Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00884	0.961
27DAP/17DAP	1.03947	0.957
39DAP/27DAP	1.61224	0.133
41DAP/39DAP	0.87112	0.496
42DAP/41DAP	1.14611	0.941
43DAP/42DAP	0.91297	0.833
47DAP/43DAP	1.06799	0.999
52DAP/47DAP	0.85798	0.617
57DAP/52DAP	1.22568	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2075	0.008
17DAP/reference	0.95323	0.567
27DAP/reference	1.26507	0.025
39DAP/reference	0.91929	0.267
41DAP/reference	0.85941	0.014
42DAP/reference	1.04136	0.166
43DAP/reference	0.92286	0.36
47DAP/reference	0.93279	0.09
52DAP/reference	0.94264	0.341
57DAP/reference	1.06305	0.239

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98056	0.732
27DAP/17DAP	1.18454	0.447
39DAP/27DAP	0.90109	0.287
41DAP/39DAP	1.08968	0.748
42DAP/41DAP	1.14035	0.539
43DAP/42DAP	0.74943	0.022
47DAP/43DAP	1.12654	0.227
52DAP/47DAP	0.7962	0.188
57DAP/52DAP	0.98666	0.81
57DAP/7DAP	1.21376	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02397	0.945
17DAP/reference	0.78312	0.011
27DAP/reference	0.81325	0.01
39DAP/reference	0.93483	0.23
41DAP/reference	0.87193	0.067
42DAP/reference	0.87611	0.117
43DAP/reference	0.75626	0.011
47DAP/reference	0.88707	0.383
52DAP/reference	0.8193	0.077
57DAP/reference	0.82214	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02345	0.852
17DAP/reference	1.06246	0.33
27DAP/reference	1.11687	0.278
39DAP/reference	0.89516	0.168
41DAP/reference	1.05772	0.688
42DAP/reference	0.93831	0.289
43DAP/reference	0.81656	0.046
47DAP/reference	0.84087	0.01
52DAP/reference	0.81419	0.006
57DAP/reference	0.66992	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98377	0.607
17DAP/reference	0.98684	0.727
27DAP/reference	1.04608	0.575
39DAP/reference	0.89057	0.046
41DAP/reference	0.97164	0.512
42DAP/reference	1.0043	1
43DAP/reference	0.86499	0.131
47DAP/reference	0.92299	0.191
52DAP/reference	0.84531	0.098
57DAP/reference	1.20076	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00391	1
26DAP/20DAP	1.36744	0.182
34DAP/26DAP	0.94359	0.927
51DAP/34DAP	1.01178	0.98
52DAP/51DAP	0.8361	1
53DAP/52DAP	0.97892	0.882
55DAP/53DAP	0.9471	0.784
57DAP/55DAP	0.88861	0.508
62DAP/57DAP	1.06776	0.902
68DAP/62DAP	1.3116	0.247
68DAP/14DAP	1.27708	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95825	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40237	0.058
Mature Green Tomato/Ripe Tomato	1.17651	0.058
Immature Eggplant/Mature Eggplant	0.36809	0.062
Ripe Pepper/Ripe Tomato	12.7057	0.233
Mature Eggplant/Ripe Tomato	57.0014	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02044
12-2/M82	N/A	N/A
12-4/M82	0.82001	0.358
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	1.5753
4-3-2/M82	0.83957	0.698
4-3/M82	0.96894	0.611
5-3/M82	1.29039	0.36
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.98654
7-2/M82	0.94533
9-3-2/M82	0.84034	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.47526	0.383
IL7-5/WTpooled	0.77231
IL7-3/WTpooled	1.52365	1
IL12-4/WTpooled	0.77863	0.71
IL1-4/WTpooled	0.98054	1
WT/WTpooled	0.76761	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	1.35877	0.177

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96345	1
DC3000/delta hrp 6h	1.00985	1
DC3000/delta hrp 12h	1.10003	1
DC3000/delta hrp 24h	0.90273	0.403

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14517	0.121
DC3000 delta B/DC3000 delta AB	1.2916	0.302

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96675	1
Exp 36h	0.84499	0.504
Exp 60h	0.70651	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9976	1
Var 0h	1.02069	1
Var 12h I row2-row1	1.00457	1
Var 12h NI row2-row1	1.3309	0.649
Var 36h I row2-row1	0.91059	1
Var 36h NI row2-row1	0.95711	0.61
Var 60h I row2-row1	0.83066	0.582
Var 60h NI row2-row1	0.88212	0.756
Time course 0hI-0hNI	1.04849	0.63
Time course 12hI-12hNI	1.07792	0.381
Time course 36hI-36hNI	1.87056	0.004
Time course 60hI-60hNI	2.73112	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)	0.96672	0.454
transgenic ySAMdc/azygous control (breaker)	0.9327	1
transgenic ySAMdc/azygous control (red)	1.55907	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93504	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.97889	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.60884	0.14
Manapal/WT (break)	2.56205	0.183
Manapal/WT (red)	1.37077	1