Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57937	0.09
27DAP/17DAP	1.72459	0.793
39DAP/27DAP	0.95431	0.682
41DAP/39DAP	1.06837	0.833
42DAP/41DAP	1.47585	0.169
43DAP/42DAP	0.99143	0.925
47DAP/43DAP	2.86585	0.361
52DAP/47DAP	0.89325	0.619
57DAP/52DAP	1.67176	0.567

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65092	0.013
17DAP/reference	0.89302	0.208
27DAP/reference	1.03762	0.709
39DAP/reference	0.83512	0.2
41DAP/reference	0.76019	0.039
42DAP/reference	0.90575	0.014
43DAP/reference	0.91957	0.247
47DAP/reference	0.99074	0.568
52DAP/reference	0.94838	0.292
57DAP/reference	1.14735	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.45478	0.032
27DAP/17DAP	1.12663	0.494
39DAP/27DAP	1.25727	0.259
41DAP/39DAP	1.58478	0.021
42DAP/41DAP	1.02368	0.939
43DAP/42DAP	0.73476	0.032
47DAP/43DAP	1.73637	0.012
52DAP/47DAP	0.96589	0.884
57DAP/52DAP	1.10911	0.759
57DAP/7DAP	0.84918

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28973	0.065
17DAP/reference	0.98851	0.599
27DAP/reference	0.96467	0.43
39DAP/reference	0.8067	0.011
41DAP/reference	1.05299	0.723
42DAP/reference	0.9875	0.531
43DAP/reference	0.89736	0.042
47DAP/reference	0.87838	0.293
52DAP/reference	0.92294	0.115
57DAP/reference	1.217	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59023	0.129
17DAP/reference	0.90983	0.208
27DAP/reference	0.94714	0.327
39DAP/reference	0.98471	0.569
41DAP/reference	1.20741	0.07
42DAP/reference	1.17517	0.118
43DAP/reference	0.96311	0.516
47DAP/reference	0.94646	0.338
52DAP/reference	0.83346	0.011
57DAP/reference	0.99069	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18637	0.386
17DAP/reference	0.90111	0.364
27DAP/reference	1.01554	1
39DAP/reference	1.20122	0.078
41DAP/reference	1.01856	0.867
42DAP/reference	0.80655	0.049
43DAP/reference	0.81901	0.081
47DAP/reference	0.9422	0.249
52DAP/reference	1.10245	0.491
57DAP/reference	0.91175	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95929	1
26DAP/20DAP	0.68358	0.317
34DAP/26DAP	1.08528	1
51DAP/34DAP	0.817	0.532
52DAP/51DAP	0.84798	1
53DAP/52DAP	0.96151
55DAP/53DAP	0.9662	0.838
57DAP/55DAP	1.52282	0.975
62DAP/57DAP	1.1712	0.767
68DAP/62DAP	1.43235	0.808
68DAP/14DAP	0.98939	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.935	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45918	0.136
Mature Green Tomato/Ripe Tomato	0.36023	0.03
Immature Eggplant/Mature Eggplant	1.10329	0.222
Ripe Pepper/Ripe Tomato	0.38485	0.224
Mature Eggplant/Ripe Tomato	0.3625	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.79187
12-2/M82	N/A	N/A
12-4/M82	0.88158	1
1-3/M82	2.42616	0.248
2-1-1/M82	1.34587	0.422
2-1/M82	2.59836	1
2-6/M82	0.97487	1
3-2/M82	N/A	N/A
4-1-1/M82	0.87247	1
4-1/M82	N/A	N/A
4-3-2/M82	1.00315
4-3/M82	1.21781	1
5-3/M82	1.33486	0.572
6-2/M82	0.94202
6-3/M82	0.51021
7-1/M82	N/A	N/A
7-2/M82	1.42648
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81304	0.321
IL2-6/WTpooled	0.94275	1
IL7-5/WTpooled	0.87379	1
IL7-3/WTpooled	0.7449	0.31
IL12-4/WTpooled	0.84741	0.71
IL1-4/WTpooled	0.85835	0.562
WT/WTpooled	0.96264	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	1.38934	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00457	1
DC3000/delta hrp 6h	0.77423	0.95
DC3000/delta hrp 12h	1.06747	1
DC3000/delta hrp 24h	2.21695	0.072

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00941	1
DC3000 delta B/DC3000 delta AB	1.66703	0.124

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17172	1
Exp 36h	2.19727	0.371
Exp 60h	2.11148	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95458	1
Var 0h	1.26718	0.311
Var 12h I row2-row1	1.44145	0.324
Var 12h NI row2-row1	0.65457	0.494
Var 36h I row2-row1	1.0852	0.742
Var 36h NI row2-row1	0.9142	0.743
Var 60h I row2-row1	0.79788	0.285
Var 60h NI row2-row1	1.23333	0.904
Time course 0hI-0hNI	1.09935	0.833
Time course 12hI-12hNI	1.51751	0.007
Time course 36hI-36hNI	2.60796	0.005
Time course 60hI-60hNI	10.517	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)	1.65174	0.482
transgenic ySAMdc/azygous control (breaker)	1.61262	0.172
transgenic ySAMdc/azygous control (red)	0.87911	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01281	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.38578	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97249	1
Manapal/WT (break)	0.80602	0.333
Manapal/WT (red)	0.71275	0.181