Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.12.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08975	0.932
27DAP/17DAP	1.01928	1
39DAP/27DAP	0.82881	0.487
41DAP/39DAP	1.76222	0.134
42DAP/41DAP	1.00426	1
43DAP/42DAP	1.17716	0.793
47DAP/43DAP	0.98554	0.868
52DAP/47DAP	1.8554	0.671
57DAP/52DAP	0.98282	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98522	0.63
17DAP/reference	1.16383	0.014
27DAP/reference	1.00387	0.885
39DAP/reference	1.07486	0.557
41DAP/reference	1.04392	0.421
42DAP/reference	1.33062	0.01
43DAP/reference	1.05201	0.269
47DAP/reference	1.08131	0.84
52DAP/reference	0.83306	0.028
57DAP/reference	0.90998	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18164	0.65
27DAP/17DAP	0.81928	0.39
39DAP/27DAP	0.66019	0.035
41DAP/39DAP	1.0928	0.69
42DAP/41DAP	1.17701	0.343
43DAP/42DAP	0.83574	0.127
47DAP/43DAP	0.86347	0.29
52DAP/47DAP	2.25058	0.045
57DAP/52DAP	2.47264	0.041
57DAP/7DAP	1.73929	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86787	0.076
17DAP/reference	0.97716	0.22
27DAP/reference	0.92053	0.011
39DAP/reference	0.96435	0.064
41DAP/reference	1.00933	0.949
42DAP/reference	1.03238	0.405
43DAP/reference	0.97744	0.385
47DAP/reference	0.93399	0.128
52DAP/reference	0.91963	0.097
57DAP/reference	0.98487	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07552	0.582
17DAP/reference	1.23489	0.06
27DAP/reference	1.04163	0.822
39DAP/reference	0.97473	0.485
41DAP/reference	0.86557	0.137
42DAP/reference	0.94325	0.392
43DAP/reference	1.15799	0.239
47DAP/reference	0.94857	0.284
52DAP/reference	1.12159	0.259
57DAP/reference	1.35003	0.155

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91281	0.044
17DAP/reference	1.02254	0.665
27DAP/reference	0.97258	0.337
39DAP/reference	0.91309	0.023
41DAP/reference	1.05479	0.439
42DAP/reference	0.89524	0.108
43DAP/reference	0.99299	0.738
47DAP/reference	0.93619	0.199
52DAP/reference	0.87697	0.148
57DAP/reference	0.78821	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99537	1
26DAP/20DAP	1.67864	1
34DAP/26DAP	3.12526	0.819
51DAP/34DAP	1.61574	0.898
52DAP/51DAP	4.77725	0.035
53DAP/52DAP	0.57766	0.049
55DAP/53DAP	1.76906	0.039
57DAP/55DAP	0.51488	0.036
62DAP/57DAP	1.6848	0.115
68DAP/62DAP	3.00817	0.616
68DAP/14DAP	0.78674	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15458	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62255	0.17
Mature Green Tomato/Ripe Tomato	3.51748	0.017
Immature Eggplant/Mature Eggplant	0.94373	0.594
Ripe Pepper/Ripe Tomato	0.9423	1
Mature Eggplant/Ripe Tomato	1.72667

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	0.73763
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.10745
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	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	1.12767	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8862	0.849
DC3000/delta hrp 6h	0.90065	0.95
DC3000/delta hrp 12h	1.16459	1
DC3000/delta hrp 24h	0.85394	0.148

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94132	0.538
DC3000 delta B/DC3000 delta AB	0.79366	0.04

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88192	0.265
Exp 36h	0.7489	0.406
Exp 60h	0.68856	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0043	1
Var 0h	0.66042	0.933
Var 12h I row2-row1	0.77911	0.338
Var 12h NI row2-row1	0.91789	0.494
Var 36h I row2-row1	0.86127	1
Var 36h NI row2-row1	1.29222	0.482
Var 60h I row2-row1	1.40334	0.562
Var 60h NI row2-row1	1.00514	1
Time course 0hI-0hNI	0.94902	0.687
Time course 12hI-12hNI	1.01182	0.867
Time course 36hI-36hNI	0.88894	0.136
Time course 60hI-60hNI	0.12519	0.005

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)	1.1518	0.431
transgenic ySAMdc/azygous control (breaker)	1.22404	0.248
transgenic ySAMdc/azygous control (red)	1.00033	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93732	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40484	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.95271	0.083
Manapal/WT (break)	1.50966	0.381
Manapal/WT (red)	1.16421	0.413