/DC3000 delta AB	0.99533	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76353	0.265
Exp 36h	0.65417	0.406
Exp 60h	0.46896	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03032	1
Var 0h	1.24399	0.98
Var 12h I row2-row1	0.99503	1
Var 12h NI row2-row1	0.96438	0.627
Var 36h I row2-row1	0.98801	1
Var 36h NI row2-row1	1.64776	1
Var 60h I row2-row1	0.94378	0.374
Var 60h NI row2-row1	1.06777	1
Time course 0hI-0hNI	0.98859	0.981
Time course 12hI-12hNI	1.00664	0.885
Time course 36hI-36hNI	1.06747	0.355
Time course 60hI-60hNI	1.18019	0.015

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)	1.24497	0.455
transgenic ySAMdc/azygous control (breaker)	0.43558	0.142
transgenic ySAMdc/azygous control (red)	1.14259	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0432	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.29796	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.31362	0.14
Manapal/WT (break)	0.78499	1
Manapal/WT (red)	1.26473	0.413